diff --git a/DESCRIPTION b/DESCRIPTION index 82266c740f..88c801aaf7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ggplot2 +Version: 3.5.2.9000 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")), diff --git a/NAMESPACE b/NAMESPACE index 088da2ba6c..b7216624e3 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -470,22 +470,26 @@ export(guide_transform) export(guides) export(has_flipped_aes) export(is.Coord) -export(is.coord) 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(is.theme_element) -export(is.waiver) +export(is_coord) +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(is_theme_element) +export(is_waiver) export(label_both) export(label_bquote) export(label_context) diff --git a/NEWS.md b/NEWS.md index 696ce126b1..578c18ade4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # ggplot2 (development version) +This is a small release focusing on fixing regressions from 3.5.0 and * Facet gains a new method `setup_panel_params` to interact with the panel_params setted by Coord object (@Yunuuuu, #6397, #6380) * `position_fill()` avoids stacking observations of zero (@teunbrand, #6338) * New `layer(layout)` argument to interact with facets (@teunbrand, #3062) @@ -86,7 +87,7 @@ @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 +* 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) @@ -341,6 +342,23 @@ (@teunbrand, #6269). * The default colour and fill scales have a new `palette` argument (@teunbrand, #6064). + +# ggplot2 3.5.2 + +This is a small release focusing on providing infrastructure for other packages +to gracefully prepare for changes in the next major release. + +## Improvements + +* Standardised test functions for important classes: `is_ggproto()`, + `is_ggplot()`, `is_mapping()`, `is_layer()`, `is_geom()`, `is_stat()`, + `is_position()`, `is_coord()`, `is_facet()`, `is_scale()`, `is_guide()`, + `is_guides()`, `is_margin()`, `is_theme_element()` and `is_theme()`. +* New `get_labs()` function for retrieving completed plot labels + (@teunbrand, #6008). +* New `get_geom_defaults()` for retrieving resolved default aesthetics. +* A new `ggplot_build()` S3 method for classes was added, which + returns input unaltered (@teunbrand, #5800). # ggplot2 3.5.1 @@ -352,15 +370,15 @@ documentation updates. * Fixed bug where discrete scales could not map aesthetics only consisting of `NA`s (#5623) * Fixed spurious warnings from `sec_axis()` with `breaks = NULL` (#5713). -* Patterns and gradients are now also enabled in `geom_sf()` +* Patterns and gradients are now also enabled in `geom_sf()` (@teunbrand, #5716). -* The default behaviour of `resolution()` has been reverted to pre-3.5.0 - behaviour. Whether mapped discrete vectors should be treated as having +* The default behaviour of `resolution()` has been reverted to pre-3.5.0 + behaviour. Whether mapped discrete vectors should be treated as having resolution of 1 is controlled by the new `discrete` argument. * Fixed bug in `guide_bins()` and `guide_coloursteps()` where discrete breaks, - such as the levels produced by `cut()`, were ordered incorrectly + such as the levels produced by `cut()`, were ordered incorrectly (@teunbrand, #5757). - + ## Improvements * When facets coerce the faceting variables to factors, the 'ordered' class @@ -368,86 +386,86 @@ documentation updates. * `coord_map()` and `coord_polar()` throw informative warnings when used with the guide system (#5707). * When passing a function to `stat_contour(breaks)`, that function is used to - calculate the breaks even if `bins` and `binwidth` are missing + calculate the breaks even if `bins` and `binwidth` are missing (@teunbrand, #5686). -* `geom_step()` now supports `lineend`, `linejoin` and `linemitre` parameters +* `geom_step()` now supports `lineend`, `linejoin` and `linemitre` parameters (@teunbrand, #5705). * Fixed performance loss when the `.data` pronoun is used in `aes()` (#5730). -* Facet evaluation is better at dealing with inherited errors +* Facet evaluation is better at dealing with inherited errors (@teunbrand, #5670). * `stat_bin()` deals with non-finite breaks better (@teunbrand, #5665). * While axes in `coord_radial()` don't neatly fit the top/right/bottom/left - organisation, specifying `position = "top"` or `position = "right"` + organisation, specifying `position = "top"` or `position = "right"` in the scale will flip the placement of the radial axis (#5735) * Theme elements that do not exist now throw warnings instead of errors (#5719). -* Fixed bug in `coord_radial()` where full circles were not treated as such +* Fixed bug in `coord_radial()` where full circles were not treated as such (@teunbrand, #5750). * When legends detect the presence of values in a layer, `NA` is now detected if the data contains values outside the given breaks (@teunbrand, #5749). * `annotate()` now warns about `stat` or `position` arguments (@teunbrand, #5151) -* `guide_coloursteps(even.steps = FALSE)` now works with discrete data that has +* `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 -This is a minor release that turned out quite beefy. It is focused on -overhauling the guide system: the system responsible for displaying information -from scales in the guise of axes and legends. As part of that overhaul, new -guides have been implemented and existing guides have been refined. The look -and feel of guides has been mostly preserved, but their internals and +This is a minor release that turned out quite beefy. It is focused on +overhauling the guide system: the system responsible for displaying information +from scales in the guise of axes and legends. As part of that overhaul, new +guides have been implemented and existing guides have been refined. The look +and feel of guides has been mostly preserved, but their internals and styling options have changed drastically. -Briefly summarising other highlights, we also welcome `coord_radial()` as a -successor of `coord_polar()`. Initial support for newer graphical features, -such as pattern fills has been added. The API has changed how `I()`/`` -vectors interact with the scale system, namely: not at all. +Briefly summarising other highlights, we also welcome `coord_radial()` as a +successor of `coord_polar()`. Initial support for newer graphical features, +such as pattern fills has been added. The API has changed how `I()`/`` +vectors interact with the scale system, namely: not at all. ## Breaking changes -* The guide system. As a whole. See 'new features' for more information. - While the S3 guide generics are still in place, the S3 methods for +* The guide system. As a whole. See 'new features' for more information. + While the S3 guide generics are still in place, the S3 methods for `guide_train()`, `guide_merge()`, `guide_geom()`, `guide_transform()`, `guide_gengrob()` have been superseded by the respective ggproto methods. In practice, this will mean that `NextMethod()` or sub-classing ggplot2's guides with the S3 system will no longer work. - + * By default, `guide_legend()` now only draws a key glyph for a layer when the value is in the layer's data. To revert to the old behaviour, you can still set `show.legend = c({aesthetic} = TRUE)` (@teunbrand, #3648). -* In the `scale_{colour/fill}_gradient2()` and - `scale_{colour/fill}_steps2()` functions, the `midpoint` argument is +* In the `scale_{colour/fill}_gradient2()` and + `scale_{colour/fill}_steps2()` functions, the `midpoint` argument is transformed by the scale transformation (#3198). - + * The `legend.key` theme element is set to inherit from the `panel.background` theme element. The default themes no longer set the `legend.key` element. This causes a visual change with the default `theme_gray()` (#5549). - + * The `scale_name` argument in `continuous_scale()`, `discrete_scale()` and `binned_scale()` is soft-deprecated. If you have implemented custom scales, - be advised to double-check that unnamed arguments ends up where they should - (@teunbrand, #1312). - -* The `legend.text.align` and `legend.title.align` arguments in `theme()` are - deprecated. The `hjust` setting of the `legend.text` and `legend.title` + be advised to double-check that unnamed arguments ends up where they should + (@teunbrand, #1312). + +* The `legend.text.align` and `legend.title.align` arguments in `theme()` are + deprecated. The `hjust` setting of the `legend.text` and `legend.title` elements continues to fulfill the role of text alignment (@teunbrand, #5347). - -* 'lines' units in `geom_label()`, often used in the `label.padding` argument, - are now are relative to the text size. This causes a visual change, but fixes + +* 'lines' units in `geom_label()`, often used in the `label.padding` argument, + are now are relative to the text size. This causes a visual change, but fixes a misalignment issue between the textbox and text (@teunbrand, #4753) - + * `coord_flip()` has been marked as superseded. The recommended alternative is to swap the `x` and `y` aesthetic and/or using the `orientation` argument in a layer (@teunbrand, #5130). - -* The `trans` argument in scales and secondary axes has been renamed to + +* The `trans` argument in scales and secondary axes has been renamed to `transform`. The `trans` argument itself is deprecated. To access the - transformation from the scale, a new `get_transformation()` method is + transformation from the scale, a new `get_transformation()` method is added to Scale-classes (#5558). - + * Providing a numeric vector to `theme(legend.position)` has been deprecated. - To set the default legend position inside the plot use + To set the default legend position inside the plot use `theme(legend.position = "inside", legend.position.inside = c(...))` instead. ## New features @@ -456,44 +474,44 @@ vectors interact with the scale system, namely: not at all. invoking the identity scale. This allows these columns to co-exist with other layers that need a non-identity scale for the same aesthetic. Also, it makes it easy to specify relative positions (@teunbrand, #5142). - + * The `fill` aesthetic in many geoms now accepts grid's patterns and gradients. - For developers of layer extensions, this feature can be enabled by switching - from `fill = alpha(fill, alpha)` to `fill = fill_alpha(fill, alpha)` when + For developers of layer extensions, this feature can be enabled by switching + from `fill = alpha(fill, alpha)` to `fill = fill_alpha(fill, alpha)` when providing fills to `grid::gpar()` (@teunbrand, #3997). - -* New function `check_device()` for testing the availability of advanced + +* New function `check_device()` for testing the availability of advanced graphics features introduced in R 4.1.0 onward (@teunbrand, #5332). - -* `coord_radial()` is a successor to `coord_polar()` with more customisation + +* `coord_radial()` is a successor to `coord_polar()` with more customisation options. `coord_radial()` can: - + * integrate with the new guide system via a dedicated `guide_axis_theta()` to display the angle coordinate. - * in addition to drawing full circles, also draw circle sectors by using the + * in addition to drawing full circles, also draw circle sectors by using the `end` argument. - * avoid data vanishing in the center of the plot by setting the `donut` + * avoid data vanishing in the center of the plot by setting the `donut` argument. - * adjust the `angle` aesthetic of layers, such as `geom_text()`, to align + * adjust the `angle` aesthetic of layers, such as `geom_text()`, to align with the coordinate system using the `rotate_angle` argument. - + ### The guide system -The guide system encompassing axes and legends, as the last remaining chunk of -ggplot2, has been rewritten to use the `` system instead of the S3 -system. This change was a necessary step to officially break open the guide -system for extension package developers. The axes and legends now inherit from -a `` class, which makes them extensible in the same manner as geoms, +The guide system encompassing axes and legends, as the last remaining chunk of +ggplot2, has been rewritten to use the `` system instead of the S3 +system. This change was a necessary step to officially break open the guide +system for extension package developers. The axes and legends now inherit from +a `` class, which makes them extensible in the same manner as geoms, stats, facets and coords (#3329, @teunbrand) * The most user-facing change is that the styling of guides is rewired through - the theme system. Guides now have a `theme` argument that can style + the theme system. Guides now have a `theme` argument that can style individual guides, while `theme()` has gained additional arguments to style guides. Theme elements declared in the guide override theme elements set - through the plot. The new theme elements for guides are: - `legend.key.spacing{.x/.y}`, `legend.frame`, `legend.axis.line`, - `legend.ticks`, `legend.ticks.length`, `legend.text.position` and - `legend.title.position`. Previous style options in the arguments of + through the plot. The new theme elements for guides are: + `legend.key.spacing{.x/.y}`, `legend.frame`, `legend.axis.line`, + `legend.ticks`, `legend.ticks.length`, `legend.text.position` and + `legend.title.position`. Previous style options in the arguments of `guide_*()` functions are soft-deprecated. * Unfortunately, we could not fully preserve the function of pre-existing @@ -502,20 +520,20 @@ stats, facets and coords (#3329, @teunbrand) The S3 methods have been removed as part of cleaning up, so the old guides will still work if the S3 methods are reimplemented, but we encourage to switch to the new system (#2728). - -* The `order` argument of guides now strictly needs to be a length-1 + +* The `order` argument of guides now strictly needs to be a length-1 integer (#4958). - + #### Axes * New `guide_axis_stack()` to combine other axis guides on top of one another. -* New `guide_axis_theta()` to draw an axis in a circular arc in - `coord_radial()`. The guide can be controlled by adding +* New `guide_axis_theta()` to draw an axis in a circular arc in + `coord_radial()`. The guide can be controlled by adding `guides(theta = guide_axis_theta(...))` to a plot. * New `guide_axis_logticks()` can be used to draw logarithmic tick marks as - an axis. It supersedes the `annotation_logticks()` function + an axis. It supersedes the `annotation_logticks()` function (@teunbrand, #5325). * `guide_axis()` gains a `minor.ticks` argument to draw minor ticks (#4387). @@ -526,36 +544,36 @@ stats, facets and coords (#3329, @teunbrand) * Primary axis titles are now placed at the primary guide, so that `guides(x = guide_axis(position = "top"))` will display the title at the top by default (#4650). - + * The default `vjust` for the `axis.title.y.right` element is now 1 instead of 0. - -* Unknown secondary axis guide positions are now inferred as the opposite + +* Unknown secondary axis guide positions are now inferred as the opposite of the primary axis guide when the latter has a known `position` (#4650). - + #### Legends * New `guide_custom()` function for drawing custom graphical objects (grobs) unrelated to scales in legend positions (#5416). - + * All legends have acquired a `position` argument, that allows individual guides to deviate from the `legend.position` set in the `theme()` function. This means that legends can now be placed at multiple sides of the plot (#5488). - + * The spacing between legend keys and their labels, in addition to legends and their titles, is now controlled by the text's `margin` setting. Not specifying margins will automatically add appropriate text margins. To - control the spacing within a legend between keys, the new - `legend.key.spacing.{x/y}` argument can be used in `theme()`. This leaves the - `legend.spacing` theme setting dedicated to solely controlling the spacing + control the spacing within a legend between keys, the new + `legend.key.spacing.{x/y}` argument can be used in `theme()`. This leaves the + `legend.spacing` theme setting dedicated to solely controlling the spacing between different guides (#5455). - + * `guide_colourbar()` and `guide_coloursteps()` gain an `alpha` argument to set the transparency of the bar (#5085). * New `display` argument in `guide_colourbar()` supplants the `raster` argument. In R 4.1.0 and above, `display = "gradient"` will draw a gradient. - + * Legend keys that can draw arrows have their size adjusted for arrows. * When legend titles are larger than the legend, title justification extends @@ -564,8 +582,8 @@ stats, facets and coords (#3329, @teunbrand) * Glyph drawing functions of the `draw_key_*()` family can now set `"width"` and `"height"` attributes (in centimetres) to the produced keys to control their displayed size in the legend. - -* `coord_sf()` now uses customisable guides provided in the scales or + +* `coord_sf()` now uses customisable guides provided in the scales or `guides()` function (@teunbrand). ## Improvements @@ -577,34 +595,34 @@ stats, facets and coords (#3329, @teunbrand) * `position_stack()` no longer silently removes missing data, which is now handled by the geom instead of position (#3532). - -* The `minor_breaks` function argument in scales can now also take a function + +* The `minor_breaks` function argument in scales can now also take a function with two arguments: the scale's limits and the scale's major breaks (#3583). - + * Failing to fit or predict in `stat_smooth()` now gives a warning and omits the failed group, instead of throwing an error (@teunbrand, #5352). - + * `labeller()` now handles unspecified entries from lookup tables (@92amartins, #4599). - + * `fortify.default()` now accepts a data-frame-like object granted the object exhibits healthy `dim()`, `colnames()`, and `as.data.frame()` behaviours (@hpages, #5390). -* `geom_violin()` gains a `bounds` argument analogous to `geom_density()`s +* `geom_violin()` gains a `bounds` argument analogous to `geom_density()`s (@eliocamp, #5493). * To apply dodging more consistently in violin plots, `stat_ydensity()` now has a `drop` argument to keep or discard groups with 1 observation. - + * `geom_boxplot()` gains a new argument, `staplewidth` that can draw staples at the ends of whiskers (@teunbrand, #5126) - + * `geom_boxplot()` gains an `outliers` argument to switch outliers on or off, in a manner that does affects the scale range. For hiding outliers that does - not affect the scale range, you can continue to use `outlier.shape = NA` + not affect the scale range, you can continue to use `outlier.shape = NA` (@teunbrand, #4892). - + * Nicer error messages for xlim/ylim arguments in coord-* functions (@92amartins, #4601, #5297). @@ -612,66 +630,66 @@ stats, facets and coords (#3329, @teunbrand) of these is now required. If one is missing, it will be filled from the `x` and `y` aesthetics respectively. This makes drawing horizontal or vertical segments a little bit more convenient (@teunbrand, #5140). - + * When `geom_path()` has aesthetics varying within groups, the `arrow()` is applied to groups instead of individual segments (@teunbrand, #4935). - -* `geom_text()` and `geom_label()` gained a `size.unit` parameter that set the - text size to millimetres, points, centimetres, inches or picas + +* `geom_text()` and `geom_label()` gained a `size.unit` parameter that set the + text size to millimetres, points, centimetres, inches or picas (@teunbrand, #3799). - + * `geom_label()` now uses the `angle` aesthetic (@teunbrand, #2785) * The `label.padding` argument in `geom_label()` now supports inputs created with the `margin()` function (#5030). - + * `ScaleContinuous$get_breaks()` now only calls `scales::zero_range()` on limits in transformed space, rather than in data space (#5304). - + * Scales throw more informative messages (@teunbrand, #4185, #4258) - + * `scale_*_manual()` with a named `values` argument now emits a warning when none of those names match the values found in the data (@teunbrand, #5298). - -* The `name` argument in most scales is now explicitly the first argument + +* The `name` argument in most scales is now explicitly the first argument (#5535) - + * The `translate_shape_string()` internal function is now exported for use in extensions of point layers (@teunbrand, #5191). - -* To improve `width` calculation in bar plots with empty factor levels, - `resolution()` considers `mapped_discrete` values as having resolution 1 + +* To improve `width` calculation in bar plots with empty factor levels, + `resolution()` considers `mapped_discrete` values as having resolution 1 (@teunbrand, #5211) - + * In `theme()`, some elements can be specified with `rel()` to inherit from `unit`-class objects in a relative fashion (@teunbrand, #3951). - + * `theme()` now supports splicing a list of arguments (#5542). * In the theme element hierarchy, parent elements that are a strict subclass of child elements now confer their subclass upon the children (#5457). - + * New `plot.tag.location` in `theme()` can control placement of the plot tag in the `"margin"`, `"plot"` or the new `"panel"` option (#4297). - + * `coord_munch()` can now close polygon shapes (@teunbrand, #3271) - + * Aesthetics listed in `geom_*()` and `stat_*()` layers now point to relevant documentation (@teunbrand, #5123). - + * The new argument `axes` in `facet_grid()` and `facet_wrap()` controls the display of axes at interior panel positions. Additionally, the `axis.labels` - argument can be used to only draw tick marks or fully labelled axes + argument can be used to only draw tick marks or fully labelled axes (@teunbrand, #4064). - + * `coord_polar()` can have free scales in facets (@teunbrand, #2815). * The `get_guide_data()` function can be used to extract position and label information from the plot (#5004). - + * Improve performance of layers without positional scales (@zeehio, #4990) -* More informative error for mismatched +* More informative error for mismatched `direction`/`theme(legend.direction = ...)` arguments (#4364, #4930). ## Bug fixes @@ -681,95 +699,95 @@ stats, facets and coords (#3329, @teunbrand) * In `guide_bins()`, the title no longer arbitrarily becomes offset from the guide when it has long labels. - + * `guide_colourbar()` and `guide_coloursteps()` merge properly when one of the aesthetics is dropped (#5324). * When using `geom_dotplot(binaxis = "x")` with a discrete y-variable, dots are now stacked from the y-position rather than from 0 (@teunbrand, #5462) - -* `stat_count()` treats `x` as unique in the same manner `unique()` does + +* `stat_count()` treats `x` as unique in the same manner `unique()` does (#4609). - + * The plot's title, subtitle and caption now obey horizontal text margins (#5533). - + * Contour functions will not fail when `options("OutDec")` is not `.` (@eliocamp, #5555). * Lines where `linewidth = NA` are now dropped in `geom_sf()` (#5204). -* `ggsave()` no longer sometimes creates new directories, which is now +* `ggsave()` no longer sometimes creates new directories, which is now controlled by the new `create.dir` argument (#5489). - -* Legend titles no longer take up space if they've been removed by setting + +* Legend titles no longer take up space if they've been removed by setting `legend.title = element_blank()` (@teunbrand, #3587). - -* `resolution()` has a small tolerance, preventing spuriously small resolutions + +* `resolution()` has a small tolerance, preventing spuriously small resolutions due to rounding errors (@teunbrand, #2516). - -* `stage()` now works correctly, even with aesthetics that do not have scales + +* `stage()` now works correctly, even with aesthetics that do not have scales (#5408) - -* `stat_ydensity()` with incomplete groups calculates the default `width` + +* `stat_ydensity()` with incomplete groups calculates the default `width` parameter more stably (@teunbrand, #5396) - + * The `size` argument in `annotation_logticks()` has been deprecated in favour of the `linewidth` argument (#5292). - -* Binned scales now treat `NA`s in limits the same way continuous scales do + +* Binned scales now treat `NA`s in limits the same way continuous scales do (#5355). * Binned scales work better with `trans = "reverse"` (#5355). * Integers are once again valid input to theme arguments that expect numeric input (@teunbrand, #5369) - + * Legends in `scale_*_manual()` can show `NA` values again when the `values` is a named vector (@teunbrand, #5214, #5286). - -* Fixed bug in `coord_sf()` where graticule lines didn't obey + +* Fixed bug in `coord_sf()` where graticule lines didn't obey `panel.grid.major`'s linewidth setting (@teunbrand, #5179) - + * Fixed bug in `annotation_logticks()` when no suitable tick positions could be found (@teunbrand, #5248). - + * The default width of `geom_bar()` is now based on panel-wise resolution of the data, rather than global resolution (@teunbrand, #4336). - + * `stat_align()` is now applied per panel instead of globally, preventing issues when facets have different ranges (@teunbrand, #5227). - + * A stacking bug in `stat_align()` was fixed (@teunbrand, #5176). * `stat_contour()` and `stat_contour_filled()` now warn about and remove duplicated coordinates (@teunbrand, #5215). - -* `guide_coloursteps()` and `guide_bins()` sort breaks (#5152). - + +* `guide_coloursteps()` and `guide_bins()` sort breaks (#5152). + ## Internal changes - + * The `ScaleContinuous$get_breaks()` method no longer censors the computed breaks. - + * The ggplot object now contains `$layout` which points to the `Layout` ggproto object and will be used by the `ggplot_build.ggplot` method. This was exposed - so that package developers may extend the behaviour of the `Layout` ggproto - object without needing to develop an entirely new `ggplot_build` method + so that package developers may extend the behaviour of the `Layout` ggproto + object without needing to develop an entirely new `ggplot_build` method (@jtlandis, #5077). - -* Guide building is now part of `ggplot_build()` instead of + +* Guide building is now part of `ggplot_build()` instead of `ggplot_gtable()` to allow guides to observe unmapped data (#5483). - + * The `titleGrob()` function has been refactored to be faster and less complicated. * The `scales_*()` functions related to managing the `` class have been implemented as methods in the `` class, rather than stray functions (#1310). - + # ggplot2 3.4.4 -This hotfix release adapts to a change in r-devel's `base::is.atomic()` and +This hotfix release adapts to a change in r-devel's `base::is.atomic()` and the upcoming retirement of maptools. * `fortify()` for sp objects (e.g., `SpatialPolygonsDataFrame`) is now deprecated @@ -788,121 +806,121 @@ changes and a few bug fixes as well. ## Minor improvements -* Various type checks and their messages have been standardised +* Various type checks and their messages have been standardised (@teunbrand, #4834). - + * ggplot2 now uses `scales::DiscreteRange` and `scales::ContinuousRange`, which are available to write scale extensions from scratch (@teunbrand, #2710). - + * The `layer_data()`, `layer_scales()` and `layer_grob()` now have the default `plot = last_plot()` (@teunbrand, #5166). - + * The `datetime_scale()` scale constructor is now exported for use in extension packages (@teunbrand, #4701). - + ## Bug fixes -* `update_geom_defaults()` and `update_stat_defaults()` now return properly +* `update_geom_defaults()` and `update_stat_defaults()` now return properly classed objects and have updated docs (@dkahle, #5146). -* For the purposes of checking required or non-missing aesthetics, character +* For the purposes of checking required or non-missing aesthetics, character vectors are no longer considered non-finite (@teunbrand, @4284). * `annotation_logticks()` skips drawing ticks when the scale range is non-finite instead of throwing an error (@teunbrand, #5229). - -* Fixed spurious warnings when the `weight` was used in `stat_bin_2d()`, + +* Fixed spurious warnings when the `weight` was used in `stat_bin_2d()`, `stat_boxplot()`, `stat_contour()`, `stat_bin_hex()` and `stat_quantile()` (@teunbrand, #5216). -* To prevent changing the plotting order, `stat_sf()` is now computed per panel +* To prevent changing the plotting order, `stat_sf()` is now computed per panel instead of per group (@teunbrand, #4340). -* Fixed bug in `coord_sf()` where graticule lines didn't obey +* Fixed bug in `coord_sf()` where graticule lines didn't obey `panel.grid.major`'s linewidth setting (@teunbrand, #5179). * `geom_text()` drops observations where `angle = NA` instead of throwing an error (@teunbrand, #2757). - + # ggplot2 3.4.1 This is a small release focusing on fixing regressions in the 3.4.0 release and minor polishes. ## Breaking changes -* The computed variable `y` in `stat_ecdf()` has been superseded by `ecdf` to +* The computed variable `y` in `stat_ecdf()` has been superseded by `ecdf` to prevent incorrect scale transformations (@teunbrand, #5113 and #5112). - + ## New features * Added `scale_linewidth_manual()` and `scale_linewidth_identity()` to support the `linewidth` aesthetic (@teunbrand, #5050). - + * `ggsave()` warns when multiple `filename`s are given, and only writes to the first file (@teunbrand, #5114). ## Bug fixes -* Fixed a regression in `geom_hex()` where aesthetics were replicated across +* Fixed a regression in `geom_hex()` where aesthetics were replicated across bins (@thomasp85, #5037 and #5044). - -* Using two ordered factors as facetting variables in + +* Using two ordered factors as facetting variables in `facet_grid(..., as.table = FALSE)` now throws a warning instead of an error (@teunbrand, #5109). - -* Fixed misbehaviour of `draw_key_boxplot()` and `draw_key_crossbar()` with + +* Fixed misbehaviour of `draw_key_boxplot()` and `draw_key_crossbar()` with skewed key aspect ratio (@teunbrand, #5082). - -* Fixed spurious warning when `weight` aesthetic was used in `stat_smooth()` + +* Fixed spurious warning when `weight` aesthetic was used in `stat_smooth()` (@teunbrand based on @clauswilke's suggestion, #5053). - -* The `lwd` alias is now correctly replaced by `linewidth` instead of `size` + +* The `lwd` alias is now correctly replaced by `linewidth` instead of `size` (@teunbrand based on @clauswilke's suggestion #5051). - -* Fixed a regression in `Coord$train_panel_guides()` where names of guides were + +* Fixed a regression in `Coord$train_panel_guides()` where names of guides were dropped (@maxsutton, #5063). In binned scales: * Automatic breaks should no longer be out-of-bounds, and automatic limits are adjusted to include breaks (@teunbrand, #5082). - + * Zero-range limits no longer throw an error and are treated akin to continuous scales with zero-range limits (@teunbrand, #5066). - + * The `trans = "date"` and `trans = "time"` transformations were made compatible (@teunbrand, #4217). # ggplot2 3.4.0 This is a minor release focusing on tightening up the internals and ironing out -some inconsistencies in the API. The biggest change is the addition of the -`linewidth` aesthetic that takes of sizing the width of any line from `size`. -This change, while attempting to be as non-breaking as possible, has the +some inconsistencies in the API. The biggest change is the addition of the +`linewidth` aesthetic that takes of sizing the width of any line from `size`. +This change, while attempting to be as non-breaking as possible, has the potential to change the look of some of your plots. Other notable changes is a complete redo of the error and warning messaging in -ggplot2 using the cli package. Messaging is now better contextualised and it +ggplot2 using the cli package. Messaging is now better contextualised and it should be easier to identify which layer an error is coming from. Last, we have -now made the switch to using the vctrs package internally which means that -support for vctrs classes as variables should improve, along with some small +now made the switch to using the vctrs package internally which means that +support for vctrs classes as variables should improve, along with some small gains in rendering speed. ## Breaking changes -* A `linewidth` aesthetic has been introduced and supersedes the `size` - aesthetic for scaling the width of lines in line based geoms. `size` will - remain functioning but deprecated for these geoms and it is recommended to - update all code to reflect the new aesthetic. For geoms that have _both_ point - sizing and linewidth sizing (`geom_pointrange()` and `geom_sf`) `size` now +* A `linewidth` aesthetic has been introduced and supersedes the `size` + aesthetic for scaling the width of lines in line based geoms. `size` will + remain functioning but deprecated for these geoms and it is recommended to + update all code to reflect the new aesthetic. For geoms that have _both_ point + sizing and linewidth sizing (`geom_pointrange()` and `geom_sf`) `size` now **only** refers to sizing of points which can leads to a visual change in old code (@thomasp85, #3672) - -* The default line width for polygons in `geom_sf()` have been decreased to 0.2 - to reflect that this is usually used for demarking borders where a thinner - line is better suited. This change was made since we already induced a - visual change in `geom_sf()` with the introduction of the `linewidth` + +* The default line width for polygons in `geom_sf()` have been decreased to 0.2 + to reflect that this is usually used for demarking borders where a thinner + line is better suited. This change was made since we already induced a + visual change in `geom_sf()` with the introduction of the `linewidth` aesthetic. - + * The dot-dot notation (`..var..`) and `stat()`, which have been superseded by `after_stat()`, are now formally deprecated (@yutannihilation, #3693). @@ -913,7 +931,7 @@ gains in rendering speed. values for some reason, you have to apply the same transformation by yourself, e.g. `sqrt()` for `scale_{x,y}_sqrt()` (@yutannihilation and @teunbrand, #4155). -* Use `rlang::hash()` instead of `digest::digest()`. This update may lead to +* Use `rlang::hash()` instead of `digest::digest()`. This update may lead to changes in the automatic sorting of legends. In order to enforce a specific legend order use the `order` argument in the guide. (@thomasp85, #4458) @@ -922,10 +940,10 @@ gains in rendering speed. * The `ticks.linewidth` and `frame.linewidth` parameters of `guide_colourbar()` are now multiplied with `.pt` like elsewhere in ggplot2. It can cause visual - changes when these arguments are not the defaults and these changes can be + changes when these arguments are not the defaults and these changes can be restored to their previous behaviour by adding `/ .pt` (@teunbrand #4314). -* `scale_*_viridis_b()` now uses the full range of the viridis scales +* `scale_*_viridis_b()` now uses the full range of the viridis scales (@gregleleu, #4737) ## New features @@ -938,18 +956,18 @@ gains in rendering speed. * `geom_density()` and `stat_density()` now support `bounds` argument to estimate density with boundary correction (@echasnovski, #4013). -* ggplot now checks during statistical transformations whether any data +* ggplot now checks during statistical transformations whether any data columns were dropped and warns about this. If stats intend to drop data columns they can declare them in the new field `dropped_aes`. (@clauswilke, #3250) -* `...` supports `rlang::list2` dynamic dots in all public functions. - (@mone27, #4764) +* `...` supports `rlang::list2` dynamic dots in all public functions. + (@mone27, #4764) -* `theme()` now has a `strip.clip` argument, that can be set to `"off"` to +* `theme()` now has a `strip.clip` argument, that can be set to `"off"` to prevent the clipping of strip text and background borders (@teunbrand, #4118) - -* `geom_contour()` now accepts a function in the `breaks` argument + +* `geom_contour()` now accepts a function in the `breaks` argument (@eliocamp, #4652). ## Minor improvements and bug fixes @@ -959,31 +977,31 @@ gains in rendering speed. * `geom_linerange()` now respects the `na.rm` argument (#4927, @thomasp85) -* Improve the support for `guide_axis()` on `coord_trans()` +* Improve the support for `guide_axis()` on `coord_trans()` (@yutannihilation, #3959) - + * Added `stat_align()` to align data without common x-coordinates prior to stacking. This is now the default stat for `geom_area()` (@thomasp85, #4850) -* Fix a bug in `stat_contour_filled()` where break value differences below a - certain number of digits would cause the computations to fail (@thomasp85, +* Fix a bug in `stat_contour_filled()` where break value differences below a + certain number of digits would cause the computations to fail (@thomasp85, #4874) * Secondary axis ticks are now positioned more precisely, removing small visual artefacts with alignment between grid and ticks (@thomasp85, #3576) -* Improve `stat_function` documentation regarding `xlim` argument. +* Improve `stat_function` documentation regarding `xlim` argument. (@92amartins, #4474) * Fix various issues with how `labels`, `breaks`, `limits`, and `show.limits` interact in the different binning guides (@thomasp85, #4831) * Automatic break calculation now squishes the scale limits to the domain - of the transformation. This allows `scale_{x/y}_sqrt()` to find breaks at 0 + of the transformation. This allows `scale_{x/y}_sqrt()` to find breaks at 0 when appropriate (@teunbrand, #980). -* Using multiple modified aesthetics correctly will no longer trigger warnings. - If used incorrectly, the warning will now report the duplicated aesthetic +* Using multiple modified aesthetics correctly will no longer trigger warnings. + If used incorrectly, the warning will now report the duplicated aesthetic instead of `NA` (@teunbrand, #4707). * `aes()` now supports the `!!!` operator in its first two arguments @@ -1005,9 +1023,9 @@ gains in rendering speed. * `geom_tile()` now correctly recognises missing data in `xmin`, `xmax`, `ymin`, and `ymax` (@thomasp85 and @sigmapi, #4495) -* `geom_hex()` will now use the binwidth from `stat_bin_hex()` if present, +* `geom_hex()` will now use the binwidth from `stat_bin_hex()` if present, instead of deriving it (@thomasp85, #4580) - + * `geom_hex()` now works on non-linear coordinate systems (@thomasp85) * Fixed a bug throwing errors when trying to render an empty plot with secondary @@ -1016,28 +1034,28 @@ gains in rendering speed. * Axes are now added correctly in `facet_wrap()` when `as.table = FALSE` (@thomasp85, #4553) -* Better compatibility of custom device functions in `ggsave()` +* Better compatibility of custom device functions in `ggsave()` (@thomasp85, #4539) * Binning scales are now more resilient to calculated limits that ends up being `NaN` after transformations (@thomasp85, #4510) -* Strip padding in `facet_grid()` is now only in effect if - `strip.placement = "outside"` _and_ an axis is present between the strip and +* Strip padding in `facet_grid()` is now only in effect if + `strip.placement = "outside"` _and_ an axis is present between the strip and the panel (@thomasp85, #4610) -* Aesthetics of length 1 are now recycled to 0 if the length of the data is 0 +* Aesthetics of length 1 are now recycled to 0 if the length of the data is 0 (@thomasp85, #4588) -* Setting `size = NA` will no longer cause `guide_legend()` to error +* Setting `size = NA` will no longer cause `guide_legend()` to error (@thomasp85, #4559) * Setting `stroke` to `NA` in `geom_point()` will no longer impair the sizing of the points (@thomasp85, #4624) -* `stat_bin_2d()` now correctly recognises the `weight` aesthetic +* `stat_bin_2d()` now correctly recognises the `weight` aesthetic (@thomasp85, #4646) - + * All geoms now have consistent exposure of linejoin and lineend parameters, and the guide keys will now respect these settings (@thomasp85, #4653) @@ -1046,13 +1064,13 @@ gains in rendering speed. * Updated documentation for `print.ggplot` to reflect that it returns the original plot, not the result of `ggplot_build()`. (@r2evans, #4390) -* `scale_*_manual()` no longer displays extra legend keys, or changes their +* `scale_*_manual()` no longer displays extra legend keys, or changes their order, when a named `values` argument has more items than the data. To display all `values` on the legend instead, use - `scale_*_manual(values = vals, limits = names(vals))`. (@teunbrand, @banfai, + `scale_*_manual(values = vals, limits = names(vals))`. (@teunbrand, @banfai, #4511, #4534) -* Updated documentation for `geom_contour()` to correctly reflect argument +* Updated documentation for `geom_contour()` to correctly reflect argument precedence between `bins` and `binwidth`. (@eliocamp, #4651) * Dots in `geom_dotplot()` are now correctly aligned to the baseline when @@ -1060,43 +1078,43 @@ gains in rendering speed. * Key glyphs for `geom_boxplot()`, `geom_crossbar()`, `geom_pointrange()`, and `geom_linerange()` are now orientation-aware (@mjskay, #4732) - -* Updated documentation for `geom_smooth()` to more clearly describe effects of + +* Updated documentation for `geom_smooth()` to more clearly describe effects of the `fullrange` parameter (@thoolihan, #4399). # ggplot2 3.3.6 -This is a very small release only applying an internal change to comply with +This is a very small release only applying an internal change to comply with R 4.2 and its deprecation of `default.stringsAsFactors()`. There are no user facing changes and no breaking changes. # ggplot2 3.3.5 -This is a very small release focusing on fixing a couple of untenable issues +This is a very small release focusing on fixing a couple of untenable issues that surfaced with the 3.3.4 release -* Revert changes made in #4434 (apply transform to intercept in `geom_abline()`) - as it introduced undesirable issues far worse than the bug it fixed +* Revert changes made in #4434 (apply transform to intercept in `geom_abline()`) + as it introduced undesirable issues far worse than the bug it fixed (@thomasp85, #4514) -* Fixes an issue in `ggsave()` when producing emf/wmf files (@yutannihilation, +* Fixes an issue in `ggsave()` when producing emf/wmf files (@yutannihilation, #4521) -* Warn when grDevices specific arguments are passed to ragg devices (@thomasp85, +* Warn when grDevices specific arguments are passed to ragg devices (@thomasp85, #4524) * Fix an issue where `coord_sf()` was reporting that it is non-linear even when data is provided in projected coordinates (@clauswilke, #4527) # ggplot2 3.3.4 -This is a larger patch release fixing a huge number of bugs and introduces a +This is a larger patch release fixing a huge number of bugs and introduces a small selection of feature refinements. ## Features -* Alt-text can now be added to a plot using the `alt` label, i.e - `+ labs(alt = ...)`. Currently this alt text is not automatically propagated, - but we plan to integrate into Shiny, RMarkdown, and other tools in the future. +* Alt-text can now be added to a plot using the `alt` label, i.e + `+ labs(alt = ...)`. Currently this alt text is not automatically propagated, + but we plan to integrate into Shiny, RMarkdown, and other tools in the future. (@thomasp85, #4477) * Add support for the BrailleR package for creating descriptions of the plot when rendered (@thomasp85, #4459) - + * `coord_sf()` now has an argument `default_crs` that specifies the coordinate reference system (CRS) for non-sf layers and scale/coord limits. This argument defaults to `NULL`, which means non-sf layers are assumed to be in projected @@ -1108,7 +1126,7 @@ small selection of feature refinements. hints to `coord_sf()` (@clauswilke, #3659). * `ggsave()` now uses ragg to render raster output if ragg is available. It also - handles custom devices that sets a default unit (e.g. `ragg::agg_png`) + handles custom devices that sets a default unit (e.g. `ragg::agg_png`) correctly (@thomasp85, #4388) * `ggsave()` now returns the saved file location invisibly (#3379, @eliocamp). @@ -1116,51 +1134,51 @@ small selection of feature refinements. no longer works (#4513). * The scale arguments `limits`, `breaks`, `minor_breaks`, `labels`, `rescaler` - and `oob` now accept purrr style lambda notation (@teunbrand, #4427). The same - is true for `as_labeller()` (and therefore also `labeller()`) + and `oob` now accept purrr style lambda notation (@teunbrand, #4427). The same + is true for `as_labeller()` (and therefore also `labeller()`) (@netique, #4188). -* Manual scales now allow named vectors passed to `values` to contain fewer +* Manual scales now allow named vectors passed to `values` to contain fewer elements than existing in the data. Elements not present in values will be set to `NA` (@thomasp85, #3451) - -* Date and datetime position scales support out-of-bounds (oob) arguments to + +* Date and datetime position scales support out-of-bounds (oob) arguments to control how limits affect data outside those limits (@teunbrand, #4199). - + ## Fixes * Fix a bug that `after_stat()` and `after_scale()` cannot refer to aesthetics if it's specified in the plot-global mapping (@yutannihilation, #4260). - + * Fix bug in `annotate_logticks()` that would cause an error when used together with `coord_flip()` (@thomasp85, #3954) - + * Fix a bug in `geom_abline()` that resulted in `intercept` not being subjected to the transformation of the y scale (@thomasp85, #3741) - + * Extent the range of the line created by `geom_abline()` so that line ending is not visible for large linewidths (@thomasp85, #4024) -* Fix bug in `geom_dotplot()` where dots would be positioned wrong with +* Fix bug in `geom_dotplot()` where dots would be positioned wrong with `stackgroups = TRUE` (@thomasp85, #1745) * Fix calculation of confidence interval for locfit smoothing in `geom_smooth()` (@topepo, #3806) - -* Fix bug in `geom_text()` where `"outward"` and `"inward"` justification for + +* Fix bug in `geom_text()` where `"outward"` and `"inward"` justification for some `angle` values was reversed (@aphalo, #4169, #4447) * `ggsave()` now sets the default background to match the fill value of the `plot.background` theme element (@karawoo, #4057) * It is now deprecated to specify `guides( = FALSE)` or - `scale_*(guide = FALSE)` to remove a guide. Please use - `guides( = "none")` or `scale_*(guide = "none")` instead + `scale_*(guide = FALSE)` to remove a guide. Please use + `guides( = "none")` or `scale_*(guide = "none")` instead (@yutannihilation, #4097) - -* Fix a bug in `guide_bins()` where keys would disappear if the guide was + +* Fix a bug in `guide_bins()` where keys would disappear if the guide was reversed (@thomasp85, #4210) - + * Fix bug in `guide_coloursteps()` that would repeat the terminal bins if the breaks coincided with the limits of the scale (@thomasp85, #4019) @@ -1169,12 +1187,12 @@ small selection of feature refinements. * Fix bug in `labeller()` where parsing was turned off if `.multiline = FALSE` (@thomasp85, #4084) - -* Make sure `label_bquote()` has access to the calling environment when + +* Make sure `label_bquote()` has access to the calling environment when evaluating the labels (@thomasp85, #4141) -* Fix a bug in the layer implementation that introduced a new state after the - first render which could lead to a different look when rendered the second +* Fix a bug in the layer implementation that introduced a new state after the + first render which could lead to a different look when rendered the second time (@thomasp85, #4204) * Fix a bug in legend justification where justification was lost of the legend @@ -1183,57 +1201,57 @@ small selection of feature refinements. * Fix a bug in `position_dodge2()` where `NA` values in thee data would cause an error (@thomasp85, #2905) -* Make sure `position_jitter()` creates the same jittering independent of +* Make sure `position_jitter()` creates the same jittering independent of whether it is called by name or with constructor (@thomasp85, #2507) -* Fix a bug in `position_jitter()` where different jitters would be applied to +* Fix a bug in `position_jitter()` where different jitters would be applied to different position aesthetics of the same axis (@thomasp85, #2941) - -* Fix a bug in `qplot()` when supplying `c(NA, NA)` as axis limits + +* Fix a bug in `qplot()` when supplying `c(NA, NA)` as axis limits (@thomasp85, #4027) - + * Remove cross-inheritance of default discrete colour/fill scales and check the - type and aesthetic of function output if `type` is a function + type and aesthetic of function output if `type` is a function (@thomasp85, #4149) * Fix bug in `scale_[x|y]_date()` where custom breaks functions that resulted in fractional dates would get misaligned (@thomasp85, #3965) - -* Fix bug in `scale_[x|y]_datetime()` where a specified timezone would be + +* Fix bug in `scale_[x|y]_datetime()` where a specified timezone would be ignored by the scale (@thomasp85, #4007) - -* Fix issue in `sec_axis()` that would throw warnings in the absence of any + +* Fix issue in `sec_axis()` that would throw warnings in the absence of any secondary breaks (@thomasp85, #4368) * `stat_bin()`'s computed variable `width` is now documented (#3522). - -* `stat_count()` now computes width based on the full dataset instead of per + +* `stat_count()` now computes width based on the full dataset instead of per group (@thomasp85, #2047) -* Extended `stat_ecdf()` to calculate the cdf from either x or y instead from y +* Extended `stat_ecdf()` to calculate the cdf from either x or y instead from y only (@jgjl, #4005) - + * Fix a bug in `stat_summary_bin()` where one more than the requested number of bins would be created (@thomasp85, #3824) -* Only drop groups in `stat_ydensity()` when there are fewer than two data +* Only drop groups in `stat_ydensity()` when there are fewer than two data points and throw a warning (@andrewwbutler, #4111). * Fixed a bug in strip assembly when theme has `strip.text = element_blank()` and plots are faceted with multi-layered strips (@teunbrand, #4384). - + * Using `theme(aspect.ratio = ...)` together with free space in `facet_grid()` now correctly throws an error (@thomasp85, #3834) * Fixed a bug in `labeller()` so that `.default` is passed to `as_labeller()` when labellers are specified by naming faceting variables. (@waltersom, #4031) - + * Updated style for example code (@rjake, #4092) * ggplot2 now requires R >= 3.3 (#4247). * ggplot2 now uses `rlang::check_installed()` to check if a suggested package is - installed, which will offer to install the package before continuing (#4375, + installed, which will offer to install the package before continuing (#4375, @malcolmbarrett) * Improved error with hint when piping a `ggplot` object into a facet function @@ -1260,18 +1278,18 @@ This is a small release focusing on fixing regressions introduced in 3.3.1. * `annotation_raster()` adds support for native rasters. For large rasters, native rasters render significantly faster than arrays (@kent37, #3388) - -* Facet strips now have dedicated position-dependent theme elements - (`strip.text.x.top`, `strip.text.x.bottom`, `strip.text.y.left`, - `strip.text.y.right`) that inherit from `strip.text.x` and `strip.text.y`, - respectively. As a consequence, some theme stylings now need to be applied to - the position-dependent elements rather than to the parent elements. This - change was already introduced in ggplot2 3.3.0 but not listed in the + +* Facet strips now have dedicated position-dependent theme elements + (`strip.text.x.top`, `strip.text.x.bottom`, `strip.text.y.left`, + `strip.text.y.right`) that inherit from `strip.text.x` and `strip.text.y`, + respectively. As a consequence, some theme stylings now need to be applied to + the position-dependent elements rather than to the parent elements. This + change was already introduced in ggplot2 3.3.0 but not listed in the changelog. (@thomasp85, #3683) * Facets now handle layers containing no data (@yutannihilation, #3853). - -* A newly added geom `geom_density_2d_filled()` and associated stat + +* A newly added geom `geom_density_2d_filled()` and associated stat `stat_density_2d_filled()` can draw filled density contours (@clauswilke, #3846). @@ -1282,36 +1300,36 @@ This is a small release focusing on fixing regressions introduced in 3.3.1. * Fixed a bug in `geom_sf()` that caused problems with legend-type autodetection (@clauswilke, #3963). - -* Support graphics devices that use the `file` argument instead of `fileneame` + +* Support graphics devices that use the `file` argument instead of `fileneame` in `ggsave()` (@bwiernik, #3810) - -* Default discrete color scales are now configurable through the `options()` of - `ggplot2.discrete.colour` and `ggplot2.discrete.fill`. When set to a character - vector of colour codes (or list of character vectors) with sufficient length, - these colours are used for the default scale. See `help(scale_colour_discrete)` + +* Default discrete color scales are now configurable through the `options()` of + `ggplot2.discrete.colour` and `ggplot2.discrete.fill`. When set to a character + vector of colour codes (or list of character vectors) with sufficient length, + these colours are used for the default scale. See `help(scale_colour_discrete)` for more details and examples (@cpsievert, #3833). -* Default continuous colour scales (i.e., the `options()` - `ggplot2.continuous.colour` and `ggplot2.continuous.fill`, which inform the - `type` argument of `scale_fill_continuous()` and `scale_colour_continuous()`) - now accept a function, which allows more control over these default +* Default continuous colour scales (i.e., the `options()` + `ggplot2.continuous.colour` and `ggplot2.continuous.fill`, which inform the + `type` argument of `scale_fill_continuous()` and `scale_colour_continuous()`) + now accept a function, which allows more control over these default `continuous_scale()`s (@cpsievert, #3827). -* A bug was fixed in `stat_contour()` when calculating breaks based on +* A bug was fixed in `stat_contour()` when calculating breaks based on the `bins` argument (@clauswilke, #3879, #4004). - -* Data columns can now contain `Vector` S4 objects, which are widely used in the + +* Data columns can now contain `Vector` S4 objects, which are widely used in the Bioconductor project. (@teunbrand, #3837) # ggplot2 3.3.1 -This is a small release with no code change. It removes all malicious links to a +This is a small release with no code change. It removes all malicious links to a site that got hijacked from the readme and pkgdown site. # ggplot2 3.3.0 -This is a minor release but does contain a range of substantial new features, +This is a minor release but does contain a range of substantial new features, along with the standard bug fixes. The release contains a few visual breaking changes, along with breaking changes for extension developers due to a shift in internal representation of the position scales and their axes. No user breaking @@ -1320,21 +1338,21 @@ changes are included. This release also adds Dewey Dunnington (@paleolimbot) to the core team. ## Breaking changes -There are no user-facing breaking changes, but a change in some internal -representations that extension developers may have relied on, along with a few -breaking visual changes which may cause visual tests in downstream packages to +There are no user-facing breaking changes, but a change in some internal +representations that extension developers may have relied on, along with a few +breaking visual changes which may cause visual tests in downstream packages to fail. -* The `panel_params` field in the `Layout` now contains a list of list of +* The `panel_params` field in the `Layout` now contains a list of list of `ViewScale` objects, describing the trained coordinate system scales, instead of the list object used before. Any extensions that use this field will likely break, as will unit tests that checks aspects of this. -* `element_text()` now issues a warning when vectorized arguments are provided, - as in `colour = c("red", "green", "blue")`. Such use is discouraged and not +* `element_text()` now issues a warning when vectorized arguments are provided, + as in `colour = c("red", "green", "blue")`. Such use is discouraged and not officially supported (@clauswilke, #3492). -* Changed `theme_grey()` setting for legend key so that it creates no border +* Changed `theme_grey()` setting for legend key so that it creates no border (`NA`) rather than drawing a white one. (@annennenne, #3180) * `geom_ribbon()` now draws separate lines for the upper and lower intervals if @@ -1344,56 +1362,56 @@ fail. ## New features -* The evaluation time of aesthetics can now be controlled to a finer degree. +* The evaluation time of aesthetics can now be controlled to a finer degree. `after_stat()` supersedes the use of `stat()` and `..var..`-notation, and is - joined by `after_scale()` to allow for mapping to scaled aesthetic values. - Remapping of the same aesthetic is now supported with `stage()`, so you can - map a data variable to a stat aesthetic, and remap the same aesthetic to + joined by `after_scale()` to allow for mapping to scaled aesthetic values. + Remapping of the same aesthetic is now supported with `stage()`, so you can + map a data variable to a stat aesthetic, and remap the same aesthetic to something else after statistical transformation (@thomasp85, #3534) * All `coord_*()` functions with `xlim` and `ylim` arguments now accept vectors with `NA` as a placeholder for the minimum or maximum value - (e.g., `ylim = c(0, NA)` would zoom the y-axis from 0 to the + (e.g., `ylim = c(0, NA)` would zoom the y-axis from 0 to the maximum value observed in the data). This mimics the behaviour of the `limits` argument in continuous scale functions (@paleolimbot, #2907). -* Allowed reversing of discrete scales by re-writing `get_limits()` +* Allowed reversing of discrete scales by re-writing `get_limits()` (@AnneLyng, #3115) - -* All geoms and stats that had a direction (i.e. where the x and y axes had + +* All geoms and stats that had a direction (i.e. where the x and y axes had different interpretation), can now freely choose their direction, instead of - relying on `coord_flip()`. The direction is deduced from the aesthetic - mapping, but can also be specified directly with the new `orientation` + relying on `coord_flip()`. The direction is deduced from the aesthetic + mapping, but can also be specified directly with the new `orientation` argument (@thomasp85, #3506). - -* Position guides can now be customized using the new `guide_axis()`, which can - be passed to position `scale_*()` functions or via `guides()`. The new axis - guide (`guide_axis()`) comes with arguments `check.overlap` (automatic removal + +* Position guides can now be customized using the new `guide_axis()`, which can + be passed to position `scale_*()` functions or via `guides()`. The new axis + guide (`guide_axis()`) comes with arguments `check.overlap` (automatic removal of overlapping labels), `angle` (easy rotation of axis labels), and `n.dodge` (dodge labels into multiple rows/columns) (@paleolimbot, #3322). - -* A new scale type has been added, that allows binning of aesthetics at the + +* A new scale type has been added, that allows binning of aesthetics at the scale level. It has versions for both position and non-position aesthetics and - comes with two new guides (`guide_bins` and `guide_coloursteps`) + comes with two new guides (`guide_bins` and `guide_coloursteps`) (@thomasp85, #3096) - + * `scale_x_continuous()` and `scale_y_continuous()` gains an `n.breaks` argument guiding the number of automatic generated breaks (@thomasp85, #3102) -* Added `stat_contour_filled()` and `geom_contour_filled()`, which compute - and draw filled contours of gridded data (@paleolimbot, #3044). +* Added `stat_contour_filled()` and `geom_contour_filled()`, which compute + and draw filled contours of gridded data (@paleolimbot, #3044). `geom_contour()` and `stat_contour()` now use the isoband package to compute contour lines. The `complete` parameter (which was undocumented and has been unused for at least four years) was removed (@paleolimbot, #3044). - -* Themes have gained two new parameters, `plot.title.position` and + +* Themes have gained two new parameters, `plot.title.position` and `plot.caption.position`, that can be used to customize how plot title/subtitle and plot caption are positioned relative to the overall plot (@clauswilke, #3252). ## Extensions - + * `Geom` now gains a `setup_params()` method in line with the other ggproto classes (@thomasp85, #3509) @@ -1404,35 +1422,35 @@ fail. ## Minor improvements and bug fixes * `coord_trans()` now draws second axes and accepts `xlim`, `ylim`, - and `expand` arguments to bring it up to feature parity with - `coord_cartesian()`. The `xtrans` and `ytrans` arguments that were - deprecated in version 1.0.1 in favour of `x` and `y` + and `expand` arguments to bring it up to feature parity with + `coord_cartesian()`. The `xtrans` and `ytrans` arguments that were + deprecated in version 1.0.1 in favour of `x` and `y` were removed (@paleolimbot, #2990). -* `coord_trans()` now calculates breaks using the expanded range - (previously these were calculated using the unexpanded range, +* `coord_trans()` now calculates breaks using the expanded range + (previously these were calculated using the unexpanded range, which resulted in differences between plots made with `coord_trans()` - and those made with `coord_cartesian()`). The expansion for discrete axes + and those made with `coord_cartesian()`). The expansion for discrete axes in `coord_trans()` was also updated such that it behaves identically to that in `coord_cartesian()` (@paleolimbot, #3338). * `expand_scale()` was deprecated in favour of `expansion()` for setting the `expand` argument of `x` and `y` scales (@paleolimbot). -* `geom_abline()`, `geom_hline()`, and `geom_vline()` now issue +* `geom_abline()`, `geom_hline()`, and `geom_vline()` now issue more informative warnings when supplied with set aesthetics (i.e., `slope`, `intercept`, `yintercept`, and/or `xintercept`) and mapped aesthetics (i.e., `data` and/or `mapping`). -* Fix a bug in `geom_raster()` that squeezed the image when it went outside +* Fix a bug in `geom_raster()` that squeezed the image when it went outside scale limits (#3539, @thomasp85) * `geom_sf()` now determines the legend type automatically (@microly, #3646). - -* `geom_sf()` now removes rows that can't be plotted due to `NA` aesthetics + +* `geom_sf()` now removes rows that can't be plotted due to `NA` aesthetics (#3546, @thomasp85) -* `geom_sf()` now applies alpha to linestring geometries +* `geom_sf()` now applies alpha to linestring geometries (#3589, @yutannihilation). * `gg_dep()` was deprecated (@perezp44, #3382). @@ -1440,10 +1458,10 @@ fail. * Added function `ggplot_add.by()` for lists created with `by()`, allowing such lists to be added to ggplot objects (#2734, @Maschette) -* ggplot2 no longer depends on reshape2, which means that it no longer +* ggplot2 no longer depends on reshape2, which means that it no longer (recursively) needs plyr, stringr, or stringi packages. -* Increase the default `nbin` of `guide_colourbar()` to place the ticks more +* Increase the default `nbin` of `guide_colourbar()` to place the ticks more precisely (#3508, @yutannihilation). * `manual_scale()` now matches `values` with the order of `breaks` whenever @@ -1455,13 +1473,13 @@ fail. * `scale_manual_*(limits = ...)` now actually limits the scale (#3262, @yutannihilation). -* Fix a bug when `show.legend` is a named logical vector +* Fix a bug when `show.legend` is a named logical vector (#3461, @yutannihilation). -* Added weight aesthetic option to `stat_density()` and made scaling of +* Added weight aesthetic option to `stat_density()` and made scaling of weights the default (@annennenne, #2902) - -* `stat_density2d()` can now take an `adjust` parameter to scale the default + +* `stat_density2d()` can now take an `adjust` parameter to scale the default bandwidth. (#2860, @haleyjeppson) * `stat_smooth()` uses `REML` by default, if `method = "gam"` and @@ -1469,7 +1487,7 @@ fail. * stacking text when calculating the labels and the y axis with `stat_summary()` now works (@ikosmidis, #2709) - + * `stat_summary()` and related functions now support rlang-style lambda functions (#3568, @dkahle). @@ -1487,8 +1505,8 @@ fail. This is a patch release fixing a few regressions introduced in 3.2.0 as well as fixing some unit tests that broke due to upstream changes. -* `position_stack()` no longer changes the order of the input data. Changes to - the internal behaviour of `geom_ribbon()` made this reordering problematic +* `position_stack()` no longer changes the order of the input data. Changes to + the internal behaviour of `geom_ribbon()` made this reordering problematic with ribbons that spanned `y = 0` (#3471) * Using `qplot()` with a single positional aesthetic will no longer title the non-specified scale as `"NULL"` (#3473) @@ -1496,11 +1514,11 @@ fixing some unit tests that broke due to upstream changes. # ggplot2 3.2.0 -This is a minor release with an emphasis on internal changes to make ggplot2 -faster and more consistent. The few interface changes will only affect the +This is a minor release with an emphasis on internal changes to make ggplot2 +faster and more consistent. The few interface changes will only affect the aesthetics of the plot in minor ways, and will only potentially break code of -extension developers if they have relied on internals that have been changed. -This release also sees the addition of Hiroaki Yutani (@yutannihilation) to the +extension developers if they have relied on internals that have been changed. +This release also sees the addition of Hiroaki Yutani (@yutannihilation) to the core developer team. With the release of R 3.6, ggplot2 now requires the R version to be at least 3.2, @@ -1513,7 +1531,7 @@ as the tidyverse is committed to support 5 major versions of R. eye. However, these changes are detected by the vdiffr package, and therefore any package developers who use vdiffr to test for visual correctness of ggplot2 plots will have to regenerate all reference images. - + * In some cases, ggplot2 now produces a warning or an error for code that previously produced plot output. In all these cases, the previous plot output was accidental, and the plotting code uses the ggplot2 API in a way that would lead to undefined @@ -1523,33 +1541,33 @@ as the tidyverse is committed to support 5 major versions of R. ## New features -* This release includes a range of internal changes that speeds up plot +* This release includes a range of internal changes that speeds up plot generation. None of the changes are user facing and will not break any code, but in general ggplot2 should feel much faster. The changes includes, but are not limited to: - + - Caching ascent and descent dimensions of text to avoid recalculating it for every title. - - - Using a faster data.frame constructor as well as faster indexing into + + - Using a faster data.frame constructor as well as faster indexing into data.frames - - - Removing the plyr dependency, replacing plyr functions with faster + + - Removing the plyr dependency, replacing plyr functions with faster equivalents. -* `geom_polygon()` can now draw polygons with holes using the new `subgroup` +* `geom_polygon()` can now draw polygons with holes using the new `subgroup` aesthetic. This functionality requires R 3.6.0 (@thomasp85, #3128) * Aesthetic mappings now accept functions that return `NULL` (@yutannihilation, #2997). -* `stat_function()` now accepts rlang/purrr style anonymous functions for the +* `stat_function()` now accepts rlang/purrr style anonymous functions for the `fun` parameter (@dkahle, #3159). -* `geom_rug()` gains an "outside" option to allow for moving the rug tassels to - outside the plot area (@njtierney, #3085) and a `length` option to allow for - changing the length of the rug lines (@daniel-wells, #3109). - +* `geom_rug()` gains an "outside" option to allow for moving the rug tassels to + outside the plot area (@njtierney, #3085) and a `length` option to allow for + changing the length of the rug lines (@daniel-wells, #3109). + * All geoms now take a `key_glyph` paramter that allows users to customize how legend keys are drawn (@clauswilke, #3145). In addition, a new key glyph `timeseries` is provided to draw nice legends for time series @@ -1558,21 +1576,21 @@ as the tidyverse is committed to support 5 major versions of R. ## Extensions * Layers now have a new member function `setup_layer()` which is called at the - very beginning of the plot building process and which has access to the - original input data and the plot object being built. This function allows the - creation of custom layers that autogenerate aesthetic mappings based on the + very beginning of the plot building process and which has access to the + original input data and the plot object being built. This function allows the + creation of custom layers that autogenerate aesthetic mappings based on the input data or that filter the input data in some form. For the time being, this feature is not exported, but it has enabled the development of a new layer type, `layer_sf()` (see next item). Other special-purpose layer types may be added in the future (@clauswilke, #2872). - + * A new layer type `layer_sf()` can auto-detect and auto-map sf geometry columns in the data. It should be used by extension developers who are writing new sf-based geoms or stats (@clauswilke, #3232). -* `x0` and `y0` are now recognized positional aesthetics so they will get scaled +* `x0` and `y0` are now recognized positional aesthetics so they will get scaled if used in extension geoms and stats (@thomasp85, #3168) - + * Continuous scale limits now accept functions which accept the default limits and return adjusted limits. This makes it possible to write a function that e.g. ensures the limits are always a multiple of 100, @@ -1590,13 +1608,13 @@ as the tidyverse is committed to support 5 major versions of R. * `coord_sf()`, `coord_map()`, and `coord_polar()` now squash `-Inf` and `Inf` into the min and max of the plot (@yutannihilation, #2972). -* `coord_sf()` graticule lines are now drawn in the same thickness as panel grid - lines in `coord_cartesian()`, and seting panel grid lines to `element_blank()` - now also works in `coord_sf()` +* `coord_sf()` graticule lines are now drawn in the same thickness as panel grid + lines in `coord_cartesian()`, and seting panel grid lines to `element_blank()` + now also works in `coord_sf()` (@clauswilke, #2991, #2525). * `economics` data has been regenerated. This leads to some changes in the - values of all columns (especially in `psavert`), but more importantly, strips + values of all columns (especially in `psavert`), but more importantly, strips the grouping attributes from `economics_long`. * `element_line()` now fills closed arrows (@yutannihilation, #2924). @@ -1609,23 +1627,23 @@ as the tidyverse is committed to support 5 major versions of R. * Clearer error messages for inappropriate aesthetics (@clairemcwhite, #3060). -* ggplot2 no longer attaches any external packages when using functions that - depend on packages that are suggested but not imported by ggplot2. The - affected functions include `geom_hex()`, `stat_binhex()`, - `stat_summary_hex()`, `geom_quantile()`, `stat_quantile()`, and `map_data()` +* ggplot2 no longer attaches any external packages when using functions that + depend on packages that are suggested but not imported by ggplot2. The + affected functions include `geom_hex()`, `stat_binhex()`, + `stat_summary_hex()`, `geom_quantile()`, `stat_quantile()`, and `map_data()` (@clauswilke, #3126). - -* `geom_area()` and `geom_ribbon()` now sort the data along the x-axis in the - `setup_data()` method rather than as part of `draw_group()` (@thomasp85, + +* `geom_area()` and `geom_ribbon()` now sort the data along the x-axis in the + `setup_data()` method rather than as part of `draw_group()` (@thomasp85, #3023) -* `geom_hline()`, `geom_vline()`, and `geom_abline()` now throw a warning if the - user supplies both an `xintercept`, `yintercept`, or `slope` value and a +* `geom_hline()`, `geom_vline()`, and `geom_abline()` now throw a warning if the + user supplies both an `xintercept`, `yintercept`, or `slope` value and a mapping (@RichardJActon, #2950). * `geom_rug()` now works with `coord_flip()` (@has2k1, #2987). -* `geom_violin()` no longer throws an error when quantile lines fall outside +* `geom_violin()` no longer throws an error when quantile lines fall outside the violin polygon (@thomasp85, #3254). * `guide_legend()` and `guide_colorbar()` now use appropriate spacing between legend @@ -1635,31 +1653,31 @@ as the tidyverse is committed to support 5 major versions of R. get backticks, and long expressions are abbreviated with `...` (@yutannihilation, #2981). -* All-`Inf` layers are now ignored for picking the scale (@yutannihilation, +* All-`Inf` layers are now ignored for picking the scale (@yutannihilation, #3184). - -* Diverging Brewer colour palette now use the correct mid-point colour + +* Diverging Brewer colour palette now use the correct mid-point colour (@dariyasydykova, #3072). - -* `scale_color_continuous()` now points to `scale_colour_continuous()` so that - it will handle `type = "viridis"` as the documentation states (@hlendway, + +* `scale_color_continuous()` now points to `scale_colour_continuous()` so that + it will handle `type = "viridis"` as the documentation states (@hlendway, #3079). -* `scale_shape_identity()` now works correctly with `guide = "legend"` +* `scale_shape_identity()` now works correctly with `guide = "legend"` (@malcolmbarrett, #3029) - + * `scale_continuous` will now draw axis line even if the length of breaks is 0 (@thomasp85, #3257) -* `stat_bin()` will now error when the number of bins exceeds 1e6 to avoid +* `stat_bin()` will now error when the number of bins exceeds 1e6 to avoid accidentally freezing the user session (@thomasp85). - + * `sec_axis()` now places ticks accurately when using nonlinear transformations (@dpseidel, #2978). * `facet_wrap()` and `facet_grid()` now automatically remove NULL from facet specs, and accept empty specs (@yutannihilation, #3070, #2986). -* `stat_bin()` now handles data with only one unique value (@yutannihilation +* `stat_bin()` now handles data with only one unique value (@yutannihilation #3047). * `sec_axis()` now accepts functions as well as formulas (@yutannihilation, #3031). @@ -1683,9 +1701,9 @@ as the tidyverse is committed to support 5 major versions of R. ## Breaking changes -This is a minor release and breaking changes have been kept to a minimum. End users of -ggplot2 are unlikely to encounter any issues. However, there are a few items that developers -of ggplot2 extensions should be aware of. For additional details, see also the discussion +This is a minor release and breaking changes have been kept to a minimum. End users of +ggplot2 are unlikely to encounter any issues. However, there are a few items that developers +of ggplot2 extensions should be aware of. For additional details, see also the discussion accompanying issue #2890. * In non-user-facing internal code (specifically in the `aes()` function and in @@ -1704,7 +1722,7 @@ accompanying issue #2890. used from the generated functions, to avoid hard-to-catch errors. This may affect some users of manual scales (such as `scale_colour_manual()`, `scale_fill_manual()`, etc.) who depend on incorrect behavior (@krlmlr, #2807). - + * `Coord` objects now have a function `backtransform_range()` that returns the panel range in data coordinates. This change may affect developers of custom coords, who now should implement this function. It may also affect developers of custom @@ -1718,12 +1736,12 @@ accompanying issue #2890. be set manually, and there are two new parameters, `label_graticule` and `label_axes`, that can be used to specify which graticules to label on which side of the plot (@clauswilke, #2846, #2857, #2881). - + * Two new geoms `geom_sf_label()` and `geom_sf_text()` can draw labels and text on sf objects. Under the hood, a new `stat_sf_coordinates()` calculates the x and y coordinates from the coordinates of the sf geometries. You can customize the calculation method via `fun.geometry` argument (@yutannihilation, #2761). - + ## Minor improvements and fixes @@ -1743,27 +1761,27 @@ accompanying issue #2890. * `fortify()` now displays a more informative error message for `grouped_df()` objects when dplyr is not installed (@jimhester, #2822). -* All `geom_*()` now display an informative error message when required +* All `geom_*()` now display an informative error message when required aesthetics are missing (@dpseidel, #2637 and #2706). * `geom_boxplot()` now understands the `width` parameter even when used with a non-standard stat, such as `stat_identity()` (@clauswilke, #2893). - + * `geom_hex()` now understands the `size` and `linetype` aesthetics (@mikmart, #2488). - + * `geom_hline()`, `geom_vline()`, and `geom_abline()` now work properly with `coord_trans()` (@clauswilke, #2149, #2812). - + * `geom_text(..., parse = TRUE)` now correctly renders the expected number of items instead of silently dropping items that are empty expressions, e.g. the empty string "". If an expression spans multiple lines, we take just the first line and drop the rest. This same issue is also fixed for `geom_label()` and the axis labels for `geom_sf()` (@slowkow, #2867). -* `geom_sf()` now respects `lineend`, `linejoin`, and `linemitre` parameters +* `geom_sf()` now respects `lineend`, `linejoin`, and `linemitre` parameters for lines and polygons (@alistaire47, #2826). - + * `ggsave()` now exits without creating a new graphics device if previously none was open (@clauswilke, #2363). @@ -1780,14 +1798,14 @@ accompanying issue #2890. * `sec_axis()` now works as expected when used in combination with tidy eval (@dpseidel, #2788). -* `scale_*_date()`, `scale_*_time()` and `scale_*_datetime()` can now display +* `scale_*_date()`, `scale_*_time()` and `scale_*_datetime()` can now display a secondary axis that is a __one-to-one__ transformation of the primary axis, - implemented using the `sec.axis` argument to the scale constructor + implemented using the `sec.axis` argument to the scale constructor (@dpseidel, #2244). - + * `stat_contour()`, `stat_density2d()`, `stat_bin2d()`, `stat_binhex()` now calculate normalized statistics including `nlevel`, `ndensity`, and - `ncount`. Also, `stat_density()` now includes the calculated statistic + `ncount`. Also, `stat_density()` now includes the calculated statistic `nlevel`, an alias for `scaled`, to better match the syntax of `stat_bin()` (@bjreisman, #2679). @@ -1795,29 +1813,29 @@ accompanying issue #2890. ## Breaking changes -* ggplot2 now supports/uses tidy evaluation (as described below). This is a - major change and breaks a number of packages; we made this breaking change - because it is important to make ggplot2 more programmable, and to be more +* ggplot2 now supports/uses tidy evaluation (as described below). This is a + major change and breaks a number of packages; we made this breaking change + because it is important to make ggplot2 more programmable, and to be more consistent with the rest of the tidyverse. The best general (and detailed) introduction to tidy evaluation can be found in the meta programming chapters in [Advanced R](https://adv-r.hadley.nz). - - The primary developer facing change is that `aes()` now contains - quosures (expression + environment pairs) rather than symbols, and you'll - need to take a different approach to extracting the information you need. - A common symptom of this change are errors "undefined columns selected" or + + The primary developer facing change is that `aes()` now contains + quosures (expression + environment pairs) rather than symbols, and you'll + need to take a different approach to extracting the information you need. + A common symptom of this change are errors "undefined columns selected" or "invalid 'type' (list) of argument" (#2610). As in the previous version, constants (like `aes(x = 1)` or `aes(colour = "smoothed")`) are stored as is. - - In this version of ggplot2, if you need to describe a mapping in a string, - use `quo_name()` (to generate single-line strings; longer expressions may + + In this version of ggplot2, if you need to describe a mapping in a string, + use `quo_name()` (to generate single-line strings; longer expressions may be abbreviated) or `quo_text()` (to generate non-abbreviated strings that may span multiple lines). If you do need to extract the value of a variable - instead use `rlang::eval_tidy()`. You may want to condition on + instead use `rlang::eval_tidy()`. You may want to condition on `(packageVersion("ggplot2") <= "2.2.1")` so that your code can work with both released and development versions of ggplot2. - + We recognise that this is a big change and if you're not already familiar with rlang, there's a lot to learn. If you are stuck, or need any help, please reach out on . @@ -1831,24 +1849,24 @@ accompanying issue #2890. such as returned by `base::scale()` because of their widespread use. * Error: More than one expression parsed - - Previously `aes_string(x = c("a", "b", "c"))` silently returned + + Previously `aes_string(x = c("a", "b", "c"))` silently returned `aes(x = a)`. Now this is a clear error. * Error: `data` must be uniquely named but has duplicate columns - - If layer data contains columns with identical names an error will be + + If layer data contains columns with identical names an error will be thrown. In earlier versions the first occurring column was chosen silently, potentially masking that the wrong data was chosen. * Error: Aesthetics must be either length 1 or the same as the data - + Layers are stricter about the columns they will combine into a single data frame. Each aesthetic now must be either the same length as the data frame or a single value. This makes silent recycling errors much less likely. -* Error: `coord_*` doesn't support free scales - +* Error: `coord_*` doesn't support free scales + Free scales only work with selected coordinate systems; previously you'd get an incorrect plot. @@ -1856,28 +1874,28 @@ accompanying issue #2890. This is because the `oob` argument to scale has been set to a function that only takes a single argument; it needs to take two arguments - (`x`, and `range`). + (`x`, and `range`). * Error: unused argument (output) - + The function `guide_train()` now has an optional parameter `aesthetic` that allows you to override the `aesthetic` setting in the scale. - To make your code work with the both released and development versions of + To make your code work with the both released and development versions of ggplot2 appropriate, add `aesthetic = NULL` to the `guide_train()` method signature. - + ```R # old guide_train.legend <- function(guide, scale) {...} - - # new + + # new guide_train.legend <- function(guide, scale, aesthetic = NULL) {...} ``` - + Then, inside the function, replace `scale$aesthetics[1]`, - `aesthetic %||% scale$aesthetics[1]`. (The %||% operator is defined in the + `aesthetic %||% scale$aesthetics[1]`. (The %||% operator is defined in the rlang package). - + ```R # old setNames(list(scale$map(breaks)), scale$aesthetics[1]) @@ -1897,9 +1915,9 @@ accompanying issue #2890. * `facet_wrap()` and `facet_grid()` now support `vars()` inputs. Like `dplyr::vars()`, this helper quotes its inputs and supports quasiquotation. For instance, you can now supply faceting variables - like this: `facet_wrap(vars(am, cyl))` instead of - `facet_wrap(~am + cyl)`. Note that the formula interface is not going - away and will not be deprecated. `vars()` is simply meant to make it + like this: `facet_wrap(vars(am, cyl))` instead of + `facet_wrap(~am + cyl)`. Note that the formula interface is not going + away and will not be deprecated. `vars()` is simply meant to make it easier to create functions around `facet_wrap()` and `facet_grid()`. The first two arguments of `facet_grid()` become `rows` and `cols` @@ -1928,100 +1946,100 @@ accompanying issue #2890. ## New features -* ggplot2 now works on R 3.1 onwards, and uses the +* ggplot2 now works on R 3.1 onwards, and uses the [vdiffr](https://github.com/r-lib/vdiffr) package for visual testing. -* In most cases, accidentally using `%>%` instead of `+` will generate an +* In most cases, accidentally using `%>%` instead of `+` will generate an informative error (#2400). -* New syntax for calculated aesthetics. Instead of using `aes(y = ..count..)` - you can (and should!) use `aes(y = stat(count))`. `stat()` is a real function - with documentation which hopefully will make this part of ggplot2 less +* New syntax for calculated aesthetics. Instead of using `aes(y = ..count..)` + you can (and should!) use `aes(y = stat(count))`. `stat()` is a real function + with documentation which hopefully will make this part of ggplot2 less confusing (#2059). - - `stat()` is particularly nice for more complex calculations because you + + `stat()` is particularly nice for more complex calculations because you only need to specify it once: `aes(y = stat(count / max(count)))`, rather than `aes(y = ..count.. / max(..count..))` - -* New `tag` label for adding identification tags to plots, typically used for - labelling a subplot with a letter. Add a tag with `labs(tag = "A")`, style it + +* New `tag` label for adding identification tags to plots, typically used for + labelling a subplot with a letter. Add a tag with `labs(tag = "A")`, style it with the `plot.tag` theme element, and control position with the `plot.tag.position` theme setting (@thomasp85). ### Layers: geoms, stats, and position adjustments -* `geom_segment()` and `geom_curve()` have a new `arrow.fill` parameter which - allows you to specify a separate fill colour for closed arrowheads +* `geom_segment()` and `geom_curve()` have a new `arrow.fill` parameter which + allows you to specify a separate fill colour for closed arrowheads (@hrbrmstr and @clauswilke, #2375). * `geom_point()` and friends can now take shapes as strings instead of integers, e.g. `geom_point(shape = "diamond")` (@daniel-barnett, #2075). * `position_dodge()` gains a `preserve` argument that allows you to control - whether the `total` width at each `x` value is preserved (the current + whether the `total` width at each `x` value is preserved (the current default), or ensure that the width of a `single` element is preserved (what many people want) (#1935). * New `position_dodge2()` provides enhanced dodging for boxplots. Compared to - `position_dodge()`, `position_dodge2()` compares `xmin` and `xmax` values + `position_dodge()`, `position_dodge2()` compares `xmin` and `xmax` values to determine which elements overlap, and spreads overlapping elements evenly within the region of overlap. `position_dodge2()` is now the default position - adjustment for `geom_boxplot()`, because it handles `varwidth = TRUE`, and + adjustment for `geom_boxplot()`, because it handles `varwidth = TRUE`, and will be considered for other geoms in the future. - - The `padding` parameter adds a small amount of padding between elements - (@karawoo, #2143) and a `reverse` parameter allows you to reverse the order + + The `padding` parameter adds a small amount of padding between elements + (@karawoo, #2143) and a `reverse` parameter allows you to reverse the order of placement (@karawoo, #2171). - -* New `stat_qq_line()` makes it easy to add a simple line to a Q-Q plot, which - makes it easier to judge the fit of the theoretical distribution + +* New `stat_qq_line()` makes it easy to add a simple line to a Q-Q plot, which + makes it easier to judge the fit of the theoretical distribution (@nicksolomon). ### Scales and guides -* Improved support for mapping date/time variables to `alpha`, `size`, `colour`, - and `fill` aesthetics, including `date_breaks` and `date_labels` arguments +* Improved support for mapping date/time variables to `alpha`, `size`, `colour`, + and `fill` aesthetics, including `date_breaks` and `date_labels` arguments (@karawoo, #1526), and new `scale_alpha()` variants (@karawoo, #1526). -* Improved support for ordered factors. Ordered factors throw a warning when - mapped to shape (unordered factors do not), and do not throw warnings when - mapped to size or alpha (unordered factors do). Viridis is used as the +* Improved support for ordered factors. Ordered factors throw a warning when + mapped to shape (unordered factors do not), and do not throw warnings when + mapped to size or alpha (unordered factors do). Viridis is used as the default colour and fill scale for ordered factors (@karawoo, #1526). * The `expand` argument of `scale_*_continuous()` and `scale_*_discrete()` now accepts separate expansion values for the lower and upper range limits. The expansion limits can be specified using the convenience function `expand_scale()`. - + Separate expansion limits may be useful for bar charts, e.g. if one - wants the bottom of the bars to be flush with the x axis but still + wants the bottom of the bars to be flush with the x axis but still leave some (automatically calculated amount of) space above them: - + ```r ggplot(mtcars) + geom_bar(aes(x = factor(cyl))) + scale_y_continuous(expand = expand_scale(mult = c(0, .1))) ``` - + It can also be useful for line charts, e.g. for counts over time, where one wants to have a ’hard’ lower limit of y = 0 but leave the upper limit unspecified (and perhaps differing between panels), with - some extra space above the highest point on the line (with symmetrical - limits, the extra space above the highest point could in some cases + some extra space above the highest point on the line (with symmetrical + limits, the extra space above the highest point could in some cases cause the lower limit to be negative). - + The old syntax for the `expand` argument will, of course, continue to work (@huftis, #1669). -* `scale_colour_continuous()` and `scale_colour_gradient()` are now controlled - by global options `ggplot2.continuous.colour` and `ggplot2.continuous.fill`. +* `scale_colour_continuous()` and `scale_colour_gradient()` are now controlled + by global options `ggplot2.continuous.colour` and `ggplot2.continuous.fill`. These can be set to `"gradient"` (the default) or `"viridis"` (@karawoo). * New `scale_colour_viridis_c()`/`scale_fill_viridis_c()` (continuous) and `scale_colour_viridis_d()`/`scale_fill_viridis_d()` (discrete) make it easy to use Viridis colour scales (@karawoo, #1526). -* Guides for `geom_text()` now accept custom labels with +* Guides for `geom_text()` now accept custom labels with `guide_legend(override.aes = list(label = "foo"))` (@brianwdavis, #2458). ### Margins @@ -2037,8 +2055,8 @@ accompanying issue #2890. text, meaning that in y facets, the strip text can be placed at either end of the strip using `hjust` (@karawoo). -* Legend titles and labels get a little extra space around them, which - prevents legend titles from overlapping the legend at large font sizes +* Legend titles and labels get a little extra space around them, which + prevents legend titles from overlapping the legend at large font sizes (@karawoo, #1881). ## Extension points @@ -2050,31 +2068,31 @@ accompanying issue #2890. defined for the class of the object (@thomasp85). * Theme elements can now be subclassed. Add a `merge_element` method to control - how properties are inherited from the parent element. Add an `element_grob` + how properties are inherited from the parent element. Add an `element_grob` method to define how elements are rendered into grobs (@thomasp85, #1981). * Coords have gained new extension mechanisms. - + If you have an existing coord extension, you will need to revise the - specification of the `train()` method. It is now called - `setup_panel_params()` (better reflecting what it actually does) and now - has arguments `scale_x`, and `scale_y` (the x and y scales respectively) - and `param`, a list of plot specific parameters generated by + specification of the `train()` method. It is now called + `setup_panel_params()` (better reflecting what it actually does) and now + has arguments `scale_x`, and `scale_y` (the x and y scales respectively) + and `param`, a list of plot specific parameters generated by `setup_params()`. - What was formerly called `scale_details` (in coords), `panel_ranges` + What was formerly called `scale_details` (in coords), `panel_ranges` (in layout) and `panel_scales` (in geoms) are now consistently called `panel_params` (#1311). These are parameters of the coord that vary from panel to panel. -* `ggplot_build()` and `ggplot_gtable()` are now generics, so ggplot-subclasses +* `ggplot_build()` and `ggplot_gtable()` are now generics, so ggplot-subclasses can define additional behavior during the build stage. * `guide_train()`, `guide_merge()`, `guide_geom()`, and `guide_gengrob()` are now exported as they are needed if you want to design your own guide. They are not currently documented; use at your own risk (#2528). -* `scale_type()` generic is now exported and documented. Use this if you +* `scale_type()` generic is now exported and documented. Use this if you want to extend ggplot2 to work with a new type of vector. ## Minor bug fixes and improvements @@ -2090,22 +2108,22 @@ accompanying issue #2890. * `label_parsed()` works once again (#2279). * You can now style the background of horizontal and vertical strips - independently with `strip.background.x` and `strip.background.y` + independently with `strip.background.x` and `strip.background.y` theme settings (#2249). ### Scales -* `discrete_scale()` documentation now inherits shared definitions from +* `discrete_scale()` documentation now inherits shared definitions from `continuous_scale()` (@alistaire47, #2052). * `guide_colorbar()` shows all colours of the scale (@has2k1, #2343). * `scale_identity()` once again produces legends by default (#2112). -* Tick marks for secondary axes with strong transformations are more +* Tick marks for secondary axes with strong transformations are more accurately placed (@thomasp85, #1992). -* Missing line types now reliably generate missing lines (with standard +* Missing line types now reliably generate missing lines (with standard warning) (#2206). * Legends now ignore set aesthetics that are not length one (#1932). @@ -2114,17 +2132,17 @@ accompanying issue #2890. be used to set the aesthetic(s) the scale works with. This makes it possible to apply a colour scale to both colour and fill aesthetics at the same time, via `aesthetics = c("colour", "fill")` (@clauswilke). - -* Three new generic scales work with any aesthetic or set of aesthetics: + +* Three new generic scales work with any aesthetic or set of aesthetics: `scale_continuous_identity()`, `scale_discrete_identity()`, and `scale_discrete_manual()` (@clauswilke). -* `scale_*_gradient2()` now consistently omits points outside limits by +* `scale_*_gradient2()` now consistently omits points outside limits by rescaling after the limits are enforced (@foo-bar-baz-qux, #2230). ### Layers -* `geom_label()` now correctly produces unbordered labels when `label.size` +* `geom_label()` now correctly produces unbordered labels when `label.size` is 0, even when saving to PDF (@bfgray3, #2407). * `layer()` gives considerably better error messages for incorrectly specified @@ -2137,25 +2155,25 @@ accompanying issue #2890. (@foo-bar-baz-qux, #2110). * `geom_density()` drops groups with fewer than two data points and throws a - warning. For groups with two data points, density values are now calculated + warning. For groups with two data points, density values are now calculated with `stats::density` (@karawoo, #2127). -* `geom_segment()` now also takes a `linejoin` parameter. This allows more - control over the appearance of the segments, which is especially useful for +* `geom_segment()` now also takes a `linejoin` parameter. This allows more + control over the appearance of the segments, which is especially useful for plotting thick arrows (@Ax3man, #774). -* `geom_smooth()` now reports the formula used when `method = "auto"` - (@davharris #1951). `geom_smooth()` now orders by the `x` aesthetic, making it - easier to pass pre-computed values without manual ordering (@izahn, #2028). It - also now knows it has `ymin` and `ymax` aesthetics (#1939). The legend - correctly reflects the status of the `se` argument when used with stats +* `geom_smooth()` now reports the formula used when `method = "auto"` + (@davharris #1951). `geom_smooth()` now orders by the `x` aesthetic, making it + easier to pass pre-computed values without manual ordering (@izahn, #2028). It + also now knows it has `ymin` and `ymax` aesthetics (#1939). The legend + correctly reflects the status of the `se` argument when used with stats other than the default (@clauswilke, #1546). -* `geom_tile()` now once again interprets `width` and `height` correctly +* `geom_tile()` now once again interprets `width` and `height` correctly (@malcolmbarrett, #2510). * `position_jitter()` and `position_jitterdodge()` gain a `seed` argument that - allows the specification of a random seed for reproducible jittering + allows the specification of a random seed for reproducible jittering (@krlmlr, #1996 and @slowkow, #2445). * `stat_density()` has better behaviour if all groups are dropped because they @@ -2163,19 +2181,19 @@ accompanying issue #2890. * `stat_summary_bin()` now understands the `breaks` parameter (@karawoo, #2214). -* `stat_bin()` now accepts functions for `binwidth`. This allows better binning +* `stat_bin()` now accepts functions for `binwidth`. This allows better binning when faceting along variables with different ranges (@botanize). -* `stat_bin()` and `geom_histogram()` now sum correctly when using the `weight` +* `stat_bin()` and `geom_histogram()` now sum correctly when using the `weight` aesthetic (@jiho, #1921). -* `stat_bin()` again uses correct scaling for the computed variable `ndensity` +* `stat_bin()` again uses correct scaling for the computed variable `ndensity` (@timgoodman, #2324). -* `stat_bin()` and `stat_bin_2d()` now properly handle the `breaks` parameter +* `stat_bin()` and `stat_bin_2d()` now properly handle the `breaks` parameter when the scales are transformed (@has2k1, #2366). -* `update_geom_defaults()` and `update_stat_defaults()` allow American +* `update_geom_defaults()` and `update_stat_defaults()` allow American spelling of aesthetic parameters (@foo-bar-baz-qux, #2299). * The `show.legend` parameter now accepts a named logical vector to hide/show @@ -2186,17 +2204,17 @@ accompanying issue #2890. ### Coords * Clipping to the plot panel is now configurable, through a `clip` argument - to coordinate systems, e.g. `coord_cartesian(clip = "off")` + to coordinate systems, e.g. `coord_cartesian(clip = "off")` (@clauswilke, #2536). -* Like scales, coordinate systems now give you a message when you're +* Like scales, coordinate systems now give you a message when you're replacing an existing coordinate system (#2264). -* `coord_polar()` now draws secondary axis ticks and labels - (@dylan-stark, #2072), and can draw the radius axis on the right +* `coord_polar()` now draws secondary axis ticks and labels + (@dylan-stark, #2072), and can draw the radius axis on the right (@thomasp85, #2005). -* `coord_trans()` now generates a warning when a transformation generates +* `coord_trans()` now generates a warning when a transformation generates non-finite values (@foo-bar-baz-qux, #2147). ### Themes @@ -2205,44 +2223,44 @@ accompanying issue #2890. (@has2k1, #2058, #2079). * Themes now set default grid colour in `panel.grid` rather than individually - in `panel.grid.major` and `panel.grid.minor` individually. This makes it + in `panel.grid.major` and `panel.grid.minor` individually. This makes it slightly easier to customise the theme (#2352). -* Fixed bug when setting strips to `element_blank()` (@thomasp85). +* Fixed bug when setting strips to `element_blank()` (@thomasp85). * Axes positioned on the top and to the right can now customize their ticks and lines separately (@thomasp85, #1899). -* Built-in themes gain parameters `base_line_size` and `base_rect_size` which +* Built-in themes gain parameters `base_line_size` and `base_rect_size` which control the default sizes of line and rectangle elements (@karawoo, #2176). * Default themes use `rel()` to set line widths (@baptiste). -* Themes were tweaked for visual consistency and more graceful behavior when - changing the base font size. All absolute heights or widths were replaced - with heights or widths that are proportional to the base font size. One +* Themes were tweaked for visual consistency and more graceful behavior when + changing the base font size. All absolute heights or widths were replaced + with heights or widths that are proportional to the base font size. One relative font size was eliminated (@clauswilke). - + * The height of descenders is now calculated solely on font metrics and doesn't - change with the specific letters in the string. This fixes minor alignment + change with the specific letters in the string. This fixes minor alignment issues with plot titles, subtitles, and legend titles (#2288, @clauswilke). ### Guides * `guide_colorbar()` is more configurable: tick marks and color bar frame - can now by styled with arguments `ticks.colour`, `ticks.linewidth`, + can now by styled with arguments `ticks.colour`, `ticks.linewidth`, `frame.colour`, `frame.linewidth`, and `frame.linetype` (@clauswilke). - -* `guide_colorbar()` now uses `legend.spacing.x` and `legend.spacing.y` - correctly, and it can handle multi-line titles. Minor tweaks were made to + +* `guide_colorbar()` now uses `legend.spacing.x` and `legend.spacing.y` + correctly, and it can handle multi-line titles. Minor tweaks were made to `guide_legend()` to make sure the two legend functions behave as similarly as possible (@clauswilke, #2397 and #2398). - -* The theme elements `legend.title` and `legend.text` now respect the settings + +* The theme elements `legend.title` and `legend.text` now respect the settings of `margin`, `hjust`, and `vjust` (@clauswilke, #2465, #1502). -* Non-angle parameters of `label.theme` or `title.theme` can now be set in +* Non-angle parameters of `label.theme` or `title.theme` can now be set in `guide_legend()` and `guide_colorbar()` (@clauswilke, #2544). ### Other @@ -2250,28 +2268,28 @@ accompanying issue #2890. * `fortify()` gains a method for tbls (@karawoo, #2218). * `ggplot` gains a method for `grouped_df`s that adds a `.group` variable, - which computes a unique value for each group. Use it with + which computes a unique value for each group. Use it with `aes(group = .group)` (#2351). * `ggproto()` produces objects with class `c("ggproto", "gg")`, allowing for - a more informative error message when adding layers, scales, or other ggproto + a more informative error message when adding layers, scales, or other ggproto objects (@jrnold, #2056). * `ggsave()`'s DPI argument now supports 3 string options: "retina" (320 DPI), "print" (300 DPI), and "screen" (72 DPI) (@foo-bar-baz-qux, #2156). - `ggsave()` now uses full argument names to avoid partial match warnings + `ggsave()` now uses full argument names to avoid partial match warnings (#2355), and correctly restores the previous graphics device when several graphics devices are open (#2363). -* `print.ggplot()` now returns the original ggplot object, instead of the - output from `ggplot_build()`. Also, the object returned from +* `print.ggplot()` now returns the original ggplot object, instead of the + output from `ggplot_build()`. Also, the object returned from `ggplot_build()` now has the class `"ggplot_built"` (#2034). * `map_data()` now works even when purrr is loaded (tidyverse#66). -* New functions `summarise_layout()`, `summarise_coord()`, and - `summarise_layers()` summarise the layout, coordinate systems, and layers - of a built ggplot object (#2034, @wch). This provides a tested API that +* New functions `summarise_layout()`, `summarise_coord()`, and + `summarise_layers()` summarise the layout, coordinate systems, and layers + of a built ggplot object (#2034, @wch). This provides a tested API that (e.g.) shiny can depend on. * Updated startup messages reflect new resources (#2410, @mine-cetinkaya-rundel). @@ -2286,88 +2304,88 @@ accompanying issue #2890. ### Subtitle and caption -Thanks to @hrbrmstr plots now have subtitles and captions, which can be set with -the `subtitle` and `caption` arguments to `ggtitle()` and `labs()`. You can -control their appearance with the theme settings `plot.caption` and -`plot.subtitle`. The main plot title is now left-aligned to better work better +Thanks to @hrbrmstr plots now have subtitles and captions, which can be set with +the `subtitle` and `caption` arguments to `ggtitle()` and `labs()`. You can +control their appearance with the theme settings `plot.caption` and +`plot.subtitle`. The main plot title is now left-aligned to better work better with a subtitle. The caption is right-aligned (@hrbrmstr). ### Stacking -`position_stack()` and `position_fill()` now sort the stacking order to match -grouping order. This allows you to control the order through grouping, and -ensures that the default legend matches the plot (#1552, #1593). If you want the -opposite order (useful if you have horizontal bars and horizontal legend), you -can request reverse stacking by using `position = position_stack(reverse = TRUE)` +`position_stack()` and `position_fill()` now sort the stacking order to match +grouping order. This allows you to control the order through grouping, and +ensures that the default legend matches the plot (#1552, #1593). If you want the +opposite order (useful if you have horizontal bars and horizontal legend), you +can request reverse stacking by using `position = position_stack(reverse = TRUE)` (#1837). - -`position_stack()` and `position_fill()` now accepts negative values which will + +`position_stack()` and `position_fill()` now accepts negative values which will create stacks extending below the x-axis (#1691). -`position_stack()` and `position_fill()` gain a `vjust` argument which makes it +`position_stack()` and `position_fill()` gain a `vjust` argument which makes it easy to (e.g.) display labels in the middle of stacked bars (#1821). ### Layers -`geom_col()` was added to complement `geom_bar()` (@hrbrmstr). It uses -`stat="identity"` by default, making the `y` aesthetic mandatory. It does not -support any other `stat_()` and does not provide fallback support for the +`geom_col()` was added to complement `geom_bar()` (@hrbrmstr). It uses +`stat="identity"` by default, making the `y` aesthetic mandatory. It does not +support any other `stat_()` and does not provide fallback support for the `binwidth` parameter. Examples and references in other functions were updated to -demonstrate `geom_col()` usage. +demonstrate `geom_col()` usage. -When creating a layer, ggplot2 will warn if you use an unknown aesthetic or an -unknown parameter. Compared to the previous version, this is stricter for -aesthetics (previously there was no message), and less strict for parameters +When creating a layer, ggplot2 will warn if you use an unknown aesthetic or an +unknown parameter. Compared to the previous version, this is stricter for +aesthetics (previously there was no message), and less strict for parameters (previously this threw an error) (#1585). ### Facetting -The facet system, as well as the internal panel class, has been rewritten in -ggproto. Facets are now extendable in the same manner as geoms and stats, as +The facet system, as well as the internal panel class, has been rewritten in +ggproto. Facets are now extendable in the same manner as geoms and stats, as described in `vignette("extending-ggplot2")`. We have also added the following new features. - -* `facet_grid()` and `facet_wrap()` now allow expressions in their faceting + +* `facet_grid()` and `facet_wrap()` now allow expressions in their faceting formulas (@DanRuderman, #1596). * When `facet_wrap()` results in an uneven number of panels, axes will now be drawn underneath the hanging panels (fixes #1607) -* Strips can now be freely positioned in `facet_wrap()` using the +* Strips can now be freely positioned in `facet_wrap()` using the `strip.position` argument (deprecates `switch`). -* The relative order of panel, strip, and axis can now be controlled with - the theme setting `strip.placement` that takes either `inside` (strip between +* The relative order of panel, strip, and axis can now be controlled with + the theme setting `strip.placement` that takes either `inside` (strip between panel and axis) or `outside` (strip after axis). -* The theme option `panel.margin` has been deprecated in favour of +* The theme option `panel.margin` has been deprecated in favour of `panel.spacing` to more clearly communicate intent. ### Extensions -Unfortunately there was a major oversight in the construction of ggproto which -lead to extensions capturing the super object at package build time, instead of -at package run time (#1826). This problem has been fixed, but requires +Unfortunately there was a major oversight in the construction of ggproto which +lead to extensions capturing the super object at package build time, instead of +at package run time (#1826). This problem has been fixed, but requires re-installation of all extension packages. ## Scales * The position of x and y axes can now be changed using the `position` argument in `scale_x_*`and `scale_y_*` which can take `top` and `bottom`, and `left` - and `right` respectively. The themes of top and right axes can be modified + and `right` respectively. The themes of top and right axes can be modified using the `.top` and `.right` modifiers to `axis.text.*` and `axis.title.*`. ### Continuous scales -* `scale_x_continuous()` and `scale_y_continuous()` can now display a secondary - axis that is a __one-to-one__ transformation of the primary axis (e.g. degrees - Celcius to degrees Fahrenheit). The secondary axis will be positioned opposite - to the primary axis and can be controlled with the `sec.axis` argument to +* `scale_x_continuous()` and `scale_y_continuous()` can now display a secondary + axis that is a __one-to-one__ transformation of the primary axis (e.g. degrees + Celcius to degrees Fahrenheit). The secondary axis will be positioned opposite + to the primary axis and can be controlled with the `sec.axis` argument to the scale constructor. * Scales worry less about having breaks. If no breaks can be computed, the - plot will work instead of throwing an uninformative error (#791). This + plot will work instead of throwing an uninformative error (#791). This is particularly helpful when you have facets with free scales, and not all panels contain data. @@ -2375,8 +2393,8 @@ re-installation of all extension packages. ### Date time -* `scale_*_datetime()` now supports time zones. It will use the timezone - attached to the variable by default, but can be overridden with the +* `scale_*_datetime()` now supports time zones. It will use the timezone + attached to the variable by default, but can be overridden with the `timezone` argument. * New `scale_x_time()` and `scale_y_time()` generate reasonable default @@ -2384,10 +2402,10 @@ re-installation of all extension packages. ### Discrete scales -The treatment of missing values by discrete scales has been thoroughly -overhauled (#1584). The underlying principle is that we can naturally represent -missing values on discrete variables (by treating just like another level), so -by default we should. +The treatment of missing values by discrete scales has been thoroughly +overhauled (#1584). The underlying principle is that we can naturally represent +missing values on discrete variables (by treating just like another level), so +by default we should. This principle applies to: @@ -2404,12 +2422,12 @@ Compared to the previous version of ggplot2, there are three main changes: 1. If present, `NA`s are shown in discrete legends. -1. All discrete scales gain a `na.translate` argument that allows you to +1. All discrete scales gain a `na.translate` argument that allows you to control whether `NA`s are translated to something that can be visualised, - or should be left as missing. Note that if you don't translate (i.e. - `na.translate = FALSE)` the missing values will passed on to the layer, + or should be left as missing. Note that if you don't translate (i.e. + `na.translate = FALSE)` the missing values will passed on to the layer, which will warning that it's dropping missing values. To suppress the - warnings, you'll also need to add `na.rm = TRUE` to the layer call. + warnings, you'll also need to add `na.rm = TRUE` to the layer call. There were also a number of other smaller changes @@ -2421,37 +2439,37 @@ There were also a number of other smaller changes ## Themes -* The `theme()` constructor now has named arguments rather than ellipses. This +* The `theme()` constructor now has named arguments rather than ellipses. This should make autocomplete substantially more useful. The documentation (including examples) has been considerably improved. - + * Built-in themes are more visually homogeneous, and match `theme_grey` better. (@jiho, #1679) - + * When computing the height of titles, ggplot2 now includes the height of the - descenders (i.e. the bits of `g` and `y` that hang beneath the baseline). This + descenders (i.e. the bits of `g` and `y` that hang beneath the baseline). This improves the margins around titles, particularly the y axis label (#1712). - I have also very slightly increased the inner margins of axis titles, and - removed the outer margins. + I have also very slightly increased the inner margins of axis titles, and + removed the outer margins. * Theme element inheritance is now easier to work with as modification now overrides default `element_blank` elements (#1555, #1557, #1565, #1567) - + * Horizontal legends (i.e. legends on the top or bottom) are horizontally aligned by default (#1842). Use `legend.box = "vertical"` to switch back to the previous behaviour. - + * `element_line()` now takes an `arrow` argument to specify arrows at the end of lines (#1740) There were a number of tweaks to the theme elements that control legends: - + * `legend.justification` now controls appearance will plotting the legend - outside of the plot area. For example, you can use - `theme(legend.justification = "top")` to make the legend align with the + outside of the plot area. For example, you can use + `theme(legend.justification = "top")` to make the legend align with the top of the plot. -* `panel.margin` and `legend.margin` have been renamed to `panel.spacing` and +* `panel.margin` and `legend.margin` have been renamed to `panel.spacing` and `legend.spacing` respectively, to better communicate intent (they only affect spacing between legends and panels, not the margins around them) @@ -2463,7 +2481,7 @@ There were a number of tweaks to the theme elements that control legends: ## Bug fixes and minor improvements -* ggplot2 now imports tibble. This ensures that all built-in datasets print +* ggplot2 now imports tibble. This ensures that all built-in datasets print compactly even if you haven't explicitly loaded tibble or dplyr (#1677). * Class of aesthetic mapping is preserved when adding `aes()` objects (#1624). @@ -2474,42 +2492,42 @@ There were a number of tweaks to the theme elements that control legends: * `geom_*(show.legend = FALSE)` now works for `guide_colorbar`. -* `geom_boxplot()` gains new `outlier.alpha` (@jonathan-g) and +* `geom_boxplot()` gains new `outlier.alpha` (@jonathan-g) and `outlier.fill` (@schloerke, #1787) parameters to control the alpha/fill of - outlier points independently of the alpha of the boxes. + outlier points independently of the alpha of the boxes. -* `position_jitter()` (and hence `geom_jitter()`) now correctly computes +* `position_jitter()` (and hence `geom_jitter()`) now correctly computes the jitter width/jitter when supplied by the user (#1775, @has2k1). * `geom_contour()` more clearly describes what inputs it needs (#1577). * `geom_curve()` respects the `lineend` parameter (#1852). -* `geom_histogram()` and `stat_bin()` understand the `breaks` parameter once - more. (#1665). The floating point adjustment for histogram bins is now +* `geom_histogram()` and `stat_bin()` understand the `breaks` parameter once + more. (#1665). The floating point adjustment for histogram bins is now actually used - it was previously inadvertently ignored (#1651). * `geom_violin()` no longer transforms quantile lines with the alpha aesthetic (@mnbram, #1714). It no longer errors when quantiles are requested but data - have zero range (#1687). When `trim = FALSE` it once again has a nice - range that allows the density to reach zero (by extending the range 3 + have zero range (#1687). When `trim = FALSE` it once again has a nice + range that allows the density to reach zero (by extending the range 3 bandwidths to either side of the data) (#1700). -* `geom_dotplot()` works better when faceting and binning on the y-axis. +* `geom_dotplot()` works better when faceting and binning on the y-axis. (#1618, @has2k1). - + * `geom_hexbin()` once again supports `..density..` (@mikebirdgeneau, #1688). * `geom_step()` gives useful warning if only one data point in layer (#1645). * `layer()` gains new `check.aes` and `check.param` arguments. These allow geom/stat authors to optional suppress checks for known aesthetics/parameters. - Currently this is used only in `geom_blank()` which powers `expand_limits()` + Currently this is used only in `geom_blank()` which powers `expand_limits()` (#1795). * All `stat_*()` display a better error message when required aesthetics are missing. - + * `stat_bin()` and `stat_summary_hex()` now accept length 1 `binwidth` (#1610) * `stat_density()` gains new argument `n`, which is passed to underlying function @@ -2527,7 +2545,7 @@ There were a number of tweaks to the theme elements that control legends: aesthetics they accept: `xmin_final`, `xmax_final`, `xlower`, `xmiddle` and `xupper` are now valid `x` aesthetics. -* `Scale` extensions can now override the `make_title` and `make_sec_title` +* `Scale` extensions can now override the `make_title` and `make_sec_title` methods to let the scale modify the axis/legend titles. * The random stream is now reset after calling `.onAttach()` (#2409). @@ -2536,35 +2554,35 @@ There were a number of tweaks to the theme elements that control legends: ## New features -* When mapping an aesthetic to a constant (e.g. - `geom_smooth(aes(colour = "loess")))`), the default guide title is the name +* When mapping an aesthetic to a constant (e.g. + `geom_smooth(aes(colour = "loess")))`), the default guide title is the name of the aesthetic (i.e. "colour"), not the value (i.e. "loess") (#1431). * `layer()` now accepts a function as the data argument. The function will be applied to the data passed to the `ggplot()` function and must return a - data.frame (#1527, @thomasp85). This is a more general version of the + data.frame (#1527, @thomasp85). This is a more general version of the deprecated `subset` argument. * `theme_update()` now uses the `+` operator instead of `%+replace%`, so that unspecified values will no longer be `NULL`ed out. `theme_replace()` - preserves the old behaviour if desired (@oneillkza, #1519). + preserves the old behaviour if desired (@oneillkza, #1519). -* `stat_bin()` has been overhauled to use the same algorithm as ggvis, which +* `stat_bin()` has been overhauled to use the same algorithm as ggvis, which has been considerably improved thanks to the advice of Randy Prium (@rpruim). This includes: - + * Better arguments and a better algorithm for determining the origin. You can now specify either `boundary` or the `center` of a bin. `origin` has been deprecated in favour of these arguments. - + * `drop` is deprecated in favour of `pad`, which adds extra 0-count bins - at either end (needed for frequency polygons). `geom_histogram()` defaults - to `pad = FALSE` which considerably improves the default limits for + at either end (needed for frequency polygons). `geom_histogram()` defaults + to `pad = FALSE` which considerably improves the default limits for the histogram, especially when the bins are big (#1477). - - * The default algorithm does a (somewhat) better job at picking nice widths + + * The default algorithm does a (somewhat) better job at picking nice widths and origins across a wider range of input data. - + * `bins = n` now gives a histogram with `n` bins, not `n + 1` (#1487). ## Bug fixes @@ -2572,16 +2590,16 @@ There were a number of tweaks to the theme elements that control legends: * All `\donttest{}` examples run. * All `geom_()` and `stat_()` functions now have consistent argument order: - data + mapping, then geom/stat/position, then `...`, then specific arguments, + data + mapping, then geom/stat/position, then `...`, then specific arguments, then arguments common to all layers (#1305). This may break code if you were - previously relying on partial name matching, but in the long-term should make + previously relying on partial name matching, but in the long-term should make ggplot2 easier to use. In particular, you can now set the `n` parameter in `geom_density2d()` without it partially matching `na.rm` (#1485). * For geoms with both `colour` and `fill`, `alpha` once again only affects fill (Reverts #1371, #1523). This was causing problems for people. -* `facet_wrap()`/`facet_grid()` works with multiple empty panels of data +* `facet_wrap()`/`facet_grid()` works with multiple empty panels of data (#1445). * `facet_wrap()` correctly swaps `nrow` and `ncol` when faceting vertically @@ -2593,17 +2611,17 @@ There were a number of tweaks to the theme elements that control legends: * `geom_path()` knows that "solid" (not just 1) represents a solid line (#1534). -* `geom_ribbon()` preserves missing values so they correctly generate a +* `geom_ribbon()` preserves missing values so they correctly generate a gap in the ribbon (#1549). -* `geom_tile()` once again accepts `width` and `height` parameters (#1513). - It uses `draw_key_polygon()` for better a legend, including a coloured +* `geom_tile()` once again accepts `width` and `height` parameters (#1513). + It uses `draw_key_polygon()` for better a legend, including a coloured outline (#1484). * `layer()` now automatically adds a `na.rm` parameter if none is explicitly supplied. -* `position_jitterdodge()` now works on all possible dodge aesthetics, +* `position_jitterdodge()` now works on all possible dodge aesthetics, e.g. `color`, `linetype` etc. instead of only based on `fill` (@bleutner) * `position = "nudge"` now works (although it doesn't do anything useful) @@ -2619,32 +2637,32 @@ There were a number of tweaks to the theme elements that control legends: * `scale_size()`, `scale_colour()`, and `scale_fill()` gain date and date-time variants (#1526). -* `stat_bin_hex()` and `stat_bin_summary()` now use the same underlying +* `stat_bin_hex()` and `stat_bin_summary()` now use the same underlying algorithm so results are consistent (#1383). `stat_bin_hex()` now accepts - a `weight` aesthetic. To be consistent with related stats, the output variable + a `weight` aesthetic. To be consistent with related stats, the output variable from `stat_bin_hex()` is now value instead of count. -* `stat_density()` gains a `bw` parameter which makes it easy to get consistent +* `stat_density()` gains a `bw` parameter which makes it easy to get consistent smoothing between facets (@jiho) -* `stat-density-2d()` no longer ignores the `h` parameter, and now accepts - `bins` and `binwidth` parameters to control the number of contours +* `stat-density-2d()` no longer ignores the `h` parameter, and now accepts + `bins` and `binwidth` parameters to control the number of contours (#1448, @has2k1). * `stat_ecdf()` does a better job of adding padding to -Inf/Inf, and gains an argument `pad` to suppress the padding if not needed (#1467). -* `stat_function()` gains an `xlim` parameter (#1528). It once again works +* `stat_function()` gains an `xlim` parameter (#1528). It once again works with discrete x values (#1509). * `stat_summary()` preserves sorted x order which avoids artefacts when display results with `geom_smooth()` (#1520). * All elements should now inherit correctly for all themes except `theme_void()`. - (@Katiedaisey, #1555) + (@Katiedaisey, #1555) * `theme_void()` was completely void of text but facets and legends still - need labels. They are now visible (@jiho). + need labels. They are now visible (@jiho). * You can once again set legend key and height width to unit arithmetic objects (like `2 * unit(1, "cm")`) (#1437). @@ -2659,48 +2677,48 @@ There were a number of tweaks to the theme elements that control legends: * Fixed issue where `coord_map()` fails when given an explicit `parameters` argument (@tdmcarthur, #1729) - -* Fixed issue where `geom_errorbarh()` had a required `x` aesthetic (#1933) + +* Fixed issue where `geom_errorbarh()` had a required `x` aesthetic (#1933) # ggplot2 2.0.0 ## Major changes -* ggplot no longer throws an error if your plot has no layers. Instead it +* ggplot no longer throws an error if your plot has no layers. Instead it automatically adds `geom_blank()` (#1246). - + * New `cut_width()` is a convenient replacement for the verbose `plyr::round_any()`, with the additional benefit of offering finer control. * New `geom_count()` is a convenient alias to `stat_sum()`. Use it when you - have overlapping points on a scatterplot. `stat_sum()` now defaults to + have overlapping points on a scatterplot. `stat_sum()` now defaults to using counts instead of proportions. -* New `geom_curve()` adds curved lines, with a similar specification to +* New `geom_curve()` adds curved lines, with a similar specification to `geom_segment()` (@veraanadi, #1088). * Date and datetime scales now have `date_breaks`, `date_minor_breaks` and `date_labels` arguments so that you never need to use the long `scales::date_breaks()` or `scales::date_format()`. - + * `geom_bar()` now has it's own stat, distinct from `stat_bin()` which was - also used by `geom_histogram()`. `geom_bar()` now uses `stat_count()` + also used by `geom_histogram()`. `geom_bar()` now uses `stat_count()` which counts values at each distinct value of x (i.e. it does not bin - the data first). This can be useful when you want to show exactly which + the data first). This can be useful when you want to show exactly which values are used in a continuous variable. -* `geom_point()` gains a `stroke` aesthetic which controls the border width of - shapes 21-25 (#1133, @SeySayux). `size` and `stroke` are additive so a point +* `geom_point()` gains a `stroke` aesthetic which controls the border width of + shapes 21-25 (#1133, @SeySayux). `size` and `stroke` are additive so a point with `size = 5` and `stroke = 5` will have a diameter of 10mm. (#1142) -* New `position_nudge()` allows you to slightly offset labels (or other +* New `position_nudge()` allows you to slightly offset labels (or other geoms) from their corresponding points (#1109). * `scale_size()` now maps values to _area_, not radius. Use `scale_radius()` if you want the old behaviour (not recommended, except perhaps for lines). -* New `stat_summary_bin()` works like `stat_summary()` but on binned data. +* New `stat_summary_bin()` works like `stat_summary()` but on binned data. It's a generalisation of `stat_bin()` that can compute any aggregate, not just counts (#1274). Both default to `mean_se()` if no aggregation functions are supplied (#1386). @@ -2709,84 +2727,84 @@ There were a number of tweaks to the theme elements that control legends: if you've supplied an argument that isn't an aesthetic or a parameter. This is likely to cause some short-term pain but in the long-term it will make it much easier to spot spelling mistakes and other errors (#1293). - - This change does break a handful of geoms/stats that used `...` to pass - additional arguments on to the underlying computation. Now - `geom_smooth()`/`stat_smooth()` and `geom_quantile()`/`stat_quantile()` - use `method.args` instead (#1245, #1289); and `stat_summary()` (#1242), + + This change does break a handful of geoms/stats that used `...` to pass + additional arguments on to the underlying computation. Now + `geom_smooth()`/`stat_smooth()` and `geom_quantile()`/`stat_quantile()` + use `method.args` instead (#1245, #1289); and `stat_summary()` (#1242), `stat_summary_hex()`, and `stat_summary2d()` use `fun.args`. ### Extensibility -There is now an official mechanism for defining Stats, Geoms, and Positions in +There is now an official mechanism for defining Stats, Geoms, and Positions in other packages. See `vignette("extending-ggplot2")` for details. * All Geoms, Stats and Positions are now exported, so you can inherit from them when making your own objects (#989). -* ggplot2 no longer uses proto or reference classes. Instead, we now use +* ggplot2 no longer uses proto or reference classes. Instead, we now use ggproto, a new OO system designed specifically for ggplot2. Unlike proto and RC, ggproto supports clean cross-package inheritance. Creating a new OO system isn't usually the right way to solve a problem, but I'm pretty sure it was necessary here. Read more about it in the vignette. -* `aes_()` replaces `aes_q()`. It also supports formulas, so the most concise +* `aes_()` replaces `aes_q()`. It also supports formulas, so the most concise SE version of `aes(carat, price)` is now `aes_(~carat, ~price)`. You may - want to use this form in packages, as it will avoid spurious `R CMD check` + want to use this form in packages, as it will avoid spurious `R CMD check` warnings about undefined global variables. ### Text * `geom_text()` has been overhauled to make labelling your data a little easier. It: - + * `nudge_x` and `nudge_y` arguments let you offset labels from their - corresponding points (#1120). - - * `check_overlap = TRUE` provides a simple way to avoid overplotting + corresponding points (#1120). + + * `check_overlap = TRUE` provides a simple way to avoid overplotting of labels: labels that would otherwise overlap are omitted (#1039). - - * `hjust` and `vjust` can now be character vectors: "left", "center", - "right", "bottom", "middle", "top". New options include "inward" and - "outward" which align text towards and away from the center of the plot + + * `hjust` and `vjust` can now be character vectors: "left", "center", + "right", "bottom", "middle", "top". New options include "inward" and + "outward" which align text towards and away from the center of the plot respectively. -* `geom_label()` works like `geom_text()` but draws a rounded rectangle +* `geom_label()` works like `geom_text()` but draws a rounded rectangle underneath each label (#1039). This is useful when you want to label plots that are dense with data. ### Deprecated features -* The little used `aes_auto()` has been deprecated. +* The little used `aes_auto()` has been deprecated. * `aes_q()` has been replaced with `aes_()` to be consistent with SE versions of NSE functions in other packages. -* The `order` aesthetic is officially deprecated. It never really worked, and +* The `order` aesthetic is officially deprecated. It never really worked, and was poorly documented. * The `stat` and `position` arguments to `qplot()` have been deprecated. `qplot()` is designed for quick plots - if you need to specify position or stat, use `ggplot()` instead. -* The theme setting `axis.ticks.margin` has been deprecated: now use the margin +* The theme setting `axis.ticks.margin` has been deprecated: now use the margin property of `axis.text`. - + * `stat_abline()`, `stat_hline()` and `stat_vline()` have been removed: these were never suitable for use other than with `geom_abline()` etc and were not documented. * `show_guide` has been renamed to `show.legend`: this more accurately - reflects what it does (controls appearance of layer in legend), and uses the + reflects what it does (controls appearance of layer in legend), and uses the same convention as other ggplot2 arguments (i.e. a `.` between names). (Yes, I know that's inconsistent with function names with use `_`, but it's too late to change now.) A number of geoms have been renamed to be internally consistent: -* `stat_binhex()` and `stat_bin2d()` have been renamed to `stat_bin_hex()` - and `stat_bin_2d()` (#1274). `stat_summary2d()` has been renamed to - `stat_summary_2d()`, `geom_density2d()`/`stat_density2d()` has been renamed +* `stat_binhex()` and `stat_bin2d()` have been renamed to `stat_bin_hex()` + and `stat_bin_2d()` (#1274). `stat_summary2d()` has been renamed to + `stat_summary_2d()`, `geom_density2d()`/`stat_density2d()` has been renamed to `geom_density_2d()`/`stat_density_2d()`. * `stat_spoke()` is now `geom_spoke()` since I realised it's a @@ -2800,57 +2818,57 @@ All defunct functions have been removed. ### Default appearance -* The default `theme_grey()` background colour has been changed from "grey90" +* The default `theme_grey()` background colour has been changed from "grey90" to "grey92": this makes the background a little less visually prominent. * Labels and titles have been tweaked for readability: * Axes labels are darker. - + * Legend and axis titles are given the same visual treatment. - - * The default font size dropped from 12 to 11. You might be surprised that + + * The default font size dropped from 12 to 11. You might be surprised that I've made the default text size smaller as it was already hard for - many people to read. It turns out there was a bug in RStudio (fixed in + many people to read. It turns out there was a bug in RStudio (fixed in 0.99.724), that shrunk the text of all grid based graphics. Once that was resolved the defaults seemed too big to my eyes. - + * More spacing between titles and borders. - - * Default margins scale with the theme font size, so the appearance at - larger font sizes should be considerably improved (#1228). + + * Default margins scale with the theme font size, so the appearance at + larger font sizes should be considerably improved (#1228). * `alpha` now affects both fill and colour aesthetics (#1371). * `element_text()` gains a margins argument which allows you to add additional - padding around text elements. To help see what's going on use `debug = TRUE` + padding around text elements. To help see what's going on use `debug = TRUE` to display the text region and anchors. * The default font size in `geom_text()` has been decreased from 5mm (14 pts) to 3.8 mm (11 pts) to match the new default theme sizes. * A diagonal line is no longer drawn on bar and rectangle legends. Instead, the - border has been tweaked to be more visible, and more closely match the size of + border has been tweaked to be more visible, and more closely match the size of line drawn on the plot. * `geom_pointrange()` and `geom_linerange()` get vertical (not horizontal) lines in the legend (#1389). -* The default line `size` for `geom_smooth()` has been increased from 0.5 to 1 +* The default line `size` for `geom_smooth()` has been increased from 0.5 to 1 to make it easier to see when overlaid on data. - + * `geom_bar()` and `geom_rect()` use a slightly paler shade of grey so they aren't so visually heavy. - + * `geom_boxplot()` now colours outliers the same way as the boxes. -* `geom_point()` now uses shape 19 instead of 16. This looks much better on - the default Linux graphics device. (It's very slightly smaller than the old +* `geom_point()` now uses shape 19 instead of 16. This looks much better on + the default Linux graphics device. (It's very slightly smaller than the old point, but it shouldn't affect any graphics significantly) -* Sizes in ggplot2 are measured in mm. Previously they were converted to pts - (for use in grid) by multiplying by 72 / 25.4. However, grid uses printer's - points, not Adobe (big pts), so sizes are now correctly multiplied by +* Sizes in ggplot2 are measured in mm. Previously they were converted to pts + (for use in grid) by multiplying by 72 / 25.4. However, grid uses printer's + points, not Adobe (big pts), so sizes are now correctly multiplied by 72.27 / 25.4. This is unlikely to noticeably affect display, but it's technically correct (). @@ -2878,8 +2896,8 @@ All defunct functions have been removed. * `theme_minimal()` became slightly more minimal by removing the axis ticks: labels now line up directly beneath grid lines (@tomschloss, #1084) -* New theme setting `panel.ontop` (logical) make it possible to place - background elements (i.e., gridlines) on top of data. Best used with +* New theme setting `panel.ontop` (logical) make it possible to place + background elements (i.e., gridlines) on top of data. Best used with transparent `panel.background` (@noamross. #551). ### Labelling @@ -2952,32 +2970,32 @@ version of ggplot. * Improved documentation for `aes()`, `layer()` and much much more. -* I've tried to reduce the use of `...` so that you can see all the +* I've tried to reduce the use of `...` so that you can see all the documentation in one place rather than having to integrate multiple pages. In some cases this has involved adding additional arguments to geoms to make it more clear what you can do: - + * `geom_smooth()` gains explicit `method`, `se` and `formula` arguments. - - * `geom_histogram()` gains `binwidth`, `bins`, `origin` and `right` + + * `geom_histogram()` gains `binwidth`, `bins`, `origin` and `right` arguments. - + * `geom_jitter()` gains `width` and `height` arguments to make it easier - to control the amount of jittering without using the lengthy + to control the amount of jittering without using the lengthy `position_jitter()` function (#1116) * Use of `qplot()` in examples has been minimised (#1123, @hrbrmstr). This is - inline with the 2nd edition of the ggplot2 box, which minimises the use of + inline with the 2nd edition of the ggplot2 box, which minimises the use of `qplot()` in favour of `ggplot()`. -* Tightly linked geoms and stats (e.g. `geom_boxplot()` and `stat_boxplot()`) +* Tightly linked geoms and stats (e.g. `geom_boxplot()` and `stat_boxplot()`) are now documented in the same file so you can see all the arguments in one place. Variations of the same idea (e.g. `geom_path()`, `geom_line()`, and `geom_step()`) are also documented together. * It's now obvious that you can set the `binwidth` parameter for `stat_bin_hex()`, `stat_summary_hex()`, `stat_bin_2d()`, and - `stat_summary_2d()`. + `stat_summary_2d()`. * The internals of positions have been cleaned up considerably. You're unlikely to notice any external changes, although the documentation should be a little @@ -2999,17 +3017,17 @@ version of ggplot. * New `luv_colours` dataset which contains the locations of all built-in `colors()` in Luv space. -* `movies` has been moved into its own package, ggplot2movies, because it was - large and not terribly useful. If you've used the movies dataset, you'll now +* `movies` has been moved into its own package, ggplot2movies, because it was + large and not terribly useful. If you've used the movies dataset, you'll now need to explicitly load the package with `library(ggplot2movies)`. ## Bug fixes and minor improvements -* All partially matched arguments and `$` have been been replaced with +* All partially matched arguments and `$` have been been replaced with full matches (@jimhester, #1134). -* ggplot2 now exports `alpha()` from the scales package (#1107), and `arrow()` - and `unit()` from grid (#1225). This means you don't need attach scales/grid +* ggplot2 now exports `alpha()` from the scales package (#1107), and `arrow()` + and `unit()` from grid (#1225). This means you don't need attach scales/grid or do `scales::`/`grid::` for these commonly used functions. * `aes_string()` now only parses character inputs. This fixes bugs when @@ -3019,10 +3037,10 @@ version of ggplot. making it easier to plot multiple grobs with the same name (e.g. grobs of ggplot2 graphics) in the same plot (#1256). -* `borders()` now accepts xlim and ylim arguments for specifying the geographical +* `borders()` now accepts xlim and ylim arguments for specifying the geographical region of interest (@markpayneatwork, #1392). -* `coord_cartesian()` applies the same expansion factor to limits as for scales. +* `coord_cartesian()` applies the same expansion factor to limits as for scales. You can suppress with `expand = FALSE` (#1207). * `coord_trans()` now works when breaks are suppressed (#1422). @@ -3070,7 +3088,7 @@ version of ggplot. * `geom_pointrange()` gains `fatten` argument so you can control the size of the point relative to the size of the line. -* `geom_segment()` annotations were not transforming with scales +* `geom_segment()` annotations were not transforming with scales (@BrianDiggs, #859). * `geom_smooth()` is no longer so chatty. If you want to know what the default @@ -3100,7 +3118,7 @@ version of ggplot. * New `layer_data()` function extracts the data used for plotting for a given layer. It's mostly useful for testing. -* User supplied `minor_breaks` can now be supplied on the same scale as +* User supplied `minor_breaks` can now be supplied on the same scale as the data, and will be automatically transformed with by scale (#1385). * You can now suppress the appearance of an axis/legend title (and the space @@ -3137,8 +3155,8 @@ version of ggplot. palettes. Instead the scales package now uses a much faster colour interpolation algorithm (#1022). -* `scale_*_brewer()` and `scale_*_distiller()` add new `direction` argument of - `scales::brewer_pal`, making it easier to change the order of colours +* `scale_*_brewer()` and `scale_*_distiller()` add new `direction` argument of + `scales::brewer_pal`, making it easier to change the order of colours (@jiho, #1139). * `scale_x_date()` now clips dates outside the limits in the same way as @@ -3151,11 +3169,11 @@ version of ggplot. * `stat_boxplot()` warns if a continuous variable is used for the `x` aesthetic without also supplying a `group` aesthetic (#992, @krlmlr). -* `stat_summary_2d()` and `stat_bin_2d()` now share exactly the same code for - determining breaks from `bins`, `binwidth`, and `origin`. - -* `stat_summary_2d()` and `stat_bin_2d()` now output in tile/raster compatible - form instead of rect compatible form. +* `stat_summary_2d()` and `stat_bin_2d()` now share exactly the same code for + determining breaks from `bins`, `binwidth`, and `origin`. + +* `stat_summary_2d()` and `stat_bin_2d()` now output in tile/raster compatible + form instead of rect compatible form. * Automatically computed breaks do not lead to an error for transformations like "probit" where the inverse can map to infinity (#871, @krlmlr) @@ -3164,10 +3182,10 @@ version of ggplot. Previously it computed the function on transformed scales, giving incorrect values (@BrianDiggs, #1011). -* `strip_dots` works with anonymous functions within calculated aesthetics +* `strip_dots` works with anonymous functions within calculated aesthetics (e.g. `aes(sapply(..density.., function(x) mean(x))))` (#1154, @NikNakk) -* `theme()` gains `validate = FALSE` parameter to turn off validation, and +* `theme()` gains `validate = FALSE` parameter to turn off validation, and hence store arbitrary additional data in the themes. (@tdhock, #1121) * Improved the calculation of segments needed to draw the curve representing diff --git a/R/aes.R b/R/aes.R index 25c6f8a806..33eae1de83 100644 --- a/R/aes.R +++ b/R/aes.R @@ -111,7 +111,7 @@ aes <- function(x, y, ...) { #' @export #' @rdname is_tests -is.mapping <- function(x) inherits(x, "uneval") +is_mapping <- function(x) inherits(x, "uneval") # Wrap symbolic objects in quosures but pull out constants out of # quosures for backward-compatibility @@ -302,7 +302,7 @@ aes_ <- function(x, y, ...) { caller_env <- parent.frame() as_quosure_aes <- function(x) { - if (is.formula(x) && length(x) == 2) { + if (is_formula(x) && length(x) == 2) { as_quosure(x) } else if (is.null(x) || is.call(x) || is.name(x) || is.atomic(x)) { new_aesthetic(x, caller_env) diff --git a/R/axis-secondary.R b/R/axis-secondary.R index c1d024e288..d694cf3a47 100644 --- a/R/axis-secondary.R +++ b/R/axis-secondary.R @@ -124,19 +124,19 @@ dup_axis <- function(transform = identity, name = derive(), breaks = derive(), sec_axis(transform, trans = trans, name, breaks, labels, guide) } -is.sec_axis <- function(x) { +is_sec_axis <- function(x) { inherits(x, "AxisSecondary") } set_sec_axis <- function(sec.axis, scale) { - if (!is.waiver(sec.axis)) { + if (!is_waiver(sec.axis)) { if (scale$is_discrete()) { if (!identical(.subset2(sec.axis, "trans"), identity)) { cli::cli_abort("Discrete secondary axes must have the {.fn identity} transformation.") } } - if (is.formula(sec.axis)) sec.axis <- sec_axis(sec.axis) - if (!is.sec_axis(sec.axis)) { + if (is_formula(sec.axis)) sec.axis <- sec_axis(sec.axis) + if (!is_sec_axis(sec.axis)) { cli::cli_abort("Secondary axes must be specified using {.fn sec_axis}.") } scale$secondary.axis <- sec.axis @@ -150,7 +150,7 @@ set_sec_axis <- function(sec.axis, scale) { derive <- function() { structure(list(), class = "derived") } -is.derived <- function(x) { +is_derived <- function(x) { inherits(x, "derived") } #' @rdname ggplot2-ggproto @@ -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$name) && !is.waiver(scale$name)) self$name <- scale$name - if (is.derived(self$breaks)) self$breaks <- scale$breaks - if (is.waiver(self$breaks)) { + if (is_derived(self$name) && !is_waiver(scale$name)) self$name <- scale$name + if (is_derived(self$breaks)) self$breaks <- scale$breaks + if (is_waiver(self$breaks)) { if (scale$is_discrete()) { self$breaks <- setNames(nm = scale$get_breaks()) } else { @@ -197,8 +197,8 @@ AxisSecondary <- ggproto("AxisSecondary", NULL, } } } - if (is.derived(self$labels)) self$labels <- scale$labels - if (is.derived(self$guide)) self$guide <- scale$guide + if (is_derived(self$labels)) self$labels <- scale$labels + if (is_derived(self$guide)) self$guide <- scale$guide }, transform_range = function(self, range) { diff --git a/R/bin.R b/R/bin.R index a213513b1b..1318a180e0 100644 --- a/R/bin.R +++ b/R/bin.R @@ -120,7 +120,7 @@ compute_bins <- function(x, scale = NULL, breaks = NULL, binwidth = NULL, bins = center = NULL, boundary = NULL, closed = c("right", "left")) { - range <- if (is.scale(scale)) scale$dimension() else range(x) + range <- if (is_scale(scale)) scale$dimension() else range(x) check_length(range, 2L) if (!is.null(breaks)) { @@ -128,7 +128,7 @@ compute_bins <- function(x, scale = NULL, breaks = NULL, binwidth = NULL, bins = if (is.function(breaks)) { breaks <- breaks(x) } - if (is.scale(scale) && !scale$is_discrete()) { + if (is_scale(scale) && !scale$is_discrete()) { breaks <- scale$transform(breaks) } check_numeric(breaks) diff --git a/R/coord-.R b/R/coord-.R index 6b0470e39e..2b560292c4 100644 --- a/R/coord-.R +++ b/R/coord-.R @@ -225,17 +225,16 @@ Coord <- ggproto("Coord", } ) - #' @export #' @rdname is_tests -is.coord <- function(x) inherits(x, "Coord") +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) + 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 diff --git a/R/coord-cartesian-.R b/R/coord-cartesian-.R index 23e237583c..350e9bfd86 100644 --- a/R/coord-cartesian-.R +++ b/R/coord-cartesian-.R @@ -165,7 +165,7 @@ view_scales_from_scale <- function(scale, coord_limits = NULL, expand = TRUE) { } panel_guides_grob <- function(guides, position, theme, labels = NULL) { - if (!is.guides(guides)) { + if (!is_guides(guides)) { return(zeroGrob()) } pair <- guides$get_position(position) diff --git a/R/coord-sf.R b/R/coord-sf.R index d603d57de7..ed8df5e446 100644 --- a/R/coord-sf.R +++ b/R/coord-sf.R @@ -116,7 +116,7 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, x_breaks <- graticule$degree[graticule$type == "E"] if (is.null(scale_x$labels)) { x_labels <- rep(NA, length(x_breaks)) - } else if (is.waiver(scale_x$labels)) { + } else if (is_waiver(scale_x$labels)) { x_labels <- graticule$degree_label[graticule$type == "E"] needs_autoparsing[graticule$type == "E"] <- TRUE } else { @@ -141,7 +141,7 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, y_breaks <- graticule$degree[graticule$type == "N"] if (is.null(scale_y$labels)) { y_labels <- rep(NA, length(y_breaks)) - } else if (is.waiver(scale_y$labels)) { + } else if (is_waiver(scale_y$labels)) { y_labels <- graticule$degree_label[graticule$type == "N"] needs_autoparsing[graticule$type == "N"] <- TRUE } else { @@ -334,7 +334,7 @@ CoordSf <- ggproto("CoordSf", CoordCartesian, # we don't draw the graticules if the major panel grid is # turned off - if (inherits(el, "element_blank")) { + if (is_theme_element(el, "blank")) { grobs <- list(element_render(theme, "panel.background")) } else { line_gp <- gg_par( @@ -553,7 +553,7 @@ coord_sf <- function(xlim = NULL, ylim = NULL, expand = TRUE, ndiscr = 100, default = FALSE, clip = "on", reverse = "none") { - if (is.waiver(label_graticule) && is.waiver(label_axes)) { + if (is_waiver(label_graticule) && is_waiver(label_axes)) { # if both `label_graticule` and `label_axes` are set to waive then we # use the default of labels on the left and at the bottom label_graticule <- "" @@ -640,13 +640,13 @@ sf_breaks <- function(scale_x, scale_y, bbox, crs) { bbox[is.na(bbox)] <- c(-180, -90, 180, 90)[is.na(bbox)] } - if (!(is.waiver(scale_x$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.waiver(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$get_breaks(limits = bbox[c(2, 4)]) finite <- is.finite(y_breaks) y_breaks <- if (any(finite)) y_breaks[finite] else NULL @@ -769,7 +769,7 @@ view_scales_from_graticule <- function(graticule, scale, aesthetic, if (scale$position != position) { # Try to use secondary axis' guide guide <- scale$secondary.axis$guide %||% waiver() - if (is.derived(guide)) { + if (is_derived(guide)) { guide <- scale$guide } } else { diff --git a/R/facet-.R b/R/facet-.R index d712a7ae5f..6e8c96f277 100644 --- a/R/facet-.R +++ b/R/facet-.R @@ -9,8 +9,8 @@ NULL #' rendered. #' #' Extending facets can range from the simple modifications of current facets, -#' to very laborious rewrites with a lot of [gtable()] manipulation. -#' For some examples of both, please see the extension vignette. +#' to very laborious rewrites with a lot of [`gtable()`][gtable::gtable()] +#' manipulation. For some examples of both, please see the extension vignette. #' #' `Facet` subclasses, like other extendible ggproto classes, have a range #' of methods that can be modified. Some of these are required for all new @@ -49,7 +49,7 @@ NULL #' #' - `setup_panel_params`: modifies the x and y ranges for each panel. This is #' used to allow the `Facet` to interact with the `panel_params`. -#' +#' #' - `init_scales`: Given a master scale for x and y, create panel #' specific scales for each panel defined in the layout. The default is to #' simply clone the master scale. @@ -318,10 +318,6 @@ Facet <- ggproto("Facet", NULL, } ) -#' @export -#' @rdname is_tests -is.facet <- function(x) inherits(x, "Facet") - # Helpers ----------------------------------------------------------------- #' Quote faceting variables @@ -383,6 +379,18 @@ vars <- function(...) { quos(...) } +#' @export +#' @rdname is_tests +is_facet <- function(x) inherits(x, "Facet") + +#' @export +#' @rdname is_tests +#' @usage is.facet(x) # Deprecated +is.facet <- function(x) { + deprecate_soft0("3.5.2", "is.facet()", "is_facet()") + is_facet(x) +} + #' Accessing a plot's facet strip labels #' #' This functions retrieves labels from facet strips with the labeller applied. @@ -493,7 +501,7 @@ as_facets_list <- function(x) { } check_vars <- function(x) { - if (is.mapping(x)) { + 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 diff --git a/R/facet-grid-.R b/R/facet-grid-.R index 86bbad2b04..dd91cab70f 100644 --- a/R/facet-grid-.R +++ b/R/facet-grid-.R @@ -430,7 +430,7 @@ ulevels <- function(x, na.last = TRUE) { table_has_grob <- function(table, pattern) { grobs <- table$grobs[grep(pattern, table$layout$name)] - !all(vapply(grobs, is.zero, logical(1))) + !all(vapply(grobs, is_zero, logical(1))) } seam_table <- function(table, grobs = NULL, side, shift = 1, name, z = 1, diff --git a/R/facet-null.R b/R/facet-null.R index 26b610fdfa..9110a8654b 100644 --- a/R/facet-null.R +++ b/R/facet-null.R @@ -30,9 +30,9 @@ FacetNull <- ggproto("FacetNull", Facet, layout_null() }, map_data = function(data, layout, params) { - # Need the is.waiver 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.waiver(data)) + if (is_waiver(data)) return(data_frame0(PANEL = factor())) if (empty(data)) diff --git a/R/facet-wrap.R b/R/facet-wrap.R index e1eda21cdb..76027080cc 100644 --- a/R/facet-wrap.R +++ b/R/facet-wrap.R @@ -327,7 +327,7 @@ FacetWrap <- ggproto("FacetWrap", Facet, if (length(empty_bottom) > 0) { x_axes <- original$x$bottom[matched[empty_bottom]] clash["bottom"] <- strip == "bottom" && !inside && !free$x && - !all(vapply(x_axes, is.zero, logical(1))) + !all(vapply(x_axes, is_zero, logical(1))) if (!clash["bottom"]) { bottom[empty_bottom] <- x_axes } @@ -336,7 +336,7 @@ FacetWrap <- ggproto("FacetWrap", Facet, if (length(empty_top) > 0) { x_axes <- original$x$top[matched[empty_top]] clash["top"] <- strip == "top" && !inside && !free$x && - !all(vapply(x_axes, is.zero, logical(1))) + !all(vapply(x_axes, is_zero, logical(1))) if (!clash["top"]) { top[empty_top] <- x_axes } @@ -345,7 +345,7 @@ FacetWrap <- ggproto("FacetWrap", Facet, if (length(empty_right) > 0) { y_axes <- original$y$right[matched[empty_right]] clash["right"] <- strip == "right" && !inside && !free$y && - !all(vapply(y_axes, is.zero, logical(1))) + !all(vapply(y_axes, is_zero, logical(1))) if (!clash["right"]) { right[empty_right] <- y_axes } @@ -354,7 +354,7 @@ FacetWrap <- ggproto("FacetWrap", Facet, if (length(empty_left) > 0) { y_axes <- original$y$left[matched[empty_left]] clash["left"] <- strip == "left" && !inside && !free$y && - !all(vapply(y_axes, is.zero, logical(1))) + !all(vapply(y_axes, is_zero, logical(1))) if (!clash["left"]) { left[empty_left] <- y_axes } @@ -410,7 +410,7 @@ FacetWrap <- ggproto("FacetWrap", Facet, if (!inside) { axes <- grepl(paste0("axis-", pos), table$layout$name) - has_axes <- !vapply(table$grobs[axes], is.zero, logical(1)) + has_axes <- !vapply(table$grobs[axes], is_zero, logical(1)) has_axes <- split(has_axes, table$layout[[pos]][axes]) has_axes <- vapply(has_axes, sum, numeric(1)) > 0 padding <- rep(padding, length(has_axes)) diff --git a/R/fortify.R b/R/fortify.R index 17d6e37b12..108be24674 100644 --- a/R/fortify.R +++ b/R/fortify.R @@ -94,7 +94,7 @@ fortify.default <- function(model, data, ...) { "or an object coercible by {.fn fortify}, or a valid ", "{.cls data.frame}-like object coercible by {.fn as.data.frame}" ) - if (is.mapping(model)) { + if (is_mapping(model)) { msg <- c( paste0(msg, ", not ", obj_type_friendly(model), "."), "i" = "Did you accidentally pass {.fn aes} to the {.arg data} argument?" diff --git a/R/geom-.R b/R/geom-.R index db3dd2d5cc..e2d8806b35 100644 --- a/R/geom-.R +++ b/R/geom-.R @@ -237,7 +237,7 @@ Geom <- ggproto("Geom", #' @export #' @rdname is_tests -is.geom <- function(x) inherits(x, "Geom") +is_geom <- function(x) inherits(x, "Geom") eval_from_theme <- function(aesthetics, theme, class = NULL) { themed <- is_themed_aes(aesthetics) diff --git a/R/geom-defaults.R b/R/geom-defaults.R index c1bc8a782f..0d4cbf9142 100644 --- a/R/geom-defaults.R +++ b/R/geom-defaults.R @@ -93,13 +93,13 @@ update_stat_defaults <- function(stat, new) { #' #' # Changed theme #' get_geom_defaults("point", theme(geom = element_geom(ink = "purple"))) -get_geom_defaults <- function(geom, theme = theme_get()) { +get_geom_defaults <- function(geom, theme = get_theme()) { theme <- theme %||% list(geom = .default_geom_element) if (is.function(geom)) { geom <- geom() } - if (is.layer(geom)) { + if (is_layer(geom)) { data <- data_frame0(.id = 1L) data <- geom$compute_geom_2(data = data, theme = theme) data$.id <- NULL @@ -108,7 +108,7 @@ get_geom_defaults <- function(geom, theme = theme_get()) { if (is.character(geom)) { geom <- validate_subclass(geom, "Geom") } - if (is.geom(geom)) { + if (is_geom(geom)) { out <- geom$use_defaults(data = NULL, theme = theme) return(out) } diff --git a/R/geom-label.R b/R/geom-label.R index 13c679ac17..a9d288996f 100644 --- a/R/geom-label.R +++ b/R/geom-label.R @@ -88,7 +88,7 @@ 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$angle) - if (!is.margin("margin")) { + if (!is_margin("margin")) { label.padding <- rep(label.padding, length.out = 4) } diff --git a/R/ggproto.R b/R/ggproto.R index 6165a9707d..853a440f9f 100644 --- a/R/ggproto.R +++ b/R/ggproto.R @@ -1,6 +1,6 @@ #' Create a new ggproto object #' -#' Construct a new object with `ggproto()`, test with `is.ggproto()`, +#' Construct a new object with `ggproto()`, test with `is_ggproto()`, #' and access parent methods/fields with `ggproto_parent()`. #' #' ggproto implements a protype based OO system which blurs the lines between @@ -52,7 +52,7 @@ #' self$x #' } #' ) -#' is.ggproto(Adder) +#' is_ggproto(Adder) #' #' Adder$add(10) #' Adder$add(10) @@ -88,7 +88,7 @@ ggproto <- function(`_class` = NULL, `_inherit` = NULL, ...) { super <- find_super() if (!is.null(super)) { - check_object(super, is.ggproto, "a {.cls ggproto} object", arg = "_inherit") + check_object(super, is_ggproto, "a {.cls ggproto} object", arg = "_inherit") e$super <- find_super class(e) <- c(`_class`, class(super)) } else { @@ -98,10 +98,6 @@ ggproto <- function(`_class` = NULL, `_inherit` = NULL, ...) { e } -#' @export -#' @rdname is_tests -is.ggproto <- function(x) inherits(x, "ggproto") - #' @export #' @rdname ggproto #' @param parent,self Access parent class `parent` of object `self`. @@ -109,6 +105,18 @@ ggproto_parent <- function(parent, self) { structure(list(parent = parent, self = self), class = "ggproto_parent") } +#' @export +#' @rdname is_tests +is_ggproto <- function(x) inherits(x, "ggproto") + +#' @export +#' @rdname is_tests +#' @usage is.ggproto(x) # Deprecated +is.ggproto <- function(x) { + deprecate_soft0("3.5.2", "is.ggproto()", "is_ggproto()") + is_ggproto(x) +} + fetch_ggproto <- function(x, name) { res <- NULL @@ -303,7 +311,7 @@ object_summaries <- function(x, exclude = NULL, flat = TRUE) { values <- vapply(obj_names, function(name) { obj <- x[[name]] if (is.function(obj)) "function" - else if (is.ggproto(obj)) format(obj, flat = flat) + else if (is_ggproto(obj)) format(obj, flat = flat) else if (is.environment(obj)) "environment" else if (is.null(obj)) "NULL" else if (is.atomic(obj)) trim(paste(as.character(obj), collapse = " ")) diff --git a/R/grob-null.R b/R/grob-null.R index 217c5a7560..d7cc328b75 100644 --- a/R/grob-null.R +++ b/R/grob-null.R @@ -23,4 +23,9 @@ grobHeight.zeroGrob <- function(x) unit(0, "cm") #' @method drawDetails zeroGrob drawDetails.zeroGrob <- function(x, recording) {} -is.zero <- function(x) is.null(x) || inherits(x, "zeroGrob") +is_zero <- function(x) is.null(x) || inherits(x, "zeroGrob") + +is.zero <- function(x) { + deprecate_warn0("4.0.0", "is.zero()", "is_zero()") + is_zero(x) +} diff --git a/R/grouping.R b/R/grouping.R index 80b9d18121..7db4807a0f 100644 --- a/R/grouping.R +++ b/R/grouping.R @@ -12,7 +12,7 @@ add_group <- function(data) { if (empty(data)) return(data) if (is.null(data[["group"]])) { - disc <- vapply(data, is.discrete, logical(1)) + disc <- vapply(data, is_discrete, logical(1)) disc[names(disc) %in% c("label", "PANEL")] <- FALSE if (any(disc)) { diff --git a/R/guide-.R b/R/guide-.R index 54cae7c873..b1e432d923 100644 --- a/R/guide-.R +++ b/R/guide-.R @@ -50,7 +50,7 @@ new_guide <- function(..., available_aes = "any", super) { # Validate theme settings if (!is.null(params$theme)) { - check_object(params$theme, is.theme, what = "a {.cls theme} object") + check_object(params$theme, is_theme, what = "a {.cls theme} object") check_theme(params$theme, call = caller_env()) params$direction <- params$direction %||% params$theme$legend.direction } @@ -68,7 +68,7 @@ new_guide <- function(..., available_aes = "any", super) { #' @export #' @rdname is_tests -is.guide <- function(x) inherits(x, "Guide") +is_guide <- function(x) inherits(x, "Guide") #' @section Guides: #' @@ -376,10 +376,10 @@ Guide <- ggproto( # Renders tickmarks build_ticks = function(key, elements, params, position = params$position, length = elements$ticks_length) { - if (!is.theme_element(elements)) { + if (!is_theme_element(elements)) { elements <- elements$ticks } - if (!inherits(elements, "element_line")) { + if (!is_theme_element(elements, "line")) { return(zeroGrob()) } @@ -421,7 +421,7 @@ Guide <- ggproto( }, add_title = function(gtable, title, position, just) { - if (is.zero(title)) { + if (is_zero(title)) { return(gtable) } diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R index 37273cba06..cddc61920e 100644 --- a/R/guide-axis-logticks.R +++ b/R/guide-axis-logticks.R @@ -108,7 +108,7 @@ guide_axis_logticks <- function( if (is_bare_numeric(mid)) mid <- rel(mid) if (is_bare_numeric(short)) short <- rel(short) - check_fun <- function(x) (is.rel(x) || is.unit(x)) && length(x) == 1 + check_fun <- function(x) (is_rel(x) || is.unit(x)) && length(x) == 1 what <- "a {.cls rel} or {.cls unit} object of length 1" check_object(long, check_fun, what) check_object(mid, check_fun, what) diff --git a/R/guide-axis-stack.R b/R/guide-axis-stack.R index a58a4344cc..23136cdf18 100644 --- a/R/guide-axis-stack.R +++ b/R/guide-axis-stack.R @@ -195,7 +195,7 @@ GuideAxisStack <- ggproto( } # Remove empty grobs - grobs <- grobs[!vapply(grobs, is.zero, logical(1))] + grobs <- grobs[!vapply(grobs, is_zero, logical(1))] if (length(grobs) == 0) { return(zeroGrob()) } diff --git a/R/guide-axis-theta.R b/R/guide-axis-theta.R index af96a337b6..ccad321d6a 100644 --- a/R/guide-axis-theta.R +++ b/R/guide-axis-theta.R @@ -183,7 +183,7 @@ GuideAxisTheta <- ggproto( build_labels = function(key, elements, params) { - if (inherits(elements$text, "element_blank")) { + if (is_theme_element(elements$text, "blank")) { return(zeroGrob()) } @@ -196,7 +196,7 @@ GuideAxisTheta <- ggproto( } # Resolve text angle - if (is.waiver(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)) @@ -267,12 +267,12 @@ GuideAxisTheta <- ggproto( key <- params$key key <- vec_slice(key, !is.na(key$.label) & nzchar(key$.label)) labels <- validate_labels(key$.label) - if (length(labels) == 0 || inherits(elements$text, "element_blank")) { + if (length(labels) == 0 || is_theme_element(elements$text, "blank")) { return(list(offset = offset)) } # Resolve text angle - if (is.waiver(params$angle %||% waiver())) { + if (is_waiver(params$angle %||% waiver())) { angle <- elements$text$angle } else { angle <- flip_text_angle(params$angle - rad2deg(key$theta)) @@ -364,7 +364,7 @@ GuideAxisTheta <- ggproto( theta_tickmarks <- function(key, element, length, offset = NULL) { n_breaks <- nrow(key) - if (n_breaks < 1 || inherits(element, "element_blank")) { + if (n_breaks < 1 || is_theme_element(element, "blank")) { return(zeroGrob()) } diff --git a/R/guide-axis.R b/R/guide-axis.R index d445900071..bba3c1388c 100644 --- a/R/guide-axis.R +++ b/R/guide-axis.R @@ -259,10 +259,10 @@ GuideAxis <- ggproto( override_elements = function(params, elements, theme) { elements$text <- label_angle_heuristic(elements$text, params$position, params$angle) - if (inherits(elements$ticks, "element_blank")) { + if (is_theme_element(elements$ticks, "blank")) { elements$major_length <- unit(0, "cm") } - if (inherits(elements$minor, "element_blank") || isFALSE(params$minor.ticks)) { + if (is_theme_element(elements$minor, "blank") || isFALSE(params$minor.ticks)) { elements$minor_length <- unit(0, "cm") } return(elements) @@ -379,7 +379,7 @@ GuideAxis <- ggproto( # Ticks major_cm <- convertUnit(elements$major_length, "cm", valueOnly = TRUE) range <- range(0, major_cm) - if (params$minor.ticks && !inherits(elements$minor, "element_blank")) { + if (params$minor.ticks && !is_theme_element(elements$minor, "blank")) { minor_cm <- convertUnit(elements$minor_length, "cm", valueOnly = TRUE) range <- range(range, minor_cm) } @@ -420,7 +420,7 @@ 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$labels[[1]]) + has_labels <- !is_zero(grobs$labels[[1]]) grobs <- c(list(grobs$ticks), grobs$labels, list(grobs$title)) # Initialise empty gtable @@ -590,7 +590,7 @@ axis_label_priority_between <- function(x, y) { #' overridden from the user- or theme-supplied element. #' @noRd label_angle_heuristic <- function(element, position, angle) { - if (!inherits(element, "element_text") + if (!is_theme_element(element, "text") || is.null(position) || is.null(angle %|W|% NULL)) { return(element) diff --git a/R/guide-bins.R b/R/guide-bins.R index b83494fb77..67857d9f7c 100644 --- a/R/guide-bins.R +++ b/R/guide-bins.R @@ -341,7 +341,7 @@ GuideBins <- ggproto( parse_binned_breaks <- function(scale, breaks = scale$get_breaks()) { - if (is.waiver(scale$labels) || is.function(scale$labels)) { + if (is_waiver(scale$labels) || is.function(scale$labels)) { breaks <- breaks[!is.na(breaks)] } if (length(breaks) == 0) { diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R index 5116e1b24b..096901e9a8 100644 --- a/R/guide-colorbar.R +++ b/R/guide-colorbar.R @@ -5,8 +5,6 @@ NULL #' #' Colour bar guide shows continuous colour scales mapped onto values. #' Colour bar is available with `scale_fill` and `scale_colour`. -#' For more information, see the inspiration for this function: -#' \href{http://www.mathworks.com/help/techdoc/ref/colorbar.html}{Matlab's colorbar function}. #' #' Guides can be specified in each `scale_*` or in [guides()]. #' `guide="legend"` in `scale_*` is syntactic sugar for diff --git a/R/guide-custom.R b/R/guide-custom.R index f602bfc843..67cf648e6f 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.waiver(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/guide-legend.R b/R/guide-legend.R index c8bf395f0a..a6f6ca134a 100644 --- a/R/guide-legend.R +++ b/R/guide-legend.R @@ -544,7 +544,7 @@ GuideLegend <- ggproto( gt <- gtable(widths = widths, heights = heights) # Add keys - if (!is.zero(grobs$decor)) { + if (!is_zero(grobs$decor)) { n_key_layers <- params$n_key_layers %||% 1L key_cols <- rep(layout$key_col, each = n_key_layers) key_rows <- rep(layout$key_row, each = n_key_layers) @@ -560,7 +560,7 @@ GuideLegend <- ggproto( ) } - if (!is.zero(grobs$labels)) { + if (!is_zero(grobs$labels)) { gt <- gtable_add_grob( gt, grobs$labels, name = names(labels) %||% @@ -579,7 +579,7 @@ GuideLegend <- ggproto( gt <- gtable_add_padding(gt, unit(elements$padding, "cm")) # Add background - if (!is.zero(elements$background)) { + if (!is_zero(elements$background)) { gt <- gtable_add_grob( gt, elements$background, name = "background", clip = "off", @@ -647,7 +647,7 @@ set_key_size <- function(key, linewidth = NULL, size = NULL, default = NULL) { keep_key_data <- function(key, data, aes, show) { # First, can we exclude based on anything else than actually checking the # data that we should include or drop the key? - if (!is.discrete(key$.value)) { + if (!is_discrete(key$.value)) { return(TRUE) } if (is_named(show)) { @@ -810,7 +810,7 @@ deprecated_guide_args <- function( # Set as theme theme <- compact(theme) - if (!is.theme(theme)) { + if (!is_theme(theme)) { theme <- inject(theme(!!!theme)) } theme diff --git a/R/guides-.R b/R/guides-.R index b6da9f723d..2f7cd6d317 100644 --- a/R/guides-.R +++ b/R/guides-.R @@ -109,7 +109,7 @@ guides <- function(...) { #' @export #' @rdname is_tests -is.guides <- function(x) inherits(x, "Guides") +is_guides <- function(x) inherits(x, "Guides") # Class ------------------------------------------------------------------- @@ -140,7 +140,7 @@ Guides <- ggproto( if (is.null(guides)) { return(invisible()) } - if (is.guides(guides)) { + if (is_guides(guides)) { guides <- guides$guides } self$guides <- defaults(guides, self$guides) @@ -492,7 +492,7 @@ Guides <- ggproto( ) grobs <- self$draw(theme, positions, theme$legend.direction) - keep <- !vapply(grobs, is.zero, logical(1), USE.NAMES = FALSE) + keep <- !vapply(grobs, is_zero, logical(1), USE.NAMES = FALSE) grobs <- grobs[keep] if (length(grobs) < 1) { return(zeroGrob()) @@ -590,7 +590,7 @@ Guides <- ggproto( # arguments to collect guides package_box = function(grobs, position, theme) { - if (is.zero(grobs) || length(grobs) == 0) { + if (is_zero(grobs) || length(grobs) == 0) { return(zeroGrob()) } @@ -912,7 +912,7 @@ validate_guide <- function(guide) { guide <- fun() } } - if (is.guide(guide)) { + if (is_guide(guide)) { return(guide) } if (inherits(guide, "guide") && is.list(guide)) { diff --git a/R/guides-grid.R b/R/guides-grid.R index 1b2f1a4a99..9e70adaf37 100644 --- a/R/guides-grid.R +++ b/R/guides-grid.R @@ -30,7 +30,7 @@ guide_grid <- function(theme, panel_params, coord, square = TRUE) { grill <- compact(grill) background <- element_render(theme, "panel.background") - if (!isTRUE(square) && !is.zero(background)) { + if (!isTRUE(square) && !is_zero(background)) { gp <- background$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) diff --git a/R/labeller.R b/R/labeller.R index 9afd572da0..6d3c1b10ae 100644 --- a/R/labeller.R +++ b/R/labeller.R @@ -296,7 +296,7 @@ as_labeller <- function(x, default = label_value, multi_line = TRUE) { x(labels) } else if (is.function(x)) { default(lapply(labels, x)) - } else if (is.formula(x)) { + } else if (is_formula(x)) { default(lapply(labels, as_function(x))) } else if (is.character(x)) { default(lapply(labels, function(label) x[label])) @@ -546,7 +546,7 @@ build_strip <- function(label_df, labeller, theme, horizontal) { #' #' @noRd assemble_strips <- function(grobs, theme, horizontal = TRUE, clip) { - if (length(grobs) == 0 || is.zero(grobs[[1]])) { + if (length(grobs) == 0 || is_zero(grobs[[1]])) { # Subsets matrix of zeroGrobs to correct length (#4050) grobs <- grobs[seq_len(NROW(grobs))] return(grobs) diff --git a/R/labels.R b/R/labels.R index 27c1e96de6..17374aafbd 100644 --- a/R/labels.R +++ b/R/labels.R @@ -189,7 +189,7 @@ labs <- function(..., title = waiver(), subtitle = waiver(), caption = waiver(), tag = tag, alt = allow_lambda(alt), alt_insight = alt_insight, dictionary = dictionary, .ignore_empty = "all") - is_waive <- vapply(args, is.waiver, 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 cb81e84b58..f50658819b 100644 --- a/R/layer.R +++ b/R/layer.R @@ -199,12 +199,8 @@ 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 (!is.mapping(mapping)) { + 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 @@ -252,7 +248,7 @@ Layer <- ggproto("Layer", NULL, }, layer_data = function(self, plot_data) { - if (is.waiver(self$data)) { + if (is_waiver(self$data)) { data <- plot_data } else if (is.function(self$data)) { data <- self$data(plot_data) @@ -262,7 +258,7 @@ Layer <- ggproto("Layer", NULL, } else { data <- self$data } - if (is.null(data) || is.waiver(data)) data else unrowname(data) + if (is.null(data) || is_waiver(data)) data else unrowname(data) }, # hook to allow a layer access to the final layer data @@ -456,6 +452,11 @@ Layer <- ggproto("Layer", NULL, } ) +#' @export +#' @rdname is_tests +is_layer <- function(x) inherits(x, "Layer") +is.layer <- function(x) lifecycle::deprecate_stop("3.5.2", "is.layer()", "is_layer()") + validate_subclass <- function(x, subclass, argname = to_lower_ascii(subclass), x_arg = caller_arg(x), @@ -496,7 +497,7 @@ validate_subclass <- function(x, subclass, return(obj) } # Try prying the class from a layer - if (inherits(obj, "Layer")) { + if (is_layer(obj)) { obj <- switch( subclass, Geom = obj$geom, diff --git a/R/layout.R b/R/layout.R index 23048609dc..ff3c065e63 100644 --- a/R/layout.R +++ b/R/layout.R @@ -276,7 +276,7 @@ Layout <- ggproto("Layout", NULL, 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)) { + if (is_derived(secondary)) { secondary <- primary } @@ -291,7 +291,7 @@ Layout <- ggproto("Layout", NULL, } else { switch(label, x = ".bottom", y = ".right") } - if (is.null(labels[[label]][[i]]) || is.waiver(labels[[label]][[i]])) + if (is.null(labels[[label]][[i]]) || is_waiver(labels[[label]][[i]])) return(zeroGrob()) element_render( diff --git a/R/margins.R b/R/margins.R index 61ea1dab43..8eb99bb691 100644 --- a/R/margins.R +++ b/R/margins.R @@ -9,22 +9,25 @@ margin <- function(t = 0, r = 0, b = 0, l = 0, unit = "pt") { u } +#' @export +#' @rdname is_tests +is_margin <- function(x) inherits(x, "margin") + +is.margin <- function(x) lifecycle::deprecate_stop("3.5.2", "is.margin()", "is_margin()") + #' @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") - #' Create a text grob with the proper location and margins #' #' `titleGrob()` is called when creating titles and labels for axes, legends, diff --git a/R/plot-build.R b/R/plot-build.R index 03ac9a5f25..9cd01b54d5 100644 --- a/R/plot-build.R +++ b/R/plot-build.R @@ -179,7 +179,7 @@ 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 -#' stores them in a special data structure called a [gtable()]. +#' stores them in a special data structure called a [`gtable`][gtable::gtable]. #' This object is amenable to programmatic manipulation, should you want #' to (e.g.) make the legend box 2 cm wide, or combine multiple plots into #' a single display, preserving aspect ratios across the plots. @@ -190,7 +190,7 @@ layer_grob <- get_layer_grob #' a ggplot2 plot. #' #' The `r link_book("gtable step section", "internals#sec-ggplotgtable")` -#' @return a [gtable()] object +#' @return a `gtable` object #' @keywords internal #' @param data plot data generated by [ggplot_build()] #' @export @@ -289,7 +289,7 @@ ggplot_gtable.ggplot_built <- function(data) { plot_margin <- calc_element("plot.margin", theme) %||% margin() plot_table <- gtable_add_padding(plot_table, plot_margin) - if (is.theme_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) @@ -348,7 +348,7 @@ table_add_tag <- function(table, label, theme) { return(table) } element <- calc_element("plot.tag", theme) - if (inherits(element, "element_blank")) { + if (is_theme_element(element, "blank")) { return(table) } @@ -454,7 +454,7 @@ table_add_tag <- function(table, label, theme) { # Add the legends to the gtable table_add_legends <- function(table, legends, theme) { - if (is.zero(legends)) { + if (is_zero(legends)) { legends <- rep(list(zeroGrob()), 5) names(legends) <- c(.trbl, "inside") } @@ -465,7 +465,7 @@ table_add_legends <- function(table, legends, theme) { names(legends) ) - empty <- vapply(legends, is.zero, logical(1)) + empty <- vapply(legends, is_zero, logical(1)) widths[!empty] <- lapply(legends[!empty], gtable_width) heights[!empty] <- lapply(legends[!empty], gtable_height) spacing <- calc_element("legend.box.spacing", theme) %||% unit(0.2, "cm") diff --git a/R/plot-construction.R b/R/plot-construction.R index cd18fc8310..b10a9f4387 100644 --- a/R/plot-construction.R +++ b/R/plot-construction.R @@ -51,9 +51,9 @@ # can be displayed in error messages e2name <- deparse(substitute(e2)) - if (is.theme(e1)) add_theme(e1, e2, e2name) - else if (is.ggplot(e1)) add_ggplot(e1, e2, e2name) - else if (is.ggproto(e1)) { + if (is_theme(e1)) add_theme(e1, e2, e2name) + else if (is_ggplot(e1)) add_ggplot(e1, e2, e2name) + else if (is_ggproto(e1)) { cli::cli_abort(c( "Cannot add {.cls ggproto} objects together.", "i" = "Did you forget to add this object to a {.cls ggplot} object?" @@ -149,7 +149,7 @@ ggplot_add.labels <- function(object, plot, object_name) { } #' @export ggplot_add.Guides <- function(object, plot, object_name) { - if (is.guides(plot$guides)) { + if (is_guides(plot$guides)) { # We clone the guides object to prevent modify-in-place of guides old <- plot$guides new <- ggproto(NULL, old) diff --git a/R/plot.R b/R/plot.R index c992530a0b..5f38f63116 100644 --- a/R/plot.R +++ b/R/plot.R @@ -111,7 +111,7 @@ ggplot <- function(data = NULL, mapping = aes(), ..., #' @export ggplot.default <- function(data = NULL, mapping = aes(), ..., environment = parent.frame()) { - if (!missing(mapping) && !is.mapping(mapping)) { + if (!missing(mapping) && !is_mapping(mapping)) { cli::cli_abort(c( "{.arg mapping} must be created with {.fn aes}.", "x" = "You've supplied {.obj_type_friendly {mapping}}." @@ -148,13 +148,6 @@ ggplot.function <- function(data = NULL, mapping = aes(), ..., )) } -#' Reports whether x is a type of object -#' @param x An object to test -#' @keywords internal -#' @export -#' @name is_tests -is.ggplot <- function(x) inherits(x, "ggplot") - plot_clone <- function(plot) { p <- plot p$scales <- plot$scales$clone() @@ -162,6 +155,21 @@ plot_clone <- function(plot) { p } +#' Reports wether `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") + +#' @export +#' @rdname is_tests +#' @usage is.ggplot(x) # Deprecated +is.ggplot <- function(x) { + deprecate_soft0("3.5.2", "is.ggplot()", "is_ggplot()") + is_ggplot(x) +} + #' 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 c78ca0fc4c..fb339b6660 100644 --- a/R/position-.R +++ b/R/position-.R @@ -103,7 +103,7 @@ Position <- ggproto("Position", #' @export #' @rdname is_tests -is.position <- function(x) inherits(x, "Position") +is_position <- function(x) inherits(x, "Position") #' Convenience function to transform all position variables. #' diff --git a/R/quick-plot.R b/R/quick-plot.R index 64e2ab460d..4dfa478be3 100644 --- a/R/quick-plot.R +++ b/R/quick-plot.R @@ -121,7 +121,7 @@ qplot <- function(x, y, ..., data, facets = NULL, margins = FALSE, geom[geom == "auto"] <- "qq" } else if (missing(y)) { x <- eval_tidy(mapping$x, data, caller_env) - if (is.discrete(x)) { + if (is_discrete(x)) { geom[geom == "auto"] <- "bar" } else { geom[geom == "auto"] <- "histogram" @@ -139,7 +139,7 @@ qplot <- function(x, y, ..., data, facets = NULL, margins = FALSE, if (is.null(facets)) { p <- p + facet_null() - } else if (is.formula(facets) && length(facets) == 2) { + } else if (is_formula(facets) && length(facets) == 2) { p <- p + facet_wrap(facets) } else { p <- p + facet_grid(rows = deparse(facets), margins = margins) diff --git a/R/save.R b/R/save.R index 523f2ef29b..2f2faec357 100644 --- a/R/save.R +++ b/R/save.R @@ -241,7 +241,7 @@ get_plot_background <- function(plot, bg = NULL, default = "transparent") { return(bg) } plot <- if (is_bare_list(plot)) plot[[1]] else plot - if (!is.ggplot(plot)) { + if (!is_ggplot(plot)) { return(default) } calc_element("plot.background", plot_theme(plot))$fill %||% default diff --git a/R/scale-.R b/R/scale-.R index 66a0c91de4..acba458034 100644 --- a/R/scale-.R +++ b/R/scale-.R @@ -228,7 +228,7 @@ discrete_scale <- function(aesthetics, scale_name = deprecated(), palette, name labels <- allow_lambda(labels) minor_breaks <- allow_lambda(minor_breaks) - if (!is.function(limits) && (length(limits) > 0) && !is.discrete(limits)) { + if (!is.function(limits) && (length(limits) > 0) && !is_discrete(limits)) { cli::cli_warn(c( "Continuous limits supplied to discrete scale.", "i" = "Did you mean {.code limits = factor(...)} or {.fn scale_*_continuous}?" @@ -370,7 +370,7 @@ binned_scale <- function(aesthetics, scale_name = deprecated(), palette, name = #' @export #' @rdname is_tests -is.scale <- function(x) inherits(x, "Scale") +is_scale <- function(x) inherits(x, "Scale") #' @section Scales: #' @@ -777,7 +777,7 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale, # don't support conversion to numeric (#5304) if (zero_range(as.numeric(transformation$transform(limits)))) { breaks <- limits[1] - } else if (is.waiver(self$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 { @@ -819,7 +819,7 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale, b <- b[is.finite(b)] transformation <- self$get_transformation() - if (is.waiver(self$minor_breaks)) { + if (is_waiver(self$minor_breaks)) { if (is.null(b)) { breaks <- NULL } else { @@ -866,7 +866,7 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale, ) } - if (is.waiver(self$labels)) { + if (is_waiver(self$labels)) { labels <- transformation$format(breaks) } else if (is.function(self$labels)) { labels <- self$labels(breaks) @@ -965,7 +965,7 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, return() } # Intercept error here to give examples and mention scale in call - if (!is.discrete(x)) { + if (!is_discrete(x)) { # These assumptions only hold for standard DiscreteRange class, so # we skip the error if another range class is used if (inherits(self$range, "DiscreteRange")) { @@ -1053,7 +1053,7 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, ) } - if (is.waiver(self$breaks)) { + if (is_waiver(self$breaks)) { breaks <- limits } else if (is.function(self$breaks)) { breaks <- self$breaks(limits) @@ -1117,7 +1117,7 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale, ) } - if (is.waiver(labels)) { + if (is_waiver(labels)) { if (!is.null(names(breaks))) { labels <- names(breaks) } else if (is.numeric(breaks)) { @@ -1273,7 +1273,7 @@ ScaleBinned <- ggproto("ScaleBinned", Scale, "Invalid {.arg breaks} specification. Use {.code NULL}, not {.code NA}.", call = self$call ) - } else if (is.waiver(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) @@ -1368,7 +1368,7 @@ ScaleBinned <- ggproto("ScaleBinned", Scale, "Invalid {.arg labels} specification. Use {.code NULL}, not {.code NA}.", call = self$call ) - } else if (is.waiver(self$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-colour.R b/R/scale-colour.R index ab5981da76..c8c468559f 100644 --- a/R/scale-colour.R +++ b/R/scale-colour.R @@ -262,7 +262,7 @@ scale_fill_discrete <- function(..., palette = NULL, aesthetics = "fill", na.val # 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) || !is.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-continuous.R b/R/scale-continuous.R index 9b0c8ec82c..d65d1c72f8 100644 --- a/R/scale-continuous.R +++ b/R/scale-continuous.R @@ -149,21 +149,21 @@ ScaleContinuousPosition <- ggproto("ScaleContinuousPosition", ScaleContinuous, }, break_info = function(self, range = NULL) { breaks <- ggproto_parent(ScaleContinuous, self)$break_info(range) - if (!(is.waiver(self$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.waiver(self$secondary.axis)) { + if (is_waiver(self$secondary.axis)) { waiver() } else { self$secondary.axis$name } }, make_sec_title = function(self, ...) { - if (!is.waiver(self$secondary.axis)) { + if (!is_waiver(self$secondary.axis)) { self$secondary.axis$make_title(...) } else { ggproto_parent(ScaleContinuous, self)$make_sec_title(...) diff --git a/R/scale-date.R b/R/scale-date.R index ac0c314e18..b7f71f0e7c 100644 --- a/R/scale-date.R +++ b/R/scale-date.R @@ -318,15 +318,15 @@ datetime_scale <- function(aesthetics, transform, trans = deprecated(), if (is.character(breaks)) breaks <- breaks_width(breaks) if (is.character(minor_breaks)) minor_breaks <- breaks_width(minor_breaks) - if (!is.waiver(date_breaks)) { + if (!is_waiver(date_breaks)) { check_string(date_breaks) breaks <- breaks_width(date_breaks) } - if (!is.waiver(date_minor_breaks)) { + if (!is_waiver(date_minor_breaks)) { check_string(date_minor_breaks) minor_breaks <- breaks_width(date_minor_breaks) } - if (!is.waiver(date_labels)) { + if (!is_waiver(date_labels)) { check_string(date_labels) if (transform == "hms") { labels <- label_time(date_labels) @@ -404,21 +404,21 @@ ScaleContinuousDatetime <- ggproto("ScaleContinuousDatetime", ScaleContinuous, }, break_info = function(self, range = NULL) { breaks <- ggproto_parent(ScaleContinuous, self)$break_info(range) - if (!(is.waiver(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$range, self)) } breaks }, sec_name = function(self) { - if (is.waiver(self$secondary.axis)) { + if (is_waiver(self$secondary.axis)) { waiver() } else { self$secondary.axis$name } }, make_sec_title = function(self, ...) { - if (!is.waiver(self$secondary.axis)) { + if (!is_waiver(self$secondary.axis)) { self$secondary.axis$make_title(...) } else { ggproto_parent(ScaleContinuous, self)$make_sec_title(...) @@ -458,21 +458,21 @@ ScaleContinuousDate <- ggproto("ScaleContinuousDate", ScaleContinuous, }, break_info = function(self, range = NULL) { breaks <- ggproto_parent(ScaleContinuous, self)$break_info(range) - if (!(is.waiver(self$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.waiver(self$secondary.axis)) { + if (is_waiver(self$secondary.axis)) { waiver() } else { self$secondary.axis$name } }, make_sec_title = function(self, ...) { - if (!is.waiver(self$secondary.axis)) { + if (!is_waiver(self$secondary.axis)) { self$secondary.axis$make_title(...) } else { ggproto_parent(ScaleContinuous, self)$make_sec_title(...) diff --git a/R/scale-discrete-.R b/R/scale-discrete-.R index adaebb96d7..6a883e677d 100644 --- a/R/scale-discrete-.R +++ b/R/scale-discrete-.R @@ -119,7 +119,7 @@ ScaleDiscretePosition <- ggproto("ScaleDiscretePosition", ScaleDiscrete, continuous_limits = NULL, train = function(self, x) { - if (is.discrete(x)) { + if (is_discrete(x)) { self$range$train(x, drop = self$drop, na.rm = !self$na.translate) } else { self$range_c$train(x) @@ -156,7 +156,7 @@ ScaleDiscretePosition <- ggproto("ScaleDiscretePosition", ScaleDiscrete, if (inherits(x, "AsIs")) { return(x) } - if (is.discrete(x)) { + if (is_discrete(x)) { values <- self$palette(length(limits)) if (!is.numeric(values)) { cli::cli_abort( @@ -185,7 +185,7 @@ ScaleDiscretePosition <- ggproto("ScaleDiscretePosition", ScaleDiscrete, }, sec_name = function(self) { - if (is.waiver(self$secondary.axis)) { + if (is_waiver(self$secondary.axis)) { waiver() } else { self$secondary.axis$name diff --git a/R/scale-expansion.R b/R/scale-expansion.R index 9c682eeaa6..89b8bd06ad 100644 --- a/R/scale-expansion.R +++ b/R/scale-expansion.R @@ -228,7 +228,7 @@ expand_limits_discrete_trans <- function(limits, expand = expansion(0, 0), range_continuous = NULL) { discrete_limits <- NULL if (length(limits) > 0) { - if (is.discrete(limits)) { + if (is_discrete(limits)) { discrete_limits <- c(1, length(limits)) # for backward compatibility } else { discrete_limits <- range(limits) diff --git a/R/scale-manual.R b/R/scale-manual.R index 9f6284361b..87b479e926 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.waiver(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 a926084cd8..db0b4bcd65 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.waiver(scale$secondary.axis) || scale$secondary.axis$empty()) { + if (is.null(scale$secondary.axis) || is_waiver(scale$secondary.axis) || scale$secondary.axis$empty()) { # if there is no second axis, return the primary scale with no guide # this guide can be overridden using guides() primary_scale <- view_scale_primary(scale, limits, continuous_range) diff --git a/R/stat-.R b/R/stat-.R index 11cdbc67d6..186341eb78 100644 --- a/R/stat-.R +++ b/R/stat-.R @@ -221,4 +221,4 @@ Stat <- ggproto("Stat", #' @export #' @rdname is_tests -is.stat <- function(x) inherits(x, "Stat") +is_stat <- function(x) inherits(x, "Stat") diff --git a/R/stat-ellipse.R b/R/stat-ellipse.R index d462bf3575..cc38cbbd0d 100644 --- a/R/stat-ellipse.R +++ b/R/stat-ellipse.R @@ -5,7 +5,7 @@ #' #' @references John Fox and Sanford Weisberg (2011). An \R Companion to #' Applied Regression, Second Edition. Thousand Oaks CA: Sage. URL: -#' \url{https://www.john-fox.ca/Companion/} +#' \url{https://uk.sagepub.com/en-gb/eur/an-r-companion-to-applied-regression/book246125} #' @references Michael Friendly. Georges Monette. John Fox. "Elliptical Insights: Understanding Statistical Methods through Elliptical Geometry." #' Statist. Sci. 28 (1) 1 - 39, February 2013. URL: \url{https://projecteuclid.org/journals/statistical-science/volume-28/issue-1/Elliptical-Insights-Understanding-Statistical-Methods-through-Elliptical-Geometry/10.1214/12-STS402.full} #' diff --git a/R/stat-function.R b/R/stat-function.R index bf6d2e4b74..2cef4a1b23 100644 --- a/R/stat-function.R +++ b/R/stat-function.R @@ -70,7 +70,7 @@ StatFunction <- ggproto("StatFunction", Stat, } } - if (is.formula(fun)) fun <- as_function(fun) + if (is_formula(fun)) fun <- as_function(fun) y_out <- inject(fun(x_trans, !!!args)) if (!is.null(scales$y) && !scales$y$is_discrete()) { diff --git a/R/theme-current.R b/R/theme-current.R index ac24ec4724..c6848c7d76 100644 --- a/R/theme-current.R +++ b/R/theme-current.R @@ -94,7 +94,7 @@ theme_get <- get_theme #' @param new new theme (a list of theme elements) #' @export set_theme <- function(new) { - check_object(new, is.theme, "a {.cls theme} object") + check_object(new, is_theme, "a {.cls theme} object") old <- ggplot_global$theme_current ggplot_global$theme_current <- new invisible(old) @@ -127,7 +127,7 @@ theme_replace <- replace_theme #' @rdname get_theme #' @export "%+replace%" <- function(e1, e2) { - if (!is.theme(e1) || !is.theme(e2)) { + if (!is_theme(e1) || !is_theme(e2)) { cli::cli_abort("{.code %+replace%} requires two theme objects") } diff --git a/R/theme-elements.R b/R/theme-elements.R index dad3927a16..aeb670edc8 100644 --- a/R/theme-elements.R +++ b/R/theme-elements.R @@ -33,6 +33,8 @@ #' a blank element among its parents will cause this element to be blank as #' well. If `FALSE` any blank parent element will be ignored when #' calculating final element state. +#' @param type For testing elements: the type of element to expect. One of +#' `"blank"`, `"rect"`, `"line"` or `"text"`. #' @return An S3 object of class `element`, `rel`, or `margin`. #' @details #' The `element_polygon()` and `element_point()` functions are not rendered @@ -247,8 +249,21 @@ element_geom <- function( ) #' @export -#' @rdname is_tests -is.theme_element <- function(x) inherits(x, "element") +#' @rdname element +is_theme_element <- function(x, type = "any") { + switch( + type %||% "any", + any = inherits(x, "element"), + rect = inherits(x, "element_rect"), + line = inherits(x, "element_line"), + text = inherits(x, "element_text"), + blank = inherits(x, "element_blank"), + polygon = inherits(x, "element_polygon"), + point = inherits(x, "element_point"), + geom = inherits(x, "element_geom"), + FALSE + ) +} #' @export print.element <- function(x, ...) utils::str(x) @@ -267,7 +282,12 @@ print.rel <- function(x, ...) print(noquote(paste(x, " *", sep = ""))) #' Reports whether x is a rel object #' @param x An object to test #' @keywords internal -is.rel <- function(x) inherits(x, "rel") +is_rel <- function(x) inherits(x, "rel") + +is.rel <- function(x) { + deprecate_warn0("4.0.0", "is.rel()", "is_rel()") + is_rel(x) +} #' Render a specified theme element into a grob #' @@ -831,7 +851,7 @@ check_element <- function(el, elname, element_tree, call = caller_env()) { if ("margin" %in% eldef$class) { if (!is.unit(el) && length(el) == 4) cli::cli_abort("The {.var {elname}} theme element must be a {.cls unit} vector of length 4.", call = call) - } else if (!inherits(el, eldef$class) && !inherits(el, "element_blank")) { + } else if (!inherits(el, eldef$class) && !is_theme_element(el, "blank")) { cli::cli_abort("The {.var {elname}} theme element must be a {.cls {eldef$class}} object.", call = call) } invisible() diff --git a/R/theme.R b/R/theme.R index 33ff8b423e..629c2d401f 100644 --- a/R/theme.R +++ b/R/theme.R @@ -475,7 +475,7 @@ theme <- function(..., # If complete theme set all non-blank elements to inherit from blanks if (complete) { elements <- lapply(elements, function(el) { - if (is.theme_element(el) && !inherits(el, "element_blank")) { + if (is_theme_element(el) && !is_theme_element(el, "blank")) { el$inherit.blank <- TRUE } el @@ -490,7 +490,7 @@ theme <- function(..., } fix_theme_deprecations <- function(elements) { - if (is.unit(elements$legend.margin) && !is.margin(elements$legend.margin)) { + if (is.unit(elements$legend.margin) && !is_margin(elements$legend.margin)) { cli::cli_warn(c( "{.var legend.margin} must be specified using {.fn margin}", "i" = "For the old behavior use {.var legend.spacing}" @@ -574,10 +574,6 @@ validate_theme_palettes <- function(elements) { elements } -#' @export -#' @rdname is_tests -is.theme <- function(x) inherits(x, "theme") - # check whether theme is complete is_theme_complete <- function(x) isTRUE(attr(x, "complete", exact = TRUE)) @@ -620,9 +616,8 @@ check_theme <- function(theme, tree = get_element_tree(), call = caller_env()) { #' complete_theme(my_theme) complete_theme <- function(theme = NULL, default = theme_get()) { if (!is_bare_list(theme)) { - check_object(theme, is.theme, "a {.cls theme} object", allow_null = TRUE) + check_object(theme, is_theme, "a {.cls theme} object", allow_null = TRUE) } - check_object(default, is.theme, "a {.cls theme} object") theme <- plot_theme(list(theme = theme), default = default) # Using `theme(!!!theme)` drops `NULL` entries, so strip most attributes and @@ -742,7 +737,7 @@ calc_element <- function(element, theme, verbose = FALSE, skip_blank = FALSE, # If result is element_blank, we skip it if `skip_blank` is `TRUE`, # and otherwise we don't inherit anything from parents - if (inherits(el_out, "element_blank")) { + if (is_theme_element(el_out, "blank")) { if (isTRUE(skip_blank)) { el_out <- NULL } else { @@ -777,7 +772,7 @@ calc_element <- function(element, theme, verbose = FALSE, skip_blank = FALSE, # if we have null properties, try to fill in from ggplot_global$theme_default el_out <- combine_elements(el_out, ggplot_global$theme_default[[element]]) nullprops <- vapply(el_out, is.null, logical(1)) - if (inherits(el_out, "element_geom")) { + if (is_theme_element(el_out, "geom")) { # Geom elements are expected to have NULL fill/colour, so allow these # to be missing nullprops[c("colour", "fill")] <- FALSE @@ -832,7 +827,7 @@ merge_element <- function(new, old) { #' @rdname merge_element #' @export merge_element.default <- function(new, old) { - if (is.null(old) || inherits(old, "element_blank")) { + if (is.null(old) || is_theme_element(old, "blank")) { # If old is NULL or element_blank, then just return new return(new) } else if (is.null(new) || is.character(new) || is.numeric(new) || is.unit(new) || @@ -855,7 +850,7 @@ merge_element.element_blank <- function(new, old) { #' @rdname merge_element #' @export merge_element.element <- function(new, old) { - if (is.null(old) || inherits(old, "element_blank")) { + if (is.null(old) || is_theme_element(old, "blank")) { # If old is NULL or element_blank, then just return new return(new) } @@ -880,7 +875,7 @@ merge_element.element <- function(new, old) { #' @rdname merge_element #' @export merge_element.margin <- function(new, old) { - if (is.null(old) || inherits(old, "element_blank")) { + if (is.null(old) || is_theme_element(old, "blank")) { return(new) } if (anyNA(new)) { @@ -899,7 +894,7 @@ merge_element.margin <- function(new, old) { combine_elements <- function(e1, e2) { # If e2 is NULL, nothing to inherit - if (is.null(e2) || inherits(e1, "element_blank")) { + if (is.null(e2) || is_theme_element(e1, "blank")) { return(e1) } @@ -909,9 +904,9 @@ combine_elements <- function(e1, e2) { } # Inheritance of rel objects - if (is.rel(e1)) { + if (is_rel(e1)) { # Both e1 and e2 are rel, give product as another rel - if (is.rel(e2)) { + if (is_rel(e2)) { return(rel(unclass(e1) * unclass(e2))) } # If e2 is a unit/numeric, return modified unit/numeric @@ -922,7 +917,7 @@ combine_elements <- function(e1, e2) { return(e1) } - if (inherits(e1, "margin") && inherits(e2, "margin")) { + if (is_margin(e1) && is_margin(e2)) { if (anyNA(e2)) { e2[is.na(e2)] <- unit(0, "pt") } @@ -932,13 +927,13 @@ combine_elements <- function(e1, e2) { } # If neither of e1 or e2 are element_* objects, return e1 - if (!inherits(e1, "element") && !inherits(e2, "element")) { + if (!is_theme_element(e1) && !is_theme_element(e2)) { return(e1) } # If e2 is element_blank, and e1 inherits blank inherit everything from e2, # otherwise ignore e2 - if (inherits(e2, "element_blank")) { + if (is_theme_element(e2, "blank")) { if (e1$inherit.blank) { return(e2) } else { @@ -951,16 +946,16 @@ combine_elements <- function(e1, e2) { e1[n] <- e2[n] # Calculate relative sizes - if (is.rel(e1$size)) { + if (is_rel(e1$size)) { e1$size <- e2$size * unclass(e1$size) } # Calculate relative linewidth - if (is.rel(e1$linewidth)) { + if (is_rel(e1$linewidth)) { e1$linewidth <- e2$linewidth * unclass(e1$linewidth) } - if (inherits(e1, "element_text")) { + if (is_theme_element(e1, "text")) { e1$margin <- combine_elements(e1$margin, e2$margin) } @@ -976,6 +971,18 @@ combine_elements <- function(e1, e2) { e1 } +#' @export +#' @rdname is_tests +is_theme <- function(x) inherits(x, "theme") + +#' @export +#' @rdname is_tests +#' @usage is.theme(x) # Deprecated +is.theme <- function(x) { + deprecate_soft0("3.5.2", "is.theme()", "is_theme()") + is_theme(x) +} + #' @export `$.theme` <- function(x, ...) { .subset2(x, ...) diff --git a/R/utilities.R b/R/utilities.R index 8f0672c142..062ec872c3 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -12,7 +12,7 @@ scales::alpha } "%|W|%" <- function(a, b) { - if (!is.waiver(a)) a else b + if (!is_waiver(a)) a else b } # Check required aesthetics are present @@ -183,7 +183,7 @@ should_stop <- function(expr) { #' 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()`). -#' `is.waiver()` reports whether an object is a waiver. +#' `is_waiver()` reports whether an object is a waiver. #' #' @export #' @keywords internal @@ -192,7 +192,12 @@ waiver <- function() structure(list(), class = "waiver") #' @param x An object to test #' @export #' @rdname waiver -is.waiver <- function(x) inherits(x, "waiver") +is_waiver <- function(x) inherits(x, "waiver") + +is.waiver <- function(x) { + deprecate_warn0("4.0.0", "is.waiver()", "is_waiver()") + is_waiver(x) +} pal_binned <- function(palette) { force(palette) @@ -279,13 +284,18 @@ snake_class <- function(x) { } empty <- function(df) { - is.null(df) || nrow(df) == 0 || ncol(df) == 0 || is.waiver(df) + is.null(df) || nrow(df) == 0 || ncol(df) == 0 || is_waiver(df) } -is.discrete <- function(x) { +is_discrete <- function(x) { is.factor(x) || is.character(x) || is.logical(x) } +is.discrete <- function(x) { + deprecate_warn0("4.0.0", "is.discrete()", "is_discrete()") + is_discrete(x) +} + 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 @@ -316,8 +326,6 @@ compact <- function(x) { x[!null] } -is.formula <- function(x) inherits(x, "formula") - dispatch_args <- function(f, ...) { args <- list(...) formals <- formals(f) diff --git a/README.Rmd b/README.Rmd index 8c601f59ea..c85299bdc5 100644 --- a/README.Rmd +++ b/README.Rmd @@ -23,7 +23,7 @@ knitr::opts_chunk$set( ## Overview -ggplot2 is a system for declaratively creating graphics, based on [The Grammar of Graphics][gg-book]. You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details. +ggplot2 is a system for declaratively creating graphics, based on [The Grammar of Graphics][gg-book]. You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details. ## Installation @@ -42,7 +42,7 @@ pak::pak("tidyverse/ggplot2") ## Cheatsheet -ggplot2 cheatsheet +ggplot2 cheatsheet ## Usage @@ -55,7 +55,7 @@ It's hard to succinctly describe how ggplot2 works because it embodies a deep ph #| per gallon are inversely correlated." library(ggplot2) -ggplot(mpg, aes(displ, hwy, colour = class)) + +ggplot(mpg, aes(displ, hwy, colour = class)) + geom_point() ``` @@ -64,7 +64,7 @@ ggplot(mpg, aes(displ, hwy, colour = class)) + [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) -ggplot2 is now over 10 years old and is used by hundreds of thousands of people to make millions of plots. That means, by-and-large, ggplot2 itself changes relatively little. When we do make changes, they will be generally to add new functions or arguments rather than changing the behaviour of existing functions, and if we do make changes to existing behaviour we will do them for compelling reasons. +ggplot2 is now over 10 years old and is used by hundreds of thousands of people to make millions of plots. That means, by-and-large, ggplot2 itself changes relatively little. When we do make changes, they will be generally to add new functions or arguments rather than changing the behaviour of existing functions, and if we do make changes to existing behaviour we will do them for compelling reasons. If you are looking for innovation, look to ggplot2's rich ecosystem of extensions. See a community maintained list at . @@ -73,25 +73,25 @@ If you are looking for innovation, look to ggplot2's rich ecosystem of extension 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 + [Communication][r4ds-comm] chapters in [R for Data Science][r4ds]. R for Data Science is designed to give you a comprehensive introduction to the [tidyverse](https://www.tidyverse.org), and these two chapters will - get you up to speed with the essentials of ggplot2 as quickly as + get you up to speed with the essentials of ggplot2 as quickly as possible. - + 1. If you'd like to take an online course, try [Data Visualization in R With ggplot2][oreilly] by Kara Woo. - + 1. If you'd like to follow a webinar, try - [Plotting Anything with ggplot2](https://youtu.be/h29g21z0a68) by Thomas Lin + [Plotting Anything with ggplot2](https://youtu.be/h29g21z0a68) by Thomas Lin Pedersen. -1. If you want to dive into making common graphics as quickly - as possible, I recommend [The R Graphics Cookbook][cookbook] +1. If you want to dive into making common graphics as quickly + as possible, I recommend [The R Graphics Cookbook][cookbook] by Winston Chang. It provides a set of recipes to solve common graphics problems. - + 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, @@ -112,7 +112,7 @@ There are two main places to get help with ggplot2: [community]: https://forum.posit.co/ [ggplot2-book]: https://ggplot2-book.org -[gg-book]: https://www.amazon.com/Grammar-Graphics-Statistics-Computing/dp/0387245448/ref=as_li_ss_tl +[gg-book]: https://link.springer.com/book/10.1007/0-387-28695-0 [so]: https://stackoverflow.com/questions/tagged/ggplot2?sort=frequent&pageSize=50 [cookbook]: https://r-graphics.org [r4ds]: https://r4ds.hadley.nz diff --git a/README.md b/README.md index 3683108c63..eed37e27ec 100644 --- a/README.md +++ b/README.md @@ -15,9 +15,9 @@ coverage](https://codecov.io/gh/tidyverse/ggplot2/graph/badge.svg)](https://app. ggplot2 is a system for declaratively creating graphics, based on [The Grammar of -Graphics](https://www.amazon.com/Grammar-Graphics-Statistics-Computing/dp/0387245448/ref=as_li_ss_tl). -You provide the data, tell ggplot2 how to map variables to aesthetics, -what graphical primitives to use, and it takes care of the details. +Graphics](https://link.springer.com/book/10.1007/0-387-28695-0). You +provide the data, tell ggplot2 how to map variables to aesthetics, what +graphical primitives to use, and it takes care of the details. ## Installation @@ -49,11 +49,13 @@ then add on layers (like `geom_point()` or `geom_histogram()`), scales ``` r library(ggplot2) -ggplot(mpg, aes(displ, hwy, colour = class)) + +ggplot(mpg, aes(displ, hwy, colour = class)) + geom_point() ``` -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. +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. ## Lifecycle diff --git a/cran-comments.md b/cran-comments.md index df78ca7e28..3423046660 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,2 +1,6 @@ -This is a small patch release fixing regressions from the last release. No -issues with reverse dependencies detected. +This is a small patch release preparing ggplot2 for changes in the ragg package. +Further it add infrastructure to help reverse dependencies gracefully prepare +for the next major ggplot2 release. + +This release breaks a test in SimNPH, but we are in contact with them and a fix +for this should land on CRAN very soon. diff --git a/man/coord_polar.Rd b/man/coord_polar.Rd index 23bbcb97ea..3bc579bcbc 100644 --- a/man/coord_polar.Rd +++ b/man/coord_polar.Rd @@ -138,14 +138,13 @@ ggplot(mtcars, aes(disp, mpg)) + # Similar with coord_cartesian(), you can set limits. ggplot(mtcars, aes(disp, mpg)) + - geom_point() + - coord_radial( - start = -0.4 * pi, - end = 0.4 * pi, inner.radius = 0.3, - thetalim = c(200, 300), - rlim = c(15, 30), - clip = "on" - ) + geom_point() + + coord_radial( + start = -0.4 * pi, + end = 0.4 * pi, inner.radius = 0.3, + thetalim = c(200, 300), + rlim = c(15, 30), + ) } \seealso{ The \href{https://ggplot2-book.org/coord#polar-coordinates-with-coord_polar}{polar coordinates section} of the online ggplot2 book. diff --git a/man/element.Rd b/man/element.Rd index 84fe10fd20..a2b716c087 100644 --- a/man/element.Rd +++ b/man/element.Rd @@ -8,6 +8,7 @@ \alias{element_polygon} \alias{element_point} \alias{element_geom} +\alias{is_theme_element} \alias{rel} \alias{margin} \alias{margin_part} @@ -89,6 +90,8 @@ element_geom( fill = NULL ) +is_theme_element(x, type = "any") + rel(x) margin(t = 0, r = 0, b = 0, l = 0, unit = "pt") @@ -155,6 +158,9 @@ is anchored.} \item{x}{A single number specifying size relative to parent element.} +\item{type}{For testing elements: the type of element to expect. One of +\code{"blank"}, \code{"rect"}, \code{"line"} or \code{"text"}.} + \item{t, r, b, l}{Dimensions of each margin. (To remember order, think trouble).} \item{unit}{Default units of dimensions. Defaults to "pt" so it diff --git a/man/figures/README-example-1.png b/man/figures/README-example-1.png index 24a035975a..96710b4627 100644 Binary files a/man/figures/README-example-1.png and b/man/figures/README-example-1.png differ diff --git a/man/get_geom_defaults.Rd b/man/get_geom_defaults.Rd index a39f80d720..ae1a7e5b63 100644 --- a/man/get_geom_defaults.Rd +++ b/man/get_geom_defaults.Rd @@ -4,7 +4,7 @@ \alias{get_geom_defaults} \title{Resolve and get geom defaults} \usage{ -get_geom_defaults(geom, theme = theme_get()) +get_geom_defaults(geom, theme = get_theme()) } \arguments{ \item{geom}{Some definition of a geom: diff --git a/man/ggplot2-ggproto.Rd b/man/ggplot2-ggproto.Rd index eae803189f..9ba1fdfdce 100644 --- a/man/ggplot2-ggproto.Rd +++ b/man/ggplot2-ggproto.Rd @@ -273,8 +273,8 @@ panels, how to apply positional scales and how to lay out the panels, once rendered. Extending facets can range from the simple modifications of current facets, -to very laborious rewrites with a lot of \code{\link[=gtable]{gtable()}} manipulation. -For some examples of both, please see the extension vignette. +to very laborious rewrites with a lot of \code{\link[gtable:gtable]{gtable()}} +manipulation. For some examples of both, please see the extension vignette. \code{Facet} subclasses, like other extendible ggproto classes, have a range of methods that can be modified. Some of these are required for all new diff --git a/man/ggplot_gtable.Rd b/man/ggplot_gtable.Rd index 6b5c5a71d7..0d608a6622 100644 --- a/man/ggplot_gtable.Rd +++ b/man/ggplot_gtable.Rd @@ -10,11 +10,11 @@ ggplot_gtable(data) \item{data}{plot data generated by \code{\link[=ggplot_build]{ggplot_build()}}} } \value{ -a \code{\link[=gtable]{gtable()}} object +a \code{gtable} object } \description{ This function builds all grobs necessary for displaying the plot, and -stores them in a special data structure called a \code{\link[=gtable]{gtable()}}. +stores them in a special data structure called a \code{\link[gtable:gtable]{gtable}}. This object is amenable to programmatic manipulation, should you want to (e.g.) make the legend box 2 cm wide, or combine multiple plots into a single display, preserving aspect ratios across the plots. diff --git a/man/ggproto.Rd b/man/ggproto.Rd index 11e3af8093..2ddf4f78d9 100644 --- a/man/ggproto.Rd +++ b/man/ggproto.Rd @@ -23,7 +23,7 @@ functions that become methods of the class or regular objects.} \item{parent, self}{Access parent class \code{parent} of object \code{self}.} } \description{ -Construct a new object with \code{ggproto()}, test with \code{is.ggproto()}, +Construct a new object with \code{ggproto()}, test with \code{is_ggproto()}, and access parent methods/fields with \code{ggproto_parent()}. } \details{ @@ -72,7 +72,7 @@ Adder <- ggproto("Adder", self$x } ) -is.ggproto(Adder) +is_ggproto(Adder) Adder$add(10) Adder$add(10) diff --git a/man/guide_colourbar.Rd b/man/guide_colourbar.Rd index 95546aa21c..bba0e628c0 100644 --- a/man/guide_colourbar.Rd +++ b/man/guide_colourbar.Rd @@ -113,8 +113,6 @@ A guide object \description{ Colour bar guide shows continuous colour scales mapped onto values. Colour bar is available with \code{scale_fill} and \code{scale_colour}. -For more information, see the inspiration for this function: -\href{http://www.mathworks.com/help/techdoc/ref/colorbar.html}{Matlab's colorbar function}. } \details{ Guides can be specified in each \verb{scale_*} or in \code{\link[=guides]{guides()}}. diff --git a/man/is.rel.Rd b/man/is_rel.Rd similarity index 86% rename from man/is.rel.Rd rename to man/is_rel.Rd index 67cda26b80..032e84f709 100644 --- a/man/is.rel.Rd +++ b/man/is_rel.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/theme-elements.R -\name{is.rel} -\alias{is.rel} +\name{is_rel} +\alias{is_rel} \title{Reports whether x is a rel object} \usage{ -is.rel(x) +is_rel(x) } \arguments{ \item{x}{An object to test} diff --git a/man/is_tests.Rd b/man/is_tests.Rd index bcb7bf0683..d6846f1ca8 100644 --- a/man/is_tests.Rd +++ b/man/is_tests.Rd @@ -1,63 +1,72 @@ % 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} +% R/facet-.R, R/stat-.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.ggproto} -\alias{is.mapping} -\alias{is.geom} -\alias{is.coord} +\alias{is_mapping} +\alias{is_geom} +\alias{is_coord} \alias{is.Coord} +\alias{is_facet} \alias{is.facet} -\alias{is.stat} -\alias{is.theme_element} -\alias{is.guide} -\alias{is.layer} -\alias{is.guides} -\alias{is.margin} +\alias{is_stat} +\alias{is_guide} +\alias{is_layer} +\alias{is_guides} +\alias{is_margin} \alias{is_tests} +\alias{is_ggplot} \alias{is.ggplot} -\alias{is.position} -\alias{is.scale} +\alias{is_position} +\alias{is_scale} +\alias{is_theme} \alias{is.theme} -\title{Reports whether x is a type of object} +\title{Reports wether \code{x} is a type of object} \usage{ -is.ggproto(x) +is_ggproto(x) -is.mapping(x) +is.ggproto(x) # Deprecated -is.geom(x) +is_mapping(x) -is.coord(x) +is_geom(x) + +is_coord(x) is.Coord(x) # Deprecated -is.facet(x) +is_facet(x) + +is.facet(x) # Deprecated + +is_stat(x) -is.stat(x) +is_guide(x) -is.theme_element(x) +is_layer(x) -is.guide(x) +is_guides(x) -is.layer(x) +is_margin(x) -is.guides(x) +is_ggplot(x) -is.margin(x) +is.ggplot(x) # Deprecated -is.ggplot(x) +is_position(x) -is.position(x) +is_scale(x) -is.scale(x) +is_theme(x) -is.theme(x) +is.theme(x) # Deprecated } \arguments{ \item{x}{An object to test} } \description{ -Reports whether x is a type of object +Reports wether \code{x} is a type of object } \keyword{internal} diff --git a/man/stat_connect.Rd b/man/stat_connect.Rd index d62ba610a5..24166744d8 100644 --- a/man/stat_connect.Rd +++ b/man/stat_connect.Rd @@ -128,11 +128,11 @@ Connect successive points with lines of different shapes. } \section{Aesthetics}{ -\code{stat_connect()} understands the following aesthetics (required aesthetics are in bold): -\itemize{ -\item \strong{\code{\link[=aes_position]{x}} \emph{or} \code{\link[=aes_position]{xmin}} \emph{or} \code{\link[=aes_position]{xmax}}} -\item \strong{\code{\link[=aes_position]{y}} \emph{or} \code{\link[=aes_position]{ymin}} \emph{or} \code{\link[=aes_position]{ymax}}} -\item \code{\link[=aes_group_order]{group}} +\code{stat_connect()} understands the following aesthetics. Required aesthetics are displayed in bold and defaults are displayed for optional aesthetics: +\tabular{rll}{ +• \tab \strong{\code{\link[=aes_position]{x}} \emph{or} \code{\link[=aes_position]{xmin}} \emph{or} \code{\link[=aes_position]{xmax}}} \tab \cr\cr +• \tab \strong{\code{\link[=aes_position]{y}} \emph{or} \code{\link[=aes_position]{ymin}} \emph{or} \code{\link[=aes_position]{ymax}}} \tab \cr\cr +• \tab \code{\link[=aes_group_order]{group}} \tab → inferred \cr\cr } Learn more about setting these aesthetics in \code{vignette("ggplot2-specs")}. } diff --git a/man/stat_ellipse.Rd b/man/stat_ellipse.Rd index fa4ecc9b05..ca8e448603 100644 --- a/man/stat_ellipse.Rd +++ b/man/stat_ellipse.Rd @@ -163,7 +163,7 @@ 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://www.john-fox.ca/Companion/} +\url{https://uk.sagepub.com/en-gb/eur/an-r-companion-to-applied-regression/book246125} 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/man/waiver.Rd b/man/waiver.Rd index 88fa06ba57..c1ecfe37bb 100644 --- a/man/waiver.Rd +++ b/man/waiver.Rd @@ -2,12 +2,12 @@ % Please edit documentation in R/utilities.R \name{waiver} \alias{waiver} -\alias{is.waiver} +\alias{is_waiver} \title{A waiver object.} \usage{ waiver() -is.waiver(x) +is_waiver(x) } \arguments{ \item{x}{An object to test} @@ -17,6 +17,6 @@ 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()}). -\code{is.waiver()} reports whether an object is a waiver. +\code{is_waiver()} reports whether an object is a waiver. } \keyword{internal} diff --git a/revdep/README.md b/revdep/README.md index ea1dc6ed4c..8faebd1cfa 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,555 +1,224 @@ # Revdeps -## Failed to check (196) +## Failed to check (206) -|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__ | | | -|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 |1.5.2 |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 |? | | | | +|package |version |error |warning |note | +|:----------------------|:-------|:-----|:-------|:----| +|abctools |1.1.7 |1 | | | +|adjustedCurves |? | | | | +|animalEKF |1.2 |1 | | | +|ANOM |0.5 |1 | | | +|aorsf |? | | | | +|atRisk |0.2.0 |1 | | | +|autoReg |? | | | | +|AutoScore |? | | | | +|bayesdfa |1.3.4 |1 | | | +|bayesDP |1.3.7 |1 | | | +|BayesGrowth |1.0.0 |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 |2.0.0 |1 | | | +|BuyseTest |? | | | | +|CAESAR.Suite |? | | | | +|CARBayesST |4.0 |1 | | | +|Certara.VPCResults |3.0.2 |1 | | | +|CGPfunctions |0.6.3 |1 | | | +|cia |? | | | | +|CIDER |0.99.4 |1 | | | +|cinaR |? | | | | +|ClusterGVis |? | | | | +|cmprskcoxmsm |0.2.1 |1 | | | +|COMMA |1.1.1 |1 | | | +|contsurvplot |? | | | | +|counterfactuals |? | | | | +|CRMetrics |0.3.2 |1 | | | +|ctsem |3.10.2 |1 | | | +|DamageDetective |? | | | | +|dartR.base |? | | | | +|dartR.captive |? | | | | +|dartR.popgen |? | | | | +|dartR.sexlinked |? | | | | +|dartR.sim |? | | | | +|dartR.spatial |? | | | | +|DepthProc |2.1.5 |1 | | | +|DFD |? | | | | +|discoveR |? | | | | +|dMrs |? | | | | +|DR.SC |3.5 |1 | | | +|dscoreMSM |? | | | | +|DynForest |? | | | | +|easybgm |0.2.1 |1 | | | +|EcoEnsemble |1.1.2 |1 | | | +|ecolottery |1.0.0 |1 | | | +|EpiEstim |2.2-4 |1 | | | +|evolqg |0.3-4 |1 | | | +|EWSmethods |? | | | | +|FARS |0.1.0 |1 | | | +|fio |0.1.6 |1 | | | +|flexrsurv |? | | | | +|fmx |? | | | | +|ForecastComb |1.3.1 |1 | | | +|gaawr2 |? | | | | +|gap |? | | | | +|gapfill |0.9.6-1 |1 | |1 | +|genekitr |? | | | | +|GeneSelectR |? | | | | +|GeomComb |1.0 |1 | | | +|geomorph |? | | | | +|GeoTox |? | | | | +|gJLS2 |0.2.0 |1 | | | +|grandR |? | | | | +|GseaVis |? | | | | +|HetSeq |0.1.0 |1 | | | +|hettx |0.1.3 |1 | | | +|Hmisc |? | | | | +|Hmsc |3.0-13 |1 | | | +|iClusterVB |0.1.4 |1 | | | +|immcp |? | | | | +|invivoPKfit |2.0.1 |1 | | | +|iNZightPlots |2.15.3 |1 | | | +|iNZightRegression |1.3.4 |1 | | | +|IRexamples |0.0.4 |1 | | | +|jmBIG |? | | | | +|joineRML |0.4.7 |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 |1.3.4 |1 | | | +|MantaID |? | | | | +|manymodelr |? | | | | +|MARVEL |? | | | | +|MaxWiK |1.0.5 |1 | | | +|mbsts |3.0 |1 | | | +|MendelianRandomization |0.10.0 |1 | | | +|mlmts |1.1.2 |1 | | | +|mlr |? | | | | +|MRZero |0.2.0 |1 | | | +|mstate |? | | | | +|multinma |0.8.0 |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 | | | +|obliqueRSF |? | | | | +|OlinkAnalyze |? | | | | +|optweight |0.2.5 |1 | | | +|ordinalsimr |? | | | | +|OVtool |1.0.3 |1 | | | +|pammtools |? | | | | +|parameters |? | | | | +|paths |0.1.1 |1 | | | +|PathwaySpace |? | | | | +|pcvr |1.1.1.0 |1 | | | +|PLMIX |2.1.1 |1 | | | +|Polychrome |? | | | | +|pould |? | | | | +|PoweREST |0.1.0 |1 | | | +|powerly |1.8.6 |1 | | | +|pre |1.0.7 |1 | | | +|ProFAST |? | | | | +|psbcSpeedUp |? | | | | +|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 | | | +|RcensusPkg |? | | | | +|RcmdrPlugin.RiskDemo |3.2 |1 | | | +|rddtools |1.6.0 |1 | | | +|relsurv |? | | | | +|ReporterScore |? | | | | +|RGraphSpace |? | | | | +|riskRegression |? | | | | +|rmlnomogram |? | | | | +|rms |? | | | | +|robber |? | | | | +|robmed |1.2.1 |1 | | | +|robmedExtra |0.1.1 |1 | | | +|ROKET |1.0.0 |1 | | | +|rplec |? | | | | +|RplotterPkg |? | | | | +|RPPanalyzer |1.4.9 |1 | | | +|RQdeltaCT |1.3.2 |1 | | | +|RRPP |? | | | | +|rshift |3.1.2 |1 | | | +|rstanarm |2.32.1 |1 | | | +|rTwig |1.4.0 |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 |3.0.0 |1 | | | +|SCpubr |? | | | | +|scRNAstat |0.1.1.1 |1 | | | +|sectorgap |0.1.0 |1 | | | +|SEERaBomb |2019.2 |1 | | | +|semicmprskcoxmsm |0.2.0 |1 | | | +|SensMap |0.7 |1 | | | +|Seurat |5.2.1 |1 | | | +|SeuratExplorer |0.1.0 |1 | | | +|shinyTempSignal |0.0.8 |1 | | | +|sievePH |1.1 |1 | | | +|SiFINeT |1.13 |1 | | | +|Signac |1.14.0 |1 | | | +|SimplyAgree |0.2.1 |1 | | | +|smer |? | | | | +|SNPassoc |? | | | | +|snplinkage |? | | | | +|SoupX |1.6.2 |1 | | | +|SpaCCI |1.0.3 |1 | | | +|sparsereg |1.2 |1 | | | +|spikeSlabGAM |1.1-20 |1 | | | +|stabiliser |1.0.6 |1 | | | +|statsr |0.3.0 |1 | | | +|streamDAG |? | | | | +|survex |? | | | | +|survHE |? | | | | +|survidm |1.3.2 |1 | | | +|SurvMetrics |? | | | | +|tempted |0.1.1 |1 | | | +|TestAnaAPP |? | | | | +|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 | | | +|ubair |? | | | | +|vdg |1.2.3 |1 | | | +|VecDep |? | | | | +|visa |1.0.0 |1 | | | +|VisualizeSimon2Stage |? | | | | +|WRTDStidal |1.1.4 |1 | | | +|xxdi |? | | | | -## New problems (347) +## New problems (6) -|package |version |error |warning |note | -|:------------------|:----------|:---------|:--------|:--------| -|[ABHgenotypeR](problems.md#abhgenotyper)|1.0.1 |__+1__ | |1 __+1__ | -|[actxps](problems.md#actxps)|1.6.0 |__+1__ | |__+1__ | -|[adklakedata](problems.md#adklakedata)|0.6.1 |__+1__ | |1 | -|[adobeanalyticsr](problems.md#adobeanalyticsr)|0.5.0 | |__+1__ |__+1__ | -|[adw](problems.md#adw)|0.4.0 |__+2__ | |__+1__ | -|[AeRobiology](problems.md#aerobiology)|2.0.1 |__+1__ | |__+1__ | -|[agricolaeplotr](problems.md#agricolaeplotr)|0.6.0 |__+2__ | |__+1__ | -|[agridat](problems.md#agridat)|1.24 |__+2__ | |__+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 | -|[APCI](problems.md#apci)|1.0.8 |__+1__ | | | -|[APCtools](problems.md#apctools)|1.0.4 |__+3__ | |__+1__ | -|[applicable](problems.md#applicable)|0.1.1 |__+1__ | | | -|[ARPALData](problems.md#arpaldata)|1.6.1 |__+1__ |__+1__ |__+1__ | -|[arulesViz](problems.md#arulesviz)|1.5.3 | |__+1__ | | -|[asremlPlus](problems.md#asremlplus)|4.4.43 |1 |__+1__ |1 __+1__ | -|[autocogs](problems.md#autocogs)|0.1.4 |__+1__ | |1 | -|[autoplotly](problems.md#autoplotly)|0.1.4 |__+2__ | | | -|[autoTS](problems.md#autots)|0.9.11 |1 | |2 __+1__ | -|[backShift](problems.md#backshift)|0.1.4.3 |__+2__ |__+1__ |1 __+2__ | -|[bayesAB](problems.md#bayesab)|1.1.3 |__+1__ | | | -|[bayesforecast](problems.md#bayesforecast)|1.0.1 |__+1__ |__+1__ |3 __+2__ | -|[BayesGrowth](problems.md#bayesgrowth)|1.0.0 |__+1__ | |2 __+1__ | -|[BayesianMCPMod](problems.md#bayesianmcpmod)|1.0.1 |__+3__ | |__+1__ | -|[BayesianReasoning](problems.md#bayesianreasoning)|0.4.2 |__+1__ | | | -|[BayesMallows](problems.md#bayesmallows)|2.2.3 |__+1__ | |1 | -|[bayesplot](problems.md#bayesplot)|1.11.1 |1 __+1__ | |1 | -|[BCEA](problems.md#bcea)|2.4.7 |__+3__ |__+1__ |__+2__ | -|[BEAMR](problems.md#beamr)|1.1.0 |__+1__ |__+1__ |__+1__ | -|[beastt](problems.md#beastt)|0.0.1 |__+2__ | |__+1__ | -|[biclust](problems.md#biclust)|2.0.3.1 |__+1__ |__+1__ |__+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__ | | | -|[brolgar](problems.md#brolgar)|1.0.1 |1 __+1__ | |1 | -|[cartograflow](problems.md#cartograflow)|1.0.5 |__+1__ | | | -|[cats](problems.md#cats)|1.0.2 |__+1__ | |1 | -|[CausalImpact](problems.md#causalimpact)|1.3.0 |__+3__ |__+1__ |__+2__ | -|[celltrackR](problems.md#celltrackr)|1.2.1 |1 | |1 __+1__ | -|[cellularautomata](problems.md#cellularautomata)|0.1.0 |__+1__ | | | -|[CensMFM](problems.md#censmfm)|3.1 | |__+1__ |__+1__ | -|[CFO](problems.md#cfo)|2.2.0 |__+1__ |__+1__ |__+1__ | -|[changepoint.geo](problems.md#changepointgeo)|1.0.2 |__+1__ | | | -|[cheem](problems.md#cheem)|0.4.0.0 |1 __+1__ | | | -|[chillR](problems.md#chillr)|0.76 |__+1__ |__+1__ |__+1__ | -|[chronicle](problems.md#chronicle)|0.3 |__+2__ | |1 __+1__ | -|[cjoint](problems.md#cjoint)|2.1.1 |__+2__ |__+1__ |1 __+1__ | -|[clickstream](problems.md#clickstream)|1.3.3 | |__+1__ | | -|[clinDataReview](problems.md#clindatareview)|1.6.1 |__+2__ | |1 __+1__ | -|[clinDR](problems.md#clindr)|2.4.1 |__+1__ | | | -|[clinUtils](problems.md#clinutils)|0.2.0 |__+1__ |-1 |1 __+1__ | -|[CLONETv2](problems.md#clonetv2)|2.2.1 | |__+1__ | | -|[ClusROC](problems.md#clusroc)|1.0.2 |__+2__ |__+1__ |__+1__ | -|[clustcurv](problems.md#clustcurv)|2.0.2 |__+1__ | |__+1__ | -|[clustMD](problems.md#clustmd)|1.2.1 | |__+1__ |1 __+1__ | -|[cnmap](problems.md#cnmap)|0.1.0 |__+2__ | |__+1__ | -|[codaredistlm](problems.md#codaredistlm)|0.1.0 |__+1__ | | | -|[codez](problems.md#codez)|1.0.0 | |__+1__ | | -|[CohortPlat](problems.md#cohortplat)|1.0.5 |__+2__ | |__+1__ | -|[colorrepel](problems.md#colorrepel)|0.4.1 |__+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__ | -|[CoSMoS](problems.md#cosmos)|2.1.0 |__+1__ | |__+1__ | -|[countfitteR](problems.md#countfitter)|1.4 |__+1__ | | | -|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 __+1__ | -|[creditmodel](problems.md#creditmodel)|1.3.1 |__+2__ |__+1__ |1 __+2__ | -|[cricketr](problems.md#cricketr)|0.0.26 | |__+1__ |__+1__ | -|[crosshap](problems.md#crosshap)|1.4.0 |__+1__ | | | -|[CRTgeeDR](problems.md#crtgeedr)|2.0.1 | |__+1__ |__+1__ | -|[ctrialsgov](problems.md#ctrialsgov)|0.2.5 |__+1__ | |1 | -|[cubble](problems.md#cubble)|1.0.0 |__+1__ | |1 __+1__ | -|[DAISIE](problems.md#daisie)|4.4.1 |__+1__ | |2 | -|[DAISIEprep](problems.md#daisieprep)|1.0.0 |__+1__ | | | -|[daltoolbox](problems.md#daltoolbox)|1.1.727 |__+1__ |__+1__ |__+1__ | -|[dawaR](problems.md#dawar)|0.2.7 |-1 __+1__ | |1 | -|[DDPNA](problems.md#ddpna)|0.3.3 |__+1__ |__+1__ |__+1__ | -|[Deducer](problems.md#deducer)|0.7-9 |__+1__ |__+1__ |__+1__ | -|[deeptime](problems.md#deeptime)|2.1.0 |__+2__ | | | -|[desplot](problems.md#desplot)|1.10 |__+3__ |__+1__ |__+2__ | -|[diceR](problems.md#dicer)|2.2.0 |__+3__ | |__+1__ | -|[directlabels](problems.md#directlabels)|2024.1.21 |__+2__ | |__+1__ | -|[distributional](problems.md#distributional)|0.5.0 |__+1__ | | | -|[dittoViz](problems.md#dittoviz)|1.0.1 |__+2__ | | | -|[divent](problems.md#divent)|0.4-4 |__+2__ | |1 __+1__ | -|[doBy](problems.md#doby)|4.6.24 |2 |__+1__ |2 __+1__ | -|[DoseFinding](problems.md#dosefinding)|1.2-1 |__+3__ |__+1__ |__+2__ | -|[dotsViolin](problems.md#dotsviolin)|0.0.1 |__+1__ | |1 | -|[dr4pl](problems.md#dr4pl)|2.0.0 |__+2__ |__+1__ |1 __+2__ | -|[DRomics](problems.md#dromics)|2.6-2 |1 __+1__ |__+1__ |1 __+2__ | -|[drpop](problems.md#drpop)|0.0.3 | |__+1__ |__+1__ | -|[duke](problems.md#duke)|0.0.3 |__+1__ | | | -|[dymo](problems.md#dymo)|1.1.0 | |__+1__ | | -|[dynr](problems.md#dynr)|0.1.16-105 | |1 __+1__ |2 __+1__ | -|[easysurv](problems.md#easysurv)|2.0.1 |__+2__ | |__+1__ | -|[EGM](problems.md#egm)|0.1.0 |__+1__ | | | -|[entropart](problems.md#entropart)|1.6-15 |__+2__ | |__+1__ | -|[epiCleanr](problems.md#epicleanr)|0.2.0 |__+1__ | |1 | -|[epiphy](problems.md#epiphy)|0.5.0 |__+1__ | | | -|[EQUALSTATS](problems.md#equalstats)|0.5.0 |__+1__ | |1 | -|[esci](problems.md#esci)|1.0.6 |__+2__ | | | -|[evalITR](problems.md#evalitr)|1.0.0 |1 | |1 __+1__ | -|[eventstudyr](problems.md#eventstudyr)|1.1.3 |__+1__ | | | -|[expirest](problems.md#expirest)|0.1.6 |__+1__ | | | -|[explainer](problems.md#explainer)|1.0.2 |__+1__ | |1 | -|[ezEDA](problems.md#ezeda)|0.1.1 |__+1__ | | | -|[fable.prophet](problems.md#fableprophet)|0.1.0 |__+1__ | |1 __+1__ | -|[fabletools](problems.md#fabletools)|0.5.0 |__+2__ | | | -|[fairmodels](problems.md#fairmodels)|1.2.1 |__+1__ | | | -|[FCPS](problems.md#fcps)|1.3.4 |__+1__ |__+1__ |1 __+1__ | -|[fdANOVA](problems.md#fdanova)|0.1.2 |__+1__ | | | -|[fddm](problems.md#fddm)|1.0-2 |__+1__ | |1 | -|[feasts](problems.md#feasts)|0.4.1 |__+1__ | | | -|[ffp](problems.md#ffp)|0.2.2 |__+1__ | | | -|[fido](problems.md#fido)|1.1.1 |1 __+2__ | |2 | -|[FielDHub](problems.md#fieldhub)|1.4.2 |__+1__ | |1 __+1__ | -|[figuRes2](problems.md#figures2)|1.0.0 |__+2__ | | | -|[flexsurv](problems.md#flexsurv)|2.3.2 |__+2__ | |2 | -|[flipr](problems.md#flipr)|0.3.3 |1 | |1 __+1__ | -|[forestmodel](problems.md#forestmodel)|0.6.2 |__+1__ |__+1__ |1 __+1__ | -|[frailtyEM](problems.md#frailtyem)|1.0.1 |__+1__ | |2 | -|[gapmap](problems.md#gapmap)|1.0.0 |__+2__ | |__+1__ | -|[gapminder](problems.md#gapminder)|1.0.0 |1 __+1__ | | | -|[GEInter](problems.md#geinter)|0.3.2 |1 |__+1__ |1 __+1__ | -|[geoheatmap](problems.md#geoheatmap)|0.1.0 |__+1__ | |__+1__ | -|[geomtextpath](problems.md#geomtextpath)|0.1.5 |__+2__ | | | -|[ggalign](problems.md#ggalign)|0.0.5 | |__+1__ |1 | -|[GGally](problems.md#ggally)|2.2.1 |__+1__ | | | -|[gganimate](problems.md#gganimate)|1.0.9 |__+2__ | |__+1__ | -|[ggblanket](problems.md#ggblanket)|12.1.0 |__+1__ | | | -|[ggdark](problems.md#ggdark)|0.2.1 |__+2__ | |1 | -|[ggdemetra](problems.md#ggdemetra)|0.2.8 | |__+1__ | | -|[ggdist](problems.md#ggdist)|3.3.2 |1 __+2__ | |1 __+1__ | -|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | | -|[ggESDA](problems.md#ggesda)|0.2.0 |__+1__ | | | -|[ggfixest](problems.md#ggfixest)|0.2.0 |__+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__ | | | -|[ggh4x](problems.md#ggh4x)|0.3.0 |__+3__ | |__+1__ | -|[gghighlight](problems.md#gghighlight)|0.4.1 |__+3__ | |__+1__ | -|[ggiraph](problems.md#ggiraph)|0.8.12 |__+2__ | |1 | -|[ggmap](problems.md#ggmap)|4.0.0 | |__+1__ |1 | -|[ggmcmc](problems.md#ggmcmc)|1.5.1.1 |1 __+1__ | |1 | -|[ggmice](problems.md#ggmice)|0.1.0 |__+1__ | |__+1__ | -|[ggmulti](problems.md#ggmulti)|1.0.7 |__+3__ | |__+1__ | -|[ggparallel](problems.md#ggparallel)|0.4.0 |__+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)|0.8.5 |__+3__ | |__+1__ | -|[ggside](problems.md#ggside)|0.3.1 |__+3__ |__+2__ |__+2__ | -|[ggsmc](problems.md#ggsmc)|0.1.2.0 |__+1__ | |1 | -|[ggspatial](problems.md#ggspatial)|1.1.9 |__+2__ | | | -|[ggstatsplot](problems.md#ggstatsplot)|0.13.0 |1 __+1__ | | | -|[ggswissmaps](problems.md#ggswissmaps)|0.1.1 | |__+1__ |__+1__ | -|[ggupset](problems.md#ggupset)|0.4.0 |__+1__ | | | -|[ggVennDiagram](problems.md#ggvenndiagram)|1.5.2 |__+1__ | |1 __+1__ | -|[Greymodels](problems.md#greymodels)|2.0.1 |__+1__ | | | -|[GWASinspector](problems.md#gwasinspector)|1.7.1 |1 |__+1__ |__+1__ | -|[GWlasso](problems.md#gwlasso)|1.0.1 |__+1__ | | | -|[harbinger](problems.md#harbinger)|1.1.707 |__+1__ |__+1__ |__+1__ | -|[HCmodelSets](problems.md#hcmodelsets)|1.1.3 |__+1__ |__+1__ |__+1__ | -|[healthyR](problems.md#healthyr)|0.2.2 |__+1__ | |1 __+1__ | -|[healthyR.ts](problems.md#healthyrts)|0.3.1 |__+2__ | |1 __+1__ | -|[heatmaply](problems.md#heatmaply)|1.5.0 |__+2__ | |1 __+1__ | -|[heemod](problems.md#heemod)|1.0.2 |__+1__ | | | -|[hesim](problems.md#hesim)|0.5.5 |__+1__ | |1 | -|[hmsidwR](problems.md#hmsidwr)|1.1.2 |__+1__ | |2 __+1__ | -|[HVT](problems.md#hvt)|24.9.1 |__+1__ |__+1__ |__+1__ | -|[hypsoLoop](problems.md#hypsoloop)|0.2.0 | |__+1__ | | -|[iCARH](problems.md#icarh)|2.0.2.1 | |__+1__ |__+1__ | -|[ICSsmoothing](problems.md#icssmoothing)|1.2.8 |__+1__ | | | -|[incidental](problems.md#incidental)|0.1 |__+1__ | |__+1__ | -|[industRial](problems.md#industrial)|0.1.0 |__+1__ | |1 | -|[infer](problems.md#infer)|1.0.7 |__+2__ | |__+1__ | -|[inferCSN](problems.md#infercsn)|1.0.8 |__+1__ | |1 | -|[injurytools](problems.md#injurytools)|1.0.3 |__+1__ | |__+1__ | -|[inTextSummaryTable](problems.md#intextsummarytable)|3.3.3 |__+2__ | |1 __+1__ | -|[inti](problems.md#inti)|0.6.6 |2 |__+1__ |1 __+1__ | -|[IPV](problems.md#ipv)|1.0.0 |__+2__ | |1 __+1__ | -|[IRon](problems.md#iron)|0.1.4 |__+1__ | |1 | -|[isoorbi](problems.md#isoorbi)|1.3.1 |__+1__ | |1 __+1__ | -|[jenga](problems.md#jenga)|1.3.0 | |__+1__ | | -|[karel](problems.md#karel)|0.1.1 |__+2__ | |1 | -|[kDGLM](problems.md#kdglm)|1.2.0 |__+1__ | | | -|[Keyboard](problems.md#keyboard)|0.1.3 |__+1__ |__+1__ |__+1__ | -|[latentcor](problems.md#latentcor)|2.0.1 |__+1__ | | | -|[lcars](problems.md#lcars)|0.4.0 |__+2__ | | | -|[lemon](problems.md#lemon)|0.5.0 |__+3__ | |__+1__ | -|[lfproQC](problems.md#lfproqc)|1.4.0 |__+2__ | |__+1__ | -|[lilikoi](problems.md#lilikoi)|2.1.1 | |__+1__ |__+1__ | -|[LMoFit](problems.md#lmofit)|0.1.7 |__+1__ | |1 __+1__ | -|[LocalCop](problems.md#localcop)|0.0.2 |1 | |1 __+1__ | -|[lognorm](problems.md#lognorm)|0.1.10 |__+1__ | |__+1__ | -|[lsl](problems.md#lsl)|0.5.6 |__+1__ | |1 | -|[MAINT.Data](problems.md#maintdata)|2.7.1 |__+2__ |__+1__ |1 __+1__ | -|[MarketMatching](problems.md#marketmatching)|1.2.1 |__+1__ | | | -|[metacart](problems.md#metacart)|2.0-3 |__+1__ |__+1__ |__+1__ | -|[MetAlyzer](problems.md#metalyzer)|1.1.0 |__+1__ | | | -|[metR](problems.md#metr)|0.17.0 |__+3__ | |1 __+1__ | -|[mgcViz](problems.md#mgcviz)|0.1.11 |__+1__ | |__+1__ | -|[migraph](problems.md#migraph)|1.4.5 |__+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)|0.10.1 |__+2__ | | | -|[misspi](problems.md#misspi)|0.1.0 |__+1__ | | | -|[mizer](problems.md#mizer)|2.5.3 |__+1__ | |1 | -|[MLEce](problems.md#mlece)|2.1.0 |__+1__ |__+1__ |__+1__ | -|[modeltime.resample](problems.md#modeltimeresample)|0.2.3 |__+1__ | |1 | -|[moreparty](problems.md#moreparty)|0.4 |__+1__ | |__+1__ | -|[mppR](problems.md#mppr)|1.5.0 |__+1__ |__+1__ |__+2__ | -|[MPTmultiverse](problems.md#mptmultiverse)|0.4-2 |__+2__ | |1 __+1__ | -|[mtb](problems.md#mtb)|0.1.8 |__+1__ | | | -|[mudfold](problems.md#mudfold)|1.1.21 | |__+1__ |__+1__ | -|[mulgar](problems.md#mulgar)|1.0.2 |__+1__ | |1 | -|[MultiTraits](problems.md#multitraits)|0.2.0 |__+2__ | |__+1__ | -|[mvSLOUCH](problems.md#mvslouch)|2.7.6 | | |__+1__ | -|[naive](problems.md#naive)|1.2.3 | |__+1__ | | -|[ncappc](problems.md#ncappc)|0.3.0 | |__+1__ |2 __+1__ | -|[neatmaps](problems.md#neatmaps)|2.1.0 |__+1__ | |1 | -|[NetFACS](problems.md#netfacs)|0.5.0 |__+2__ | | | -|[NetworkInference](problems.md#networkinference)|1.2.4 |__+3__ |__+1__ |1 __+2__ | -|[NHSRplotthedots](problems.md#nhsrplotthedots)|0.1.0 |__+1__ | |1 | -|[nichetools](problems.md#nichetools)|0.3.2 |__+1__ | |__+1__ | -|[NIMAA](problems.md#nimaa)|0.2.1 |__+3__ | |2 __+1__ | -|[nzelect](problems.md#nzelect)|0.4.0 |__+1__ | |2 | -|[oddsratio](problems.md#oddsratio)|2.0.1 |__+2__ | |1 __+1__ | -|[OmicNavigator](problems.md#omicnavigator)|1.13.13 |__+1__ | |1 | -|[ordbetareg](problems.md#ordbetareg)|0.7.2 |__+1__ | |2 | -|[pafr](problems.md#pafr)|0.0.2 |__+1__ | |1 | -|[pathviewr](problems.md#pathviewr)|1.1.7 |__+1__ | | | -|[pdxTrees](problems.md#pdxtrees)|0.4.0 |__+1__ | |1 __+1__ | -|[PeakError](problems.md#peakerror)|2023.9.4 |__+1__ | | | -|[PeakSegJoint](problems.md#peaksegjoint)|2024.12.4 |__+1__ | | | -|[PeakSegOptimal](problems.md#peaksegoptimal)|2024.10.1 |__+1__ | | | -|[personalized](problems.md#personalized)|0.2.7 |__+1__ | | | -|[Plasmidprofiler](problems.md#plasmidprofiler)|0.1.6 |__+1__ | | | -|[plotDK](problems.md#plotdk)|0.1.0 |__+1__ | |2 | -|[PlotFTIR](problems.md#plotftir)|1.0.0 |__+3__ | | | -|[plotly](problems.md#plotly)|4.10.4 |__+2__ | |1 | -|[plotthis](problems.md#plotthis)|0.5.0 |__+1__ | | | -|[pmartR](problems.md#pmartr)|2.4.6 |__+1__ | |1 | -|[pmxTools](problems.md#pmxtools)|1.3 |__+1__ | |1 | -|[pogit](problems.md#pogit)|1.3.0 | |__+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__ | -|[precintcon](problems.md#precintcon)|2.3.0 |__+1__ | | | -|[pRecipe](problems.md#precipe)|3.0.2 | |__+1__ |__+1__ | -|[PReMiuM](problems.md#premium)|3.2.13 | |__+1__ |1 __+1__ | -|[prevR](problems.md#prevr)|5.0.0 |__+2__ |__+1__ |1 __+2__ | -|[priorsense](problems.md#priorsense)|1.0.4 |__+2__ | |__+1__ | -|[probably](problems.md#probably)|1.0.3 |__+1__ | | | -|[processmapR](problems.md#processmapr)|0.5.6 |__+1__ | | | -|[psborrow](problems.md#psborrow)|0.2.1 |__+1__ | | | -|[PupilPre](problems.md#pupilpre)|0.6.2 |__+1__ | |__+1__ | -|[qgcomp](problems.md#qgcomp)|2.16.4 |__+3__ |__+1__ |__+2__ | -|[qpNCA](problems.md#qpnca)|1.1.6 |__+2__ |__+1__ |__+2__ | -|[r2dii.plot](problems.md#r2diiplot)|0.4.0 |__+1__ | | | -|[r4ss](problems.md#r4ss)|1.44.0 | |__+1__ |__+1__ | -|[r6qualitytools](problems.md#r6qualitytools)|1.0.1 |__+1__ |__+1__ |__+1__ | -|[Radviz](problems.md#radviz)|0.9.3 |__+2__ | |__+1__ | -|[rassta](problems.md#rassta)|1.0.6 |__+2__ | | | -|[rater](problems.md#rater)|1.3.1 |__+1__ | |2 | -|[ratlas](problems.md#ratlas)|0.1.0 |1 __+1__ | |1 __+1__ | -|[RclusTool](problems.md#rclustool)|0.91.6 |__+1__ |__+1__ |__+1__ | -|[RDS](problems.md#rds)|0.9-10 |__+1__ |__+1__ |__+1__ | -|[regtomean](problems.md#regtomean)|1.2 | |__+1__ |1 | -|[RKorAPClient](problems.md#rkorapclient)|0.9.0 |__+1__ | | | -|[rmcfs](problems.md#rmcfs)|1.3.6 | |__+1__ |__+1__ | -|[rnmamod](problems.md#rnmamod)|0.4.0 |__+3__ |__+1__ |1 __+2__ | -|[roahd](problems.md#roahd)|1.4.3 |__+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__ | -|[signatureSurvival](problems.md#signaturesurvival)|1.0.0 |__+1__ |__+1__ |1 __+1__ | -|[SimNPH](problems.md#simnph)|0.5.5 |__+1__ | | | -|[simRestore](problems.md#simrestore)|1.1.4 |__+1__ | | | -|[singleCellHaystack](problems.md#singlecellhaystack)|1.0.2 |__+1__ |__+1__ |__+1__ | -|[SNPannotator](problems.md#snpannotator)|0.2.6.0 | |__+1__ |__+1__ | -|[soc.ca](problems.md#socca)|0.8.0 |__+1__ |__+1__ |2 __+1__ | -|[SOMbrero](problems.md#sombrero)|1.4-2 |__+2__ |__+1__ |__+1__ | -|[spectralR](problems.md#spectralr)|0.1.3 |__+1__ | | | -|[spinifex](problems.md#spinifex)|0.3.8 |__+1__ | | | -|[spooky](problems.md#spooky)|1.4.0 | |__+1__ | | -|[sport](problems.md#sport)|0.2.1 |__+1__ | |1 | -|[SqueakR](problems.md#squeakr)|1.3.0 |1 | |1 __+1__ | -|[statgenGWAS](problems.md#statgengwas)|1.0.10 |__+1__ | |1 | -|[statgenHTP](problems.md#statgenhtp)|1.0.7 |__+1__ | |2 | -|[Superpower](problems.md#superpower)|0.2.0 |__+3__ |__+1__ |1 __+2__ | -|[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 | +|package |version |error |warning |note | +|:------------|:-------|:------|:-------|:--------| +|[CNAIM](problems.md#cnaim)|2.1.4 | | |__+1__ | +|[covidcast](problems.md#covidcast)|0.5.2 |__+1__ | |1 __+1__ | +|[embryogrowth](problems.md#embryogrowth)|9.5 | | |1 __+1__ | +|[infer](problems.md#infer)|1.0.7 |__+1__ | | | +|[PSCBS](problems.md#pscbs)|0.67.0 | | |__+1__ | +|[SimNPH](problems.md#simnph)|0.5.6 |__+1__ | | | diff --git a/revdep/cran.md b/revdep/cran.md index d521f55150..bd4bcc21fa 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,1409 +1,47 @@ ## revdepcheck results -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 checked 5632 reverse dependencies (5606 from CRAN + 26 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 347 new problems - * We failed to check 179 packages + * We saw 6 new problems + * We failed to check 180 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* ABHgenotypeR - 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 - -* 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 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 - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* agridat - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* AnalysisLin - checking examples ... ERROR - -* animbook - checking examples ... ERROR - -* ANN2 - checking tests ... ERROR - -* APCI - checking tests ... ERROR - -* APCtools - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* applicable - checking tests ... ERROR - -* ARPALData - checking examples ... ERROR - checking whether package ‘ARPALData’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* arulesViz - checking whether package ‘arulesViz’ can be installed ... WARNING - -* asremlPlus - checking whether package ‘asremlPlus’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* autocogs - checking tests ... ERROR - -* autoplotly - checking examples ... ERROR - checking tests ... ERROR - -* autoTS - checking re-building of vignette outputs ... NOTE - -* backShift - checking examples ... 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 - -* 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 - -* BayesianMCPMod - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* BayesianReasoning - checking tests ... ERROR - -* BayesMallows - checking tests ... ERROR - -* bayesplot - checking tests ... ERROR - -* BCEA - checking examples ... ERROR - checking tests ... ERROR - 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 - -* biclust - checking examples ... ERROR - checking whether package ‘biclust’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* biclustermd - checking tests ... ERROR - -* biodosetools - checking tests ... ERROR - -* boxly - checking tests ... ERROR - -* brolgar - checking examples ... ERROR - -* cartograflow - checking examples ... ERROR - -* cats - checking examples ... ERROR - -* 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 - -* celltrackR - checking re-building of vignette outputs ... NOTE - -* cellularautomata - checking running R code from vignettes ... ERROR - -* CensMFM - checking whether package ‘CensMFM’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* CFO - checking examples ... ERROR - checking whether package ‘CFO’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* changepoint.geo - checking tests ... ERROR - -* 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 - -* cjoint - checking examples ... ERROR - 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 - -* CLONETv2 - checking whether package ‘CLONETv2’ can be installed ... WARNING - -* ClusROC - checking examples ... ERROR - checking tests ... ERROR - checking whether package ‘ClusROC’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* 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 - -* cnmap - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* codaredistlm - 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 - -* colorrepel - checking examples ... ERROR - -* CoreMicrobiomeR - checking examples ... ERROR - -* correlationfunnel - checking tests ... ERROR - -* corrViz - 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 - -* covidcast - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* creditmodel - checking examples ... ERROR - 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 - -* 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 - -* cubble - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* DAISIE - checking examples ... ERROR - -* DAISIEprep - checking tests ... ERROR - -* daltoolbox - checking examples ... ERROR - 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 - -* diceR - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* directlabels - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* distributional - checking examples ... ERROR - -* dittoViz - checking examples ... ERROR - checking tests ... ERROR - -* 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 - -* 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 - -* 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 - -* epiphy - checking examples ... ERROR - -* EQUALSTATS - checking examples ... ERROR - -* esci - checking examples ... ERROR - checking tests ... ERROR - -* evalITR - checking re-building of vignette outputs ... NOTE - -* eventstudyr - checking tests ... ERROR - -* expirest - checking tests ... ERROR - -* explainer - checking examples ... ERROR - -* ezEDA - checking tests ... ERROR - -* fable.prophet - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* fabletools - checking examples ... ERROR - checking tests ... ERROR - -* fairmodels - checking tests ... ERROR - -* FCPS - checking examples ... ERROR - checking whether package ‘FCPS’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* fdANOVA - checking examples ... ERROR - -* fddm - checking running R code from vignettes ... ERROR - -* feasts - checking tests ... ERROR - -* ffp - checking examples ... ERROR - -* fido - checking examples ... ERROR - checking tests ... ERROR - -* FielDHub - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* 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 - -* forestmodel - checking examples ... ERROR - checking whether package ‘forestmodel’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* frailtyEM - checking examples ... ERROR - -* gapmap - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* 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 - -* geomtextpath - checking examples ... ERROR - checking tests ... ERROR - -* ggalign - checking for code/documentation mismatches ... WARNING - -* GGally - checking tests ... ERROR - -* gganimate - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggblanket - checking examples ... ERROR - -* ggdark - checking examples ... ERROR - checking tests ... ERROR - -* ggdemetra - checking whether package ‘ggdemetra’ can be installed ... WARNING - -* ggdist - checking examples ... ERROR - checking tests ... 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 - -* ggh4x - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* gghighlight - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggiraph - checking examples ... ERROR - checking tests ... ERROR - -* ggmap - checking whether package ‘ggmap’ can be installed ... WARNING - -* ggmcmc - checking examples ... ERROR - -* ggmice - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggmulti - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggparallel - checking tests ... ERROR - -* ggplotlyExtra - checking examples ... ERROR - -* ggpol - checking examples ... ERROR - -* ggpubr - checking tests ... ERROR - -* ggraph - checking examples ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggredist - checking examples ... ERROR - -* ggRtsy - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* ggseqplot - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - 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 - -* ggspatial - checking examples ... ERROR - checking tests ... ERROR - -* ggstatsplot - 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 - -* ggVennDiagram - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* Greymodels - checking examples ... ERROR - -* GWASinspector - checking whether package ‘GWASinspector’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* GWlasso - checking examples ... ERROR - -* harbinger - checking examples ... ERROR - checking whether package ‘harbinger’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* HCmodelSets - checking examples ... ERROR - checking whether package ‘HCmodelSets’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* healthyR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* healthyR.ts - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* heatmaply - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* heemod - checking running R code from vignettes ... ERROR - -* hesim - checking tests ... ERROR - -* 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 - -* iCARH - checking whether package ‘iCARH’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* ICSsmoothing - checking tests ... ERROR - -* incidental - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* industRial - checking examples ... ERROR - -* infer - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* inferCSN - checking examples ... ERROR - -* injurytools - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* 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 - checking re-building of vignette outputs ... NOTE - -* IRon - checking examples ... ERROR - -* isoorbi - 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 - checking tests ... ERROR - -* kDGLM - checking examples ... ERROR - -* Keyboard - checking examples ... ERROR - checking whether package ‘Keyboard’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* 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 - -* 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 - -* LocalCop - checking re-building of vignette outputs ... NOTE - -* lognorm - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* lsl - checking examples ... ERROR - -* MAINT.Data - checking examples ... ERROR - checking tests ... ERROR - checking whether package ‘MAINT.Data’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* MarketMatching - checking re-building of vignette outputs ... ERROR - -* metacart - checking examples ... ERROR - checking whether package ‘metacart’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* MetAlyzer - checking examples ... ERROR - -* metR - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* mgcViz - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* 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 - -* mizer - checking tests ... ERROR - -* MLEce - checking examples ... ERROR - checking whether package ‘MLEce’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* modeltime.resample - checking tests ... ERROR - -* moreparty - 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 - -* 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 - -* MultiTraits - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* mvSLOUCH - checking re-building of vignette outputs ... NOTE - -* naive - checking whether package ‘naive’ can be installed ... WARNING - -* ncappc - checking whether package ‘ncappc’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* neatmaps - checking examples ... ERROR - -* NetFACS - checking examples ... ERROR - checking running R code from vignettes ... ERROR - -* 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 - 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 - -* nzelect - checking examples ... ERROR - -* oddsratio - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* OmicNavigator - checking tests ... ERROR - -* ordbetareg - checking examples ... ERROR - -* pafr - checking tests ... ERROR - -* pathviewr - checking tests ... ERROR - -* pdxTrees - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* PeakError - checking examples ... ERROR - -* PeakSegJoint - checking examples ... ERROR - -* PeakSegOptimal - checking examples ... ERROR - -* personalized - checking tests ... ERROR - -* Plasmidprofiler - checking examples ... ERROR - -* plotDK - checking tests ... ERROR - -* PlotFTIR - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... 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 - checking re-building of vignette outputs ... NOTE - -* ppseq - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* precintcon - checking examples ... ERROR - -* 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 - checking examples ... ERROR - 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 - -* PupilPre - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* 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 - -* qpNCA - checking tests ... 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 - -* r2dii.plot - checking tests ... ERROR - -* r4ss - checking whether package ‘r4ss’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* 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 - -* rassta - checking examples ... ERROR - checking tests ... ERROR - -* rater - checking tests ... ERROR - -* ratlas - checking tests ... ERROR - checking re-building of vignette outputs ... NOTE - -* RclusTool - checking examples ... ERROR - checking whether package ‘RclusTool’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* RDS - checking examples ... ERROR - checking whether package ‘RDS’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* regtomean - checking whether package ‘regtomean’ can be installed ... WARNING - -* RKorAPClient - checking tests ... ERROR - -* rmcfs - checking whether package ‘rmcfs’ can be installed ... WARNING - checking R code for possible problems ... NOTE +* CNAIM + checking installed package size ... NOTE -* rnmamod - checking examples ... ERROR - checking tests ... ERROR +* covidcast 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 -* roahd - checking examples ... ERROR - -* robomit - checking examples ... ERROR - checking whether package ‘robomit’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* romic - checking tests ... ERROR - -* roptions - checking examples ... ERROR - -* rsimsum - checking whether package ‘rsimsum’ can be installed ... WARNING - -* rSRD - checking examples ... ERROR - checking whether package ‘rSRD’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* saeRobust - checking examples ... ERROR - checking tests ... ERROR - checking whether package ‘saeRobust’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* scUtils - checking tests ... ERROR - -* SCVA - checking examples ... ERROR - -* SDMtune - checking tests ... ERROR +* embryogrowth checking installed package size ... NOTE -* seAMLess - checking examples ... ERROR - -* seedreg - checking examples ... ERROR - -* segen - checking whether package ‘segen’ can be installed ... WARNING - -* sensitivity - checking examples ... ERROR - checking whether package ‘sensitivity’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* sglg - checking examples ... ERROR - -* sgsR +* infer checking tests ... ERROR -* SHAPforxgboost - checking examples ... ERROR - -* SHELF - checking whether package ‘SHELF’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* signatureSurvival - checking examples ... ERROR - checking whether package ‘signatureSurvival’ can be installed ... WARNING - checking R code for possible problems ... NOTE +* PSCBS + checking installed package size ... NOTE * SimNPH checking tests ... ERROR -* simRestore - checking tests ... ERROR - -* singleCellHaystack - checking examples ... ERROR - checking whether package ‘singleCellHaystack’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* SNPannotator - checking whether package ‘SNPannotator’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* soc.ca - checking examples ... ERROR - checking whether package ‘soc.ca’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* SOMbrero - checking examples ... ERROR - checking tests ... ERROR - checking whether package ‘SOMbrero’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* spectralR - checking tests ... ERROR - -* spinifex - checking tests ... ERROR - -* spooky - checking whether package ‘spooky’ can be installed ... WARNING - -* sport - checking tests ... ERROR - -* SqueakR - checking re-building of vignette outputs ... NOTE - -* statgenGWAS - checking tests ... ERROR - -* statgenHTP - checking tests ... ERROR - -* 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 - -* tabledown - checking examples ... ERROR - -* TCIU - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* tcplfit2 - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* tetragon - checking whether package ‘tetragon’ can be installed ... WARNING - -* 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 - -* tidyplots - 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 - -* timetk - checking tests ... ERROR - -* TOSTER - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* TransProR - checking examples ... ERROR - -* TreatmentPatterns - checking tests ... ERROR - -* TreatmentSelection - checking examples ... ERROR - checking whether package ‘TreatmentSelection’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* trelliscopejs - checking tests ... ERROR - -* tricolore - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* tsnet - checking tests ... ERROR - -* UCSCXenaShiny - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* umiAnalyzer - checking examples ... ERROR - -* usmap - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* vaccineff - checking tests ... ERROR - -* valr - checking tests ... ERROR - -* visOmopResults - checking tests ... ERROR - -* visvow - checking tests ... ERROR - checking whether package ‘visvow’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* vivaldi - checking examples ... ERROR - checking tests ... 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 - -* vvshiny - checking tests ... ERROR - -* VWPre - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* WebAnalytics - checking examples ... ERROR - checking tests ... ERROR - checking whether package ‘WebAnalytics’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* WhatsR - checking examples ... ERROR - checking tests ... ERROR - checking whether package ‘WhatsR’ can be installed ... WARNING - checking R code for possible problems ... NOTE - -* wilson - checking tests ... ERROR - -* wordmap - checking tests ... ERROR - -* xpose - checking examples ... ERROR - checking tests ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* xpose.xtras - checking examples ... ERROR - checking running R code from vignettes ... ERROR - checking re-building of vignette outputs ... NOTE - -* yamlet - checking examples ... ERROR - checking tests ... ERROR - ### Failed to check * abctools (NA) * adjustedCurves (NA) * animalEKF (NA) * ANOM (NA) +* aorsf (NA) * atRisk (NA) * autoReg (NA) * AutoScore (NA) -* bartMan (NA) +* bayesdfa (NA) * bayesDP (NA) +* BayesGrowth (NA) * BayesianFactorZoo (NA) * BayesSurvive (NA) * BCClong (NA) @@ -1416,7 +54,9 @@ Issues with CRAN packages are summarised below. * CARBayesST (NA) * Certara.VPCResults (NA) * CGPfunctions (NA) +* CIDER (NA) * cinaR (NA) +* ClusterGVis (NA) * cmprskcoxmsm (NA) * COMMA (NA) * contsurvplot (NA) @@ -1439,24 +79,25 @@ Issues with CRAN packages are summarised below. * ecolottery (NA) * EpiEstim (NA) * evolqg (NA) +* FARS (NA) +* fio (NA) * flexrsurv (NA) * ForecastComb (NA) +* gaawr2 (NA) * gap (NA) * gapfill (NA) * genekitr (NA) * GeneSelectR (NA) * GeomComb (NA) -* ggtern (NA) -* ggThemeAssist (NA) * gJLS2 (NA) * grandR (NA) * GseaVis (NA) +* HetSeq (NA) * hettx (NA) * Hmisc (NA) * Hmsc (NA) * iClusterVB (NA) * immcp (NA) -* inventorize (NA) * invivoPKfit (NA) * iNZightPlots (NA) * iNZightRegression (NA) @@ -1477,12 +118,10 @@ Issues with CRAN packages are summarised below. * MaxWiK (NA) * mbsts (NA) * MendelianRandomization (NA) -* miWQS (NA) * mlmts (NA) * mlr (NA) * MRZero (NA) * mstate (NA) -* multilevelTools (NA) * multinma (NA) * multipleOutcomes (NA) * MuPETFlow (NA) @@ -1491,23 +130,21 @@ Issues with CRAN packages are summarised below. * NetworkChange (NA) * nlmeVPC (NA) * NMADiagT (NA) -* NMF (NA) * obliqueRSF (NA) * OlinkAnalyze (NA) * optweight (NA) * OVtool (NA) * pammtools (NA) +* parameters (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) @@ -1521,8 +158,10 @@ Issues with CRAN packages are summarised below. * robber (NA) * robmed (NA) * robmedExtra (NA) +* ROKET (NA) * RPPanalyzer (NA) * RQdeltaCT (NA) +* rshift (NA) * rstanarm (NA) * rTwig (NA) * RVA (NA) @@ -1540,10 +179,10 @@ Issues with CRAN packages are summarised below. * semicmprskcoxmsm (NA) * SensMap (NA) * Seurat (NA) +* SeuratExplorer (NA) * shinyTempSignal (NA) * sievePH (NA) * SiFINeT (NA) -* sigminer (NA) * Signac (NA) * SimplyAgree (NA) * SNPassoc (NA) @@ -1551,7 +190,6 @@ Issues with CRAN packages are summarised below. * SoupX (NA) * SpaCCI (NA) * sparsereg (NA) -* spectralAnalysis (NA) * spikeSlabGAM (NA) * stabiliser (NA) * statsr (NA) @@ -1559,9 +197,9 @@ Issues with CRAN packages are summarised below. * survex (NA) * survHE (NA) * survidm (NA) +* SurvMetrics (NA) * tempted (NA) * TestAnaAPP (NA) -* tidydr (NA) * tidyEdSurvey (NA) * tidyseurat (NA) * tidyvpc (NA) @@ -1572,5 +210,4 @@ Issues with CRAN packages are summarised below. * twang (NA) * vdg (NA) * visa (NA) -* wppExplorer (NA) * WRTDStidal (NA) diff --git a/revdep/failures.md b/revdep/failures.md index 16b90a9326..b27d1332f5 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -78,7 +78,7 @@ ERROR: lazy loading failed for package ‘abctools’ * 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 +* Number of recursive dependencies: 178 Run `revdepcheck::cloud_details(, "adjustedCurves")` for more info @@ -271,6 +271,82 @@ ERROR: lazy loading failed for package ‘ANOM’ * removing ‘/tmp/workdir/ANOM/old/ANOM.Rcheck/ANOM’ +``` +# aorsf + +
+ +* Version: 0.1.5 +* GitHub: https://github.com/ropensci/aorsf +* Source code: https://github.com/cran/aorsf +* Date/Publication: 2024-05-30 03:40:02 UTC +* Number of recursive dependencies: 174 + +Run `revdepcheck::cloud_details(, "aorsf")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/aorsf/new/aorsf.Rcheck’ +* 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 ‘aorsf/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘aorsf.Rmd’ using ‘UTF-8’... OK + ‘fast.Rmd’ using ‘UTF-8’... OK + ‘oobag.Rmd’ using ‘UTF-8’... OK + ‘pd.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/aorsf/old/aorsf.Rcheck’ +* 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 ‘aorsf/DESCRIPTION’ ... OK +... +* checking for unstated dependencies in vignettes ... OK +* checking package vignettes in ‘inst/doc’ ... OK +* checking running R code from vignettes ... OK + ‘aorsf.Rmd’ using ‘UTF-8’... OK + ‘fast.Rmd’ using ‘UTF-8’... OK + ‘oobag.Rmd’ using ‘UTF-8’... OK + ‘pd.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 NOTE + + + + + ``` # atRisk @@ -342,7 +418,7 @@ ERROR: lazy loading failed for package ‘atRisk’ * 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 +* Number of recursive dependencies: 218 Run `revdepcheck::cloud_details(, "autoReg")` for more info @@ -418,7 +494,7 @@ Status: OK * 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 +* Number of recursive dependencies: 174 Run `revdepcheck::cloud_details(, "AutoScore")` for more info @@ -486,26 +562,26 @@ Status: 1 ERROR ``` -# bartMan +# bayesdfa
-* 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 +* Version: 1.3.4 +* GitHub: https://github.com/fate-ewi/bayesdfa +* Source code: https://github.com/cran/bayesdfa +* Date/Publication: 2025-03-22 20:30:21 UTC +* Number of recursive dependencies: 87 -Run `revdepcheck::cloud_details(, "bartMan")` for more info +Run `revdepcheck::cloud_details(, "bayesdfa")` for more info
-## Newly broken +## In both -* checking whether package ‘bartMan’ can be installed ... ERROR +* checking whether package ‘bayesdfa’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/bartMan/new/bartMan.Rcheck/00install.out’ for details. + See ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/00install.out’ for details. ``` ## Installation @@ -513,38 +589,28 @@ Run `revdepcheck::cloud_details(, "bartMan")` for more info ### Devel ``` -* installing *source* package ‘bartMan’ ... -** package ‘bartMan’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bayesdfa’ ... +** package ‘bayesdfa’ 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’ +Error in loadNamespace(x) : there is no package called ‘rstantools’ +Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted -ERROR: lazy loading failed for package ‘bartMan’ -* removing ‘/tmp/workdir/bartMan/new/bartMan.Rcheck/bartMan’ +ERROR: configuration failed for package ‘bayesdfa’ +* removing ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/bayesdfa’ ``` ### CRAN ``` -* installing *source* package ‘bartMan’ ... -** package ‘bartMan’ successfully unpacked and MD5 sums checked +* installing *source* package ‘bayesdfa’ ... +** package ‘bayesdfa’ 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) +Error in loadNamespace(x) : there is no package called ‘rstantools’ +Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: configuration failed for package ‘bayesdfa’ +* removing ‘/tmp/workdir/bayesdfa/old/bayesdfa.Rcheck/bayesdfa’ ``` @@ -621,6 +687,84 @@ ERROR: lazy loading failed for package ‘bayesDP’ * removing ‘/tmp/workdir/bayesDP/old/bayesDP.Rcheck/bayesDP’ +``` +# 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 + +
+ +## In both + +* checking whether package ‘BayesGrowth’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/BayesGrowth/new/BayesGrowth.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘BayesGrowth’ ... +** package ‘BayesGrowth’ 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, +... +Warning: namespace ‘BayesGrowth’ is not available and has been replaced +by .GlobalEnv when processing object ‘MCMC_example_results’ +** 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 ‘MuMIn’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘BayesGrowth’ +* removing ‘/tmp/workdir/BayesGrowth/new/BayesGrowth.Rcheck/BayesGrowth’ + + +``` +### CRAN + +``` +* installing *source* package ‘BayesGrowth’ ... +** package ‘BayesGrowth’ 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, +... +Warning: namespace ‘BayesGrowth’ is not available and has been replaced +by .GlobalEnv when processing object ‘MCMC_example_results’ +** 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 ‘MuMIn’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘BayesGrowth’ +* removing ‘/tmp/workdir/BayesGrowth/old/BayesGrowth.Rcheck/BayesGrowth’ + + ``` # BayesianFactorZoo @@ -690,11 +834,11 @@ ERROR: lazy loading failed for package ‘BayesianFactorZoo’
-* Version: 0.0.2 +* Version: 0.1.0 * 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: 118 +* Date/Publication: 2025-03-25 22:50:23 UTC +* Number of recursive dependencies: 130 Run `revdepcheck::cloud_details(, "BayesSurvive")` for more info @@ -716,7 +860,7 @@ Run `revdepcheck::cloud_details(, "BayesSurvive")` for more info * using option ‘--no-manual’ * checking for file ‘BayesSurvive/DESCRIPTION’ ... OK ... -* this is package ‘BayesSurvive’ version ‘0.0.2’ +* this is package ‘BayesSurvive’ version ‘0.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -746,7 +890,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘BayesSurvive/DESCRIPTION’ ... OK ... -* this is package ‘BayesSurvive’ version ‘0.0.2’ +* this is package ‘BayesSurvive’ version ‘0.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -770,7 +914,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/BCClong * Date/Publication: 2024-06-24 00:00:02 UTC -* Number of recursive dependencies: 148 +* Number of recursive dependencies: 149 Run `revdepcheck::cloud_details(, "BCClong")` for more info @@ -984,7 +1128,7 @@ ERROR: lazy loading failed for package ‘binsreg’ * GitHub: https://github.com/statjs/bspcov * Source code: https://github.com/cran/bspcov * Date/Publication: 2024-11-13 20:10:02 UTC -* Number of recursive dependencies: 111 +* Number of recursive dependencies: 112 Run `revdepcheck::cloud_details(, "bspcov")` for more info @@ -1042,11 +1186,11 @@ ERROR: lazy loading failed for package ‘bspcov’
-* Version: 1.0.1 +* Version: 2.0.0 * 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 +* Date/Publication: 2025-01-30 17:50:07 UTC +* Number of recursive dependencies: 111 Run `revdepcheck::cloud_details(, "BSTZINB")` for more info @@ -1106,10 +1250,10 @@ ERROR: lazy loading failed for package ‘BSTZINB’
-* Version: 3.0.5 +* Version: 3.1.0 * GitHub: https://github.com/bozenne/BuyseTest * Source code: https://github.com/cran/BuyseTest -* Date/Publication: 2024-10-13 21:40:02 UTC +* Date/Publication: 2025-03-04 14:40:02 UTC * Number of recursive dependencies: 132 Run `revdepcheck::cloud_details(, "BuyseTest")` for more info @@ -1132,7 +1276,7 @@ Run `revdepcheck::cloud_details(, "BuyseTest")` for more info * using option ‘--no-manual’ * checking for file ‘BuyseTest/DESCRIPTION’ ... OK ... -* this is package ‘BuyseTest’ version ‘3.0.5’ +* this is package ‘BuyseTest’ version ‘3.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -1162,7 +1306,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘BuyseTest/DESCRIPTION’ ... OK ... -* this is package ‘BuyseTest’ version ‘3.0.5’ +* this is package ‘BuyseTest’ version ‘3.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -1182,11 +1326,11 @@ Status: 1 ERROR
-* Version: 0.1.0 +* Version: 0.2.2 * 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 +* Date/Publication: 2025-04-01 09:00:07 UTC +* Number of recursive dependencies: 255 Run `revdepcheck::cloud_details(, "CAESAR.Suite")` for more info @@ -1208,7 +1352,7 @@ Run `revdepcheck::cloud_details(, "CAESAR.Suite")` for more info * using option ‘--no-manual’ * checking for file ‘CAESAR.Suite/DESCRIPTION’ ... OK ... -* this is package ‘CAESAR.Suite’ version ‘0.1.0’ +* this is package ‘CAESAR.Suite’ version ‘0.2.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -1238,7 +1382,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘CAESAR.Suite/DESCRIPTION’ ... OK ... -* this is package ‘CAESAR.Suite’ version ‘0.1.0’ +* this is package ‘CAESAR.Suite’ version ‘0.2.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -1334,7 +1478,7 @@ ERROR: lazy loading failed for package ‘CARBayesST’ * GitHub: NA * Source code: https://github.com/cran/Certara.VPCResults * Date/Publication: 2024-12-02 15:30:02 UTC -* Number of recursive dependencies: 141 +* Number of recursive dependencies: 142 Run `revdepcheck::cloud_details(, "Certara.VPCResults")` for more info @@ -1484,6 +1628,70 @@ Run `revdepcheck::cloud_details(, "cia")` for more info +``` +# CIDER + +
+ +* Version: 0.99.4 +* GitHub: https://github.com/zhiyuan-hu-lab/CIDER +* Source code: https://github.com/cran/CIDER +* Date/Publication: 2025-02-07 09:50:14 UTC +* Number of recursive dependencies: 168 + +Run `revdepcheck::cloud_details(, "CIDER")` for more info + +
+ +## In both + +* checking whether package ‘CIDER’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/CIDER/new/CIDER.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘CIDER’ ... +** package ‘CIDER’ 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 ‘CIDER’ +* removing ‘/tmp/workdir/CIDER/new/CIDER.Rcheck/CIDER’ + + +``` +### CRAN + +``` +* installing *source* package ‘CIDER’ ... +** package ‘CIDER’ 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 ‘CIDER’ +* removing ‘/tmp/workdir/CIDER/old/CIDER.Rcheck/CIDER’ + + ``` # cinaR @@ -1493,7 +1701,7 @@ Run `revdepcheck::cloud_details(, "cia")` for more info * 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: 171 +* Number of recursive dependencies: 172 Run `revdepcheck::cloud_details(, "cinaR")` for more info @@ -1561,60 +1769,136 @@ Status: 1 ERROR ``` -# cmprskcoxmsm +# ClusterGVis
-* 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: 0.1.2 +* GitHub: https://github.com/junjunlab/ClusterGVis +* Source code: https://github.com/cran/ClusterGVis +* Date/Publication: 2025-02-14 14:30:13 UTC +* Number of recursive dependencies: 297 -Run `revdepcheck::cloud_details(, "cmprskcoxmsm")` for more info +Run `revdepcheck::cloud_details(, "ClusterGVis")` 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 +## Error before 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’ +* using log directory ‘/tmp/workdir/ClusterGVis/new/ClusterGVis.Rcheck’ +* 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 ‘ClusterGVis/DESCRIPTION’ ... OK +... +* this is package ‘ClusterGVis’ version ‘0.1.2’ +* 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 ``` -* 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]]) : +* using log directory ‘/tmp/workdir/ClusterGVis/old/ClusterGVis.Rcheck’ +* 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 ‘ClusterGVis/DESCRIPTION’ ... OK +... +* this is package ‘ClusterGVis’ version ‘0.1.2’ +* 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 + + + + + +``` +# 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 @@ -1631,7 +1915,7 @@ ERROR: lazy loading failed for package ‘cmprskcoxmsm’ * GitHub: NA * Source code: https://github.com/cran/COMMA * Date/Publication: 2024-12-13 21:10:02 UTC -* Number of recursive dependencies: 72 +* Number of recursive dependencies: 73 Run `revdepcheck::cloud_details(, "COMMA")` for more info @@ -1695,7 +1979,7 @@ ERROR: lazy loading failed for package ‘COMMA’ * 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 +* Number of recursive dependencies: 157 Run `revdepcheck::cloud_details(, "contsurvplot")` for more info @@ -1771,7 +2055,7 @@ Status: 1 ERROR * GitHub: https://github.com/dandls/counterfactuals * Source code: https://github.com/cran/counterfactuals * Date/Publication: 2024-10-17 12:00:06 UTC -* Number of recursive dependencies: 217 +* Number of recursive dependencies: 218 Run `revdepcheck::cloud_details(, "counterfactuals")` for more info @@ -1847,7 +2131,7 @@ Status: 1 NOTE * GitHub: https://github.com/khodosevichlab/CRMetrics * Source code: https://github.com/cran/CRMetrics * Date/Publication: 2024-11-08 00:20:06 UTC -* Number of recursive dependencies: 242 +* Number of recursive dependencies: 243 Run `revdepcheck::cloud_details(, "CRMetrics")` for more info @@ -1976,16 +2260,51 @@ ERROR: compilation failed for package ‘ctsem’ * removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’ +``` +# DamageDetective + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/DamageDetective +* Number of recursive dependencies: 177 + +Run `revdepcheck::cloud_details(, "DamageDetective")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # dartR.base
-* Version: 0.98 +* Version: 1.0.5 * GitHub: NA * Source code: https://github.com/cran/dartR.base -* Date/Publication: 2024-09-19 13:20:02 UTC -* Number of recursive dependencies: 288 +* Date/Publication: 2025-03-04 03:40:02 UTC +* Number of recursive dependencies: 289 Run `revdepcheck::cloud_details(, "dartR.base")` for more info @@ -2007,7 +2326,7 @@ Run `revdepcheck::cloud_details(, "dartR.base")` for more info * using option ‘--no-manual’ * checking for file ‘dartR.base/DESCRIPTION’ ... OK ... -* this is package ‘dartR.base’ version ‘0.98’ +* this is package ‘dartR.base’ version ‘1.0.5’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -2037,7 +2356,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘dartR.base/DESCRIPTION’ ... OK ... -* this is package ‘dartR.base’ version ‘0.98’ +* this is package ‘dartR.base’ version ‘1.0.5’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -2057,11 +2376,11 @@ Status: 1 ERROR
-* Version: 0.75 +* Version: 1.0.2 * GitHub: NA * Source code: https://github.com/cran/dartR.captive -* Date/Publication: 2023-11-27 17:10:09 UTC -* Number of recursive dependencies: 152 +* Date/Publication: 2025-02-18 08:20:05 UTC +* Number of recursive dependencies: 166 Run `revdepcheck::cloud_details(, "dartR.captive")` for more info @@ -2083,11 +2402,11 @@ Run `revdepcheck::cloud_details(, "dartR.captive")` for more info * using option ‘--no-manual’ * checking for file ‘dartR.captive/DESCRIPTION’ ... OK ... -* this is package ‘dartR.captive’ version ‘0.75’ +* this is package ‘dartR.captive’ version ‘1.0.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Package required but not available: ‘dartR.base’ +Packages required but not available: 'dartR.base', 'dartR.sim' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -2113,11 +2432,11 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘dartR.captive/DESCRIPTION’ ... OK ... -* this is package ‘dartR.captive’ version ‘0.75’ +* this is package ‘dartR.captive’ version ‘1.0.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR -Package required but not available: ‘dartR.base’ +Packages required but not available: 'dartR.base', 'dartR.sim' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. @@ -2213,7 +2532,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/dartR.sexlinked * Date/Publication: 2024-06-24 15:40:02 UTC -* Number of recursive dependencies: 120 +* Number of recursive dependencies: 125 Run `revdepcheck::cloud_details(, "dartR.sexlinked")` for more info @@ -2289,7 +2608,7 @@ Status: 1 ERROR * 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 +* Number of recursive dependencies: 138 Run `revdepcheck::cloud_details(, "dartR.sim")` for more info @@ -2365,7 +2684,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/dartR.spatial * Date/Publication: 2023-11-15 00:50:02 UTC -* Number of recursive dependencies: 168 +* Number of recursive dependencies: 171 Run `revdepcheck::cloud_details(, "dartR.spatial")` for more info @@ -2441,7 +2760,7 @@ Status: 1 ERROR * 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 +* Number of recursive dependencies: 131 Run `revdepcheck::cloud_details(, "DepthProc")` for more info @@ -2515,10 +2834,10 @@ ERROR: lazy loading failed for package ‘DepthProc’
-* Version: 0.2.0 +* Version: 0.3.0 * GitHub: https://github.com/MohmedSoudy/DFD * Source code: https://github.com/cran/DFD -* Date/Publication: 2024-08-28 18:20:02 UTC +* Date/Publication: 2025-02-11 13:50:11 UTC * Number of recursive dependencies: 207 Run `revdepcheck::cloud_details(, "DFD")` for more info @@ -2541,7 +2860,7 @@ Run `revdepcheck::cloud_details(, "DFD")` for more info * using option ‘--no-manual’ * checking for file ‘DFD/DESCRIPTION’ ... OK ... -* this is package ‘DFD’ version ‘0.2.0’ +* this is package ‘DFD’ version ‘0.3.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -2571,7 +2890,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘DFD/DESCRIPTION’ ... OK ... -* this is package ‘DFD’ version ‘0.2.0’ +* this is package ‘DFD’ version ‘0.3.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -2586,6 +2905,41 @@ Status: 1 ERROR +``` +# discoveR + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/discoveR +* Number of recursive dependencies: 175 + +Run `revdepcheck::cloud_details(, "discoveR")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # dMrs @@ -2595,7 +2949,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/dMrs * Date/Publication: 2025-01-21 15:40:05 UTC -* Number of recursive dependencies: 137 +* Number of recursive dependencies: 139 Run `revdepcheck::cloud_details(, "dMrs")` for more info @@ -2667,10 +3021,10 @@ Status: OK
-* Version: 3.4 +* Version: 3.5 * GitHub: https://github.com/feiyoung/DR.SC * Source code: https://github.com/cran/DR.SC -* Date/Publication: 2024-03-19 08:40:02 UTC +* Date/Publication: 2025-03-29 15:10:02 UTC * Number of recursive dependencies: 151 Run `revdepcheck::cloud_details(, "DR.SC")` for more info @@ -2824,7 +3178,7 @@ Status: OK * Version: NA * GitHub: NA * Source code: https://github.com/cran/DynForest -* Number of recursive dependencies: 143 +* Number of recursive dependencies: 142 Run `revdepcheck::cloud_details(, "DynForest")` for more info @@ -2914,10 +3268,10 @@ ERROR: lazy loading failed for package ‘easybgm’
-* Version: 1.1.0 +* Version: 1.1.2 * GitHub: https://github.com/CefasRepRes/EcoEnsemble * Source code: https://github.com/cran/EcoEnsemble -* Date/Publication: 2024-08-19 17:20:06 UTC +* Date/Publication: 2025-03-18 18:20:02 UTC * Number of recursive dependencies: 90 Run `revdepcheck::cloud_details(, "EcoEnsemble")` for more info @@ -3218,6 +3572,126 @@ Run `revdepcheck::cloud_details(, "EWSmethods")` for more info +``` +# FARS + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/FARS +* Date/Publication: 2025-04-03 15:10:10 UTC +* Number of recursive dependencies: 139 + +Run `revdepcheck::cloud_details(, "FARS")` for more info + +
+ +## In both + +* checking whether package ‘FARS’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/FARS/new/FARS.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘FARS’ ... +** package ‘FARS’ 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 ‘FARS’ +* removing ‘/tmp/workdir/FARS/new/FARS.Rcheck/FARS’ + + +``` +### CRAN + +``` +* installing *source* package ‘FARS’ ... +** package ‘FARS’ 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 ‘FARS’ +* removing ‘/tmp/workdir/FARS/old/FARS.Rcheck/FARS’ + + +``` +# fio + +
+ +* Version: 0.1.6 +* GitHub: https://github.com/albersonmiranda/fio +* Source code: https://github.com/cran/fio +* Date/Publication: 2025-04-06 07:50:02 UTC +* Number of recursive dependencies: 90 + +Run `revdepcheck::cloud_details(, "fio")` for more info + +
+ +## In both + +* checking whether package ‘fio’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/fio/new/fio.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘fio’ ... +** package ‘fio’ successfully unpacked and MD5 sums checked +** using staged installation +Error in eval(ei, envir) : +------------------ [UNSUPPORTED RUST VERSION]------------------ +- Minimum supported Rust version is 1.77. +- Installed Rust version is 1.75.0. +--------------------------------------------------------------- +Calls: source -> withVisible -> eval -> eval +Execution halted +ERROR: configuration failed for package ‘fio’ +* removing ‘/tmp/workdir/fio/new/fio.Rcheck/fio’ + + +``` +### CRAN + +``` +* installing *source* package ‘fio’ ... +** package ‘fio’ successfully unpacked and MD5 sums checked +** using staged installation +Error in eval(ei, envir) : +------------------ [UNSUPPORTED RUST VERSION]------------------ +- Minimum supported Rust version is 1.77. +- Installed Rust version is 1.75.0. +--------------------------------------------------------------- +Calls: source -> withVisible -> eval -> eval +Execution halted +ERROR: configuration failed for package ‘fio’ +* removing ‘/tmp/workdir/fio/old/fio.Rcheck/fio’ + + ``` # flexrsurv @@ -3227,7 +3701,7 @@ Run `revdepcheck::cloud_details(, "EWSmethods")` for more info * GitHub: NA * Source code: https://github.com/cran/flexrsurv * Date/Publication: 2024-02-09 16:10:02 UTC -* Number of recursive dependencies: 129 +* Number of recursive dependencies: 130 Run `revdepcheck::cloud_details(, "flexrsurv")` for more info @@ -3392,17 +3866,17 @@ ERROR: lazy loading failed for package ‘ForecastComb’ ``` -# gap +# gaawr2
-* 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 +* Version: 0.0.3 +* GitHub: https://github.com/jinghuazhao/gaawr2 +* Source code: https://github.com/cran/gaawr2 +* Date/Publication: 2025-03-24 15:00:09 UTC +* Number of recursive dependencies: 229 -Run `revdepcheck::cloud_details(, "gap")` for more info +Run `revdepcheck::cloud_details(, "gaawr2")` for more info
@@ -3411,7 +3885,7 @@ Run `revdepcheck::cloud_details(, "gap")` for more info ### Devel ``` -* using log directory ‘/tmp/workdir/gap/new/gap.Rcheck’ +* using log directory ‘/tmp/workdir/gaawr2/new/gaawr2.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by @@ -3420,18 +3894,18 @@ Run `revdepcheck::cloud_details(, "gap")` for more info * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘gap/DESCRIPTION’ ... OK +* checking for file ‘gaawr2/DESCRIPTION’ ... OK ... ---- failed re-building ‘jss.Rnw’ +--- finished re-building ‘web.Rmd’ SUMMARY: processing the following file failed: - ‘jss.Rnw’ + ‘gaawr2.Rmd’ Error: Vignette re-building failed. Execution halted * DONE -Status: 4 NOTEs +Status: 1 WARNING, 2 NOTEs @@ -3441,7 +3915,7 @@ Status: 4 NOTEs ### CRAN ``` -* using log directory ‘/tmp/workdir/gap/old/gap.Rcheck’ +* using log directory ‘/tmp/workdir/gaawr2/old/gaawr2.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by @@ -3450,12 +3924,88 @@ Status: 4 NOTEs * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * using option ‘--no-manual’ -* checking for file ‘gap/DESCRIPTION’ ... OK +* checking for file ‘gaawr2/DESCRIPTION’ ... OK ... ---- failed re-building ‘jss.Rnw’ +--- finished re-building ‘web.Rmd’ SUMMARY: processing the following file failed: - ‘jss.Rnw’ + ‘gaawr2.Rmd’ + +Error: Vignette re-building failed. +Execution halted + +* DONE +Status: 1 WARNING, 2 NOTEs + + + + + +``` +# 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: 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 @@ -3831,153 +4381,6 @@ Run `revdepcheck::cloud_details(, "GeoTox")` for more info -``` -# 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 @@ -3987,7 +4390,7 @@ ERROR: lazy loading failed for package ‘ggThemeAssist’ * GitHub: NA * Source code: https://github.com/cran/gJLS2 * Date/Publication: 2021-09-30 09:00:05 UTC -* Number of recursive dependencies: 45 +* Number of recursive dependencies: 46 Run `revdepcheck::cloud_details(, "gJLS2")` for more info @@ -4051,7 +4454,7 @@ ERROR: lazy loading failed for package ‘gJLS2’ * 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 +* Number of recursive dependencies: 266 Run `revdepcheck::cloud_details(, "grandR")` for more info @@ -4194,6 +4597,64 @@ Status: 1 ERROR +``` +# HetSeq + +
+ +* Version: 0.1.0 +* GitHub: https://github.com/erhard-lab/HetSeq +* Source code: https://github.com/cran/HetSeq +* Date/Publication: 2025-02-03 18:00:05 UTC +* Number of recursive dependencies: 185 + +Run `revdepcheck::cloud_details(, "HetSeq")` for more info + +
+ +## In both + +* checking whether package ‘HetSeq’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/HetSeq/new/HetSeq.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘HetSeq’ ... +** package ‘HetSeq’ 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 >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘HetSeq’ +* removing ‘/tmp/workdir/HetSeq/new/HetSeq.Rcheck/HetSeq’ + + +``` +### CRAN + +``` +* installing *source* package ‘HetSeq’ ... +** package ‘HetSeq’ 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 >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘HetSeq’ +* removing ‘/tmp/workdir/HetSeq/old/HetSeq.Rcheck/HetSeq’ + + ``` # hettx @@ -4263,11 +4724,11 @@ ERROR: lazy loading failed for package ‘hettx’
-* Version: 5.2-2 +* Version: 5.2-3 * GitHub: NA * Source code: https://github.com/cran/Hmisc -* Date/Publication: 2025-01-10 23:30:03 UTC -* Number of recursive dependencies: 173 +* Date/Publication: 2025-03-16 15:40:02 UTC +* Number of recursive dependencies: 174 Run `revdepcheck::cloud_details(, "Hmisc")` for more info @@ -4407,7 +4868,7 @@ ERROR: lazy loading failed for package ‘Hmsc’ * 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 +* Number of recursive dependencies: 129 Run `revdepcheck::cloud_details(, "iClusterVB")` for more info @@ -4552,75 +5013,15 @@ 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 - -
- -## 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) - - ``` # invivoPKfit
-* Version: 2.0.0 +* Version: 2.0.1 * GitHub: NA * Source code: https://github.com/cran/invivoPKfit -* Date/Publication: 2025-01-09 14:30:02 UTC +* Date/Publication: 2025-03-24 16:00:02 UTC * Number of recursive dependencies: 172 Run `revdepcheck::cloud_details(, "invivoPKfit")` for more info @@ -4681,7 +5082,7 @@ ERROR: lazy loading failed for package ‘invivoPKfit’ * 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: 161 +* Number of recursive dependencies: 162 Run `revdepcheck::cloud_details(, "iNZightPlots")` for more info @@ -4741,7 +5142,7 @@ 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: 162 +* Number of recursive dependencies: 163 Run `revdepcheck::cloud_details(, "iNZightRegression")` for more info @@ -4801,7 +5202,7 @@ 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: 180 +* Number of recursive dependencies: 181 Run `revdepcheck::cloud_details(, "IRexamples")` for more info @@ -4875,7 +5276,7 @@ ERROR: lazy loading failed for package ‘IRexamples’ * GitHub: NA * Source code: https://github.com/cran/jmBIG * Date/Publication: 2025-01-19 21:00:02 UTC -* Number of recursive dependencies: 187 +* Number of recursive dependencies: 189 Run `revdepcheck::cloud_details(, "jmBIG")` for more info @@ -4947,10 +5348,10 @@ Status: 1 ERROR
-* Version: 0.4.6 +* Version: 0.4.7 * GitHub: https://github.com/graemeleehickey/joineRML * Source code: https://github.com/cran/joineRML -* Date/Publication: 2023-01-20 04:50:02 UTC +* Date/Publication: 2025-02-04 16:30:02 UTC * Number of recursive dependencies: 93 Run `revdepcheck::cloud_details(, "joineRML")` for more info @@ -4974,12 +5375,12 @@ Run `revdepcheck::cloud_details(, "joineRML")` for more info ** package ‘joineRML’ 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++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 +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 expW.cpp -o expW.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 gammaUpdate.cpp -o gammaUpdate.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 gammaUpdate_approx.cpp -o gammaUpdate_approx.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 lambdaUpdate.cpp -o lambdaUpdate.o ... ** data *** moving datasets to lazyload DB @@ -5001,12 +5402,12 @@ ERROR: lazy loading failed for package ‘joineRML’ ** package ‘joineRML’ 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++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 +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 expW.cpp -o expW.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 gammaUpdate.cpp -o gammaUpdate.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 gammaUpdate_approx.cpp -o gammaUpdate_approx.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 lambdaUpdate.cpp -o lambdaUpdate.o ... ** data *** moving datasets to lazyload DB @@ -5025,10 +5426,10 @@ ERROR: lazy loading failed for package ‘joineRML’
-* Version: 1.6.1 +* Version: 1.6.4 * GitHub: https://github.com/jinseob2kim/jsmodule * Source code: https://github.com/cran/jsmodule -* Date/Publication: 2025-01-08 13:10:02 UTC +* Date/Publication: 2025-03-10 06:20:02 UTC * Number of recursive dependencies: 241 Run `revdepcheck::cloud_details(, "jsmodule")` for more info @@ -5179,7 +5580,7 @@ ERROR: lazy loading failed for package ‘kmc’ * 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 +* Number of recursive dependencies: 172 Run `revdepcheck::cloud_details(, "KMunicate")` for more info @@ -5531,7 +5932,7 @@ ERROR: lazy loading failed for package ‘llbayesireg’ * GitHub: NA * Source code: https://github.com/cran/lnmixsurv * Date/Publication: 2024-09-03 15:20:08 UTC -* Number of recursive dependencies: 195 +* Number of recursive dependencies: 196 Run `revdepcheck::cloud_details(, "lnmixsurv")` for more info @@ -5553,16 +5954,16 @@ Run `revdepcheck::cloud_details(, "lnmixsurv")` for more info * using option ‘--no-manual’ * checking for file ‘lnmixsurv/DESCRIPTION’ ... OK ... ---- finished re-building ‘parallel_computation.Rmd’ - -SUMMARY: processing the following file failed: - ‘expectation_maximization.Rmd’ - -Error: Vignette re-building failed. -Execution halted - +* 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: 2 ERRORs, 5 NOTEs +Status: 4 NOTEs @@ -5607,7 +6008,7 @@ Status: 4 NOTEs * GitHub: https://github.com/AlJacq/LorenzRegression * Source code: https://github.com/cran/LorenzRegression * Date/Publication: 2024-10-11 16:50:02 UTC -* Number of recursive dependencies: 83 +* Number of recursive dependencies: 84 Run `revdepcheck::cloud_details(, "LorenzRegression")` for more info @@ -5681,10 +6082,10 @@ ERROR: lazy loading failed for package ‘LorenzRegression’
-* Version: 1.3.3 +* Version: 1.3.4 * GitHub: NA * Source code: https://github.com/cran/lsirm12pl -* Date/Publication: 2024-08-28 23:00:02 UTC +* Date/Publication: 2025-03-06 10:40:06 UTC * Number of recursive dependencies: 123 Run `revdepcheck::cloud_details(, "lsirm12pl")` for more info @@ -5762,7 +6163,7 @@ ERROR: lazy loading failed for package ‘lsirm12pl’ * Version: NA * GitHub: NA * Source code: https://github.com/cran/MantaID -* Number of recursive dependencies: 157 +* Number of recursive dependencies: 158 Run `revdepcheck::cloud_details(, "MantaID")` for more info @@ -5789,6 +6190,41 @@ Run `revdepcheck::cloud_details(, "MantaID")` for more info +``` +# manymodelr + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/manymodelr +* Number of recursive dependencies: 129 + +Run `revdepcheck::cloud_details(, "manymodelr")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # MARVEL @@ -5798,7 +6234,7 @@ 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: 229 +* Number of recursive dependencies: 230 Run `revdepcheck::cloud_details(, "MARVEL")` for more info @@ -5985,108 +6421,31 @@ 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 ‘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 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 - -``` -* 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’ +ERROR: lazy loading failed for package ‘mbsts’ +* removing ‘/tmp/workdir/mbsts/old/mbsts.Rcheck/mbsts’ ``` -# miWQS +# MendelianRandomization
-* 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: 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(, "miWQS")` for more info +Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info
## In both -* checking whether package ‘miWQS’ can be installed ... ERROR +* checking whether package ‘MendelianRandomization’ can be installed ... ERROR ``` Installation failed. - See ‘/tmp/workdir/miWQS/new/miWQS.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘wqs’ + See ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/00install.out’ for details. ``` ## Installation @@ -6094,40 +6453,48 @@ Run `revdepcheck::cloud_details(, "miWQS")` for more info ### Devel ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ 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 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 -** 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 ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/new/MendelianRandomization.Rcheck/MendelianRandomization’ ``` ### CRAN ``` -* installing *source* package ‘miWQS’ ... -** package ‘miWQS’ 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 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 -** 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 ‘MendelianRandomization’ +* removing ‘/tmp/workdir/MendelianRandomization/old/MendelianRandomization.Rcheck/MendelianRandomization’ ``` @@ -6203,7 +6570,7 @@ 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: 365 +* Number of recursive dependencies: 364 Run `revdepcheck::cloud_details(, "mlr")` for more info @@ -6234,7 +6601,7 @@ Run `revdepcheck::cloud_details(, "mlr")` for more info ‘mlr.Rmd’ using ‘UTF-8’... OK * checking re-building of vignette outputs ... OK * DONE -Status: 1 WARNING, 3 NOTEs +Status: 2 NOTEs @@ -6337,7 +6704,7 @@ ERROR: lazy loading failed for package ‘MRZero’ * 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 +* Number of recursive dependencies: 114 Run `revdepcheck::cloud_details(, "mstate")` for more info @@ -6404,86 +6771,16 @@ Status: 1 NOTE -``` -# 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: 170 - -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 -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 ‘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 -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 ‘multilevelTools’ -* removing ‘/tmp/workdir/multilevelTools/old/multilevelTools.Rcheck/multilevelTools’ - - ``` # multinma
-* Version: 0.7.2 +* Version: 0.8.0 * GitHub: https://github.com/dmphillippo/multinma * Source code: https://github.com/cran/multinma -* Date/Publication: 2024-09-16 12:20:02 UTC -* Number of recursive dependencies: 151 +* Date/Publication: 2025-03-25 22:50:16 UTC +* Number of recursive dependencies: 150 Run `revdepcheck::cloud_details(, "multinma")` for more info @@ -6561,7 +6858,7 @@ ERROR: compilation failed for package ‘multinma’ * GitHub: NA * Source code: https://github.com/cran/multipleOutcomes * Date/Publication: 2024-05-30 15:00:03 UTC -* Number of recursive dependencies: 176 +* Number of recursive dependencies: 177 Run `revdepcheck::cloud_details(, "multipleOutcomes")` for more info @@ -6637,7 +6934,7 @@ Status: OK * GitHub: NA * Source code: https://github.com/cran/MuPETFlow * Date/Publication: 2025-01-15 19:40:19 UTC -* Number of recursive dependencies: 85 +* Number of recursive dependencies: 86 Run `revdepcheck::cloud_details(, "MuPETFlow")` for more info @@ -7034,111 +7331,6 @@ ERROR: lazy loading failed for package ‘NMADiagT’ * removing ‘/tmp/workdir/NMADiagT/old/NMADiagT.Rcheck/NMADiagT’ -``` -# NMF - -
- -* Version: 0.28 -* GitHub: NA -* 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(, "NMF")` for more info - -
- -## Newly broken - -* checking whether package ‘NMF’ can be installed ... ERROR - ``` - Installation failed. - 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 - -### Devel - -``` -* installing *source* package ‘NMF’ ... -** package ‘NMF’ 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/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 ‘NMF’ -* removing ‘/tmp/workdir/NMF/new/NMF.Rcheck/NMF’ - - -``` -### CRAN - -``` -* installing *source* package ‘NMF’ ... -** package ‘NMF’ 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/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) - - ``` # obliqueRSF @@ -7220,11 +7412,11 @@ Status: OK
-* Version: 4.0.2 +* Version: 4.2.0 * 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 +* Date/Publication: 2025-02-24 21:40:08 UTC +* Number of recursive dependencies: 211 Run `revdepcheck::cloud_details(, "OlinkAnalyze")` for more info @@ -7246,16 +7438,16 @@ Run `revdepcheck::cloud_details(, "OlinkAnalyze")` for more info * using option ‘--no-manual’ * checking for file ‘OlinkAnalyze/DESCRIPTION’ ... OK ... ---- finished re-building ‘plate_randomizer.Rmd’ - -SUMMARY: processing the following file failed: - ‘Vignett.Rmd’ - -Error: Vignette re-building failed. -Execution halted - +* checking running R code from vignettes ... OK + ‘LOD.Rmd’ using ‘UTF-8’... OK + ‘OutlierExclusion.Rmd’ using ‘UTF-8’... OK + ‘Vignett.Rmd’ using ‘UTF-8’... OK + ‘bridging_crossproduct.Rmd’ using ‘UTF-8’... OK + ‘bridging_introduction.Rmd’ using ‘UTF-8’... OK + ‘plate_randomizer.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK * DONE -Status: 1 ERROR, 2 NOTEs +Status: 1 NOTE @@ -7276,16 +7468,16 @@ Status: 1 ERROR, 2 NOTEs * using option ‘--no-manual’ * checking for file ‘OlinkAnalyze/DESCRIPTION’ ... OK ... ---- finished re-building ‘plate_randomizer.Rmd’ - -SUMMARY: processing the following file failed: - ‘Vignett.Rmd’ - -Error: Vignette re-building failed. -Execution halted - +* checking running R code from vignettes ... OK + ‘LOD.Rmd’ using ‘UTF-8’... OK + ‘OutlierExclusion.Rmd’ using ‘UTF-8’... OK + ‘Vignett.Rmd’ using ‘UTF-8’... OK + ‘bridging_crossproduct.Rmd’ using ‘UTF-8’... OK + ‘bridging_introduction.Rmd’ using ‘UTF-8’... OK + ‘plate_randomizer.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK * DONE -Status: 1 ERROR, 2 NOTEs +Status: 1 NOTE @@ -7349,6 +7541,41 @@ ERROR: lazy loading failed for package ‘optweight’ * removing ‘/tmp/workdir/optweight/old/optweight.Rcheck/optweight’ +``` +# ordinalsimr + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/ordinalsimr +* Number of recursive dependencies: 120 + +Run `revdepcheck::cloud_details(, "ordinalsimr")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # OVtool @@ -7416,11 +7643,11 @@ ERROR: lazy loading failed for package ‘OVtool’
-* Version: 0.5.93 +* Version: 0.7.3 * 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 +* Date/Publication: 2025-03-24 15:20:02 UTC +* Number of recursive dependencies: 126 Run `revdepcheck::cloud_details(, "pammtools")` for more info @@ -7487,6 +7714,82 @@ Status: OK +``` +# parameters + +
+ +* Version: 0.24.2 +* GitHub: https://github.com/easystats/parameters +* Source code: https://github.com/cran/parameters +* Date/Publication: 2025-03-04 14:50:06 UTC +* Number of recursive dependencies: 474 + +Run `revdepcheck::cloud_details(, "parameters")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/parameters/new/parameters.Rcheck’ +* 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 ‘parameters/DESCRIPTION’ ... OK +... + • equivalence_test/equivalence-test-5.svg + 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 + ‘overview_of_vignettes.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 ERRORs, 2 NOTEs + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/parameters/old/parameters.Rcheck’ +* 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 ‘parameters/DESCRIPTION’ ... OK +... + • equivalence_test/equivalence-test-5.svg + 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 + ‘overview_of_vignettes.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 2 ERRORs, 2 NOTEs + + + + + ``` # paths @@ -7595,7 +7898,7 @@ Run `revdepcheck::cloud_details(, "PathwaySpace")` for more info * 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 +* Number of recursive dependencies: 193 Run `revdepcheck::cloud_details(, "pcvr")` for more info @@ -7735,67 +8038,38 @@ ERROR: lazy loading failed for package ‘PLMIX’ ``` -# popstudy +# Polychrome
-* Version: 1.0.1 +* Version: NA * GitHub: NA -* Source code: https://github.com/cran/popstudy -* Date/Publication: 2023-10-17 23:50:02 UTC -* Number of recursive dependencies: 242 +* Source code: https://github.com/cran/Polychrome +* Number of recursive dependencies: 50 -Run `revdepcheck::cloud_details(, "popstudy")` for more info +Run `revdepcheck::cloud_details(, "Polychrome")` 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 +## Error before 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’ + + + + ``` @@ -7883,7 +8157,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/PoweREST * Date/Publication: 2024-09-09 09:30:02 UTC -* Number of recursive dependencies: 171 +* Number of recursive dependencies: 183 Run `revdepcheck::cloud_details(, "PoweREST")` for more info @@ -8017,7 +8291,7 @@ 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: 153 +* Number of recursive dependencies: 154 Run `revdepcheck::cloud_details(, "pre")` for more info @@ -8077,11 +8351,11 @@ ERROR: lazy loading failed for package ‘pre’
-* Version: 1.4 +* Version: 1.6 * 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: 248 +* Date/Publication: 2025-03-27 14:40:02 UTC +* Number of recursive dependencies: 246 Run `revdepcheck::cloud_details(, "ProFAST")` for more info @@ -8103,7 +8377,7 @@ Run `revdepcheck::cloud_details(, "ProFAST")` for more info * using option ‘--no-manual’ * checking for file ‘ProFAST/DESCRIPTION’ ... OK ... -* this is package ‘ProFAST’ version ‘1.4’ +* this is package ‘ProFAST’ version ‘1.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -8133,7 +8407,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘ProFAST/DESCRIPTION’ ... OK ... -* this is package ‘ProFAST’ version ‘1.4’ +* this is package ‘ProFAST’ version ‘1.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -8224,78 +8498,6 @@ 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: 171 - -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 -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 ‘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 -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 ‘pscore’ -* removing ‘/tmp/workdir/pscore/old/pscore.Rcheck/pscore’ - - ``` # pubh @@ -8478,7 +8680,7 @@ 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: 123 +* Number of recursive dependencies: 124 Run `revdepcheck::cloud_details(, "qte")` for more info @@ -8659,6 +8861,41 @@ ERROR: lazy loading failed for package ‘quid’ * removing ‘/tmp/workdir/quid/old/quid.Rcheck/quid’ +``` +# RcensusPkg + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/RcensusPkg +* Number of recursive dependencies: 118 + +Run `revdepcheck::cloud_details(, "RcensusPkg")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # RcmdrPlugin.RiskDemo @@ -8796,11 +9033,11 @@ ERROR: lazy loading failed for package ‘rddtools’
-* Version: 2.3-1 +* Version: 2.3-2 * GitHub: NA * Source code: https://github.com/cran/relsurv -* Date/Publication: 2025-01-20 15:40:01 UTC -* Number of recursive dependencies: 112 +* Date/Publication: 2025-01-28 15:50:02 UTC +* Number of recursive dependencies: 113 Run `revdepcheck::cloud_details(, "relsurv")` for more info @@ -9062,7 +9299,7 @@ Status: 1 ERROR * Version: NA * GitHub: NA * Source code: https://github.com/cran/rmlnomogram -* Number of recursive dependencies: 181 +* Number of recursive dependencies: 182 Run `revdepcheck::cloud_details(, "rmlnomogram")` for more info @@ -9097,7 +9334,7 @@ Run `revdepcheck::cloud_details(, "rmlnomogram")` for more info * Version: NA * GitHub: NA * Source code: https://github.com/cran/rms -* Number of recursive dependencies: 148 +* Number of recursive dependencies: 151 Run `revdepcheck::cloud_details(, "rms")` for more info @@ -9133,7 +9370,7 @@ Run `revdepcheck::cloud_details(, "rms")` for more info * 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 +* Number of recursive dependencies: 144 Run `revdepcheck::cloud_details(, "robber")` for more info @@ -9205,10 +9442,10 @@ Status: OK
-* Version: 1.2.0 +* Version: 1.2.1 * GitHub: https://github.com/aalfons/robmed * Source code: https://github.com/cran/robmed -* Date/Publication: 2024-12-10 00:00:02 UTC +* Date/Publication: 2025-02-08 22:50:06 UTC * Number of recursive dependencies: 59 Run `revdepcheck::cloud_details(, "robmed")` for more info @@ -9232,94 +9469,236 @@ Run `revdepcheck::cloud_details(, "robmed")` for more info ** package ‘robmed’ successfully unpacked and MD5 sums checked ** using staged installation ** R -** data -*** moving datasets to lazyload DB +** 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: 0.1.1 +* GitHub: https://github.com/aalfons/robmedExtra +* Source code: https://github.com/cran/robmedExtra +* Date/Publication: 2024-11-03 12:10:01 UTC +* Number of recursive dependencies: 91 + +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’ + + +``` +# ROKET + +
+ +* Version: 1.0.0 +* GitHub: NA +* Source code: https://github.com/cran/ROKET +* Date/Publication: 2025-03-06 17:00:02 UTC +* Number of recursive dependencies: 172 + +Run `revdepcheck::cloud_details(, "ROKET")` for more info + +
+ +## In both + +* checking whether package ‘ROKET’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/ROKET/new/ROKET.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘ROKET’ ... +** package ‘ROKET’ 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 ROKET.cpp -o ROKET.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 ROKET.so ROKET.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/ROKET/new/ROKET.Rcheck/00LOCK-ROKET/00new/ROKET/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 ‘robmed’ -* removing ‘/tmp/workdir/robmed/new/robmed.Rcheck/robmed’ +ERROR: lazy loading failed for package ‘ROKET’ +* removing ‘/tmp/workdir/ROKET/new/ROKET.Rcheck/ROKET’ ``` ### CRAN ``` -* installing *source* package ‘robmed’ ... -** package ‘robmed’ successfully unpacked and MD5 sums checked +* installing *source* package ‘ROKET’ ... +** package ‘ROKET’ 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 ROKET.cpp -o ROKET.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 ROKET.so ROKET.o RcppExports.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR +installing to /tmp/workdir/ROKET/old/ROKET.Rcheck/00LOCK-ROKET/00new/ROKET/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 ‘robmed’ -* removing ‘/tmp/workdir/robmed/old/robmed.Rcheck/robmed’ +ERROR: lazy loading failed for package ‘ROKET’ +* removing ‘/tmp/workdir/ROKET/old/ROKET.Rcheck/ROKET’ ``` -# robmedExtra +# rplec
-* Version: 0.1.1 -* GitHub: https://github.com/aalfons/robmedExtra -* Source code: https://github.com/cran/robmedExtra -* Date/Publication: 2024-11-03 12:10:01 UTC -* Number of recursive dependencies: 91 +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/rplec +* Number of recursive dependencies: 122 -Run `revdepcheck::cloud_details(, "robmedExtra")` for more info +Run `revdepcheck::cloud_details(, "rplec")` for more info
-## In both +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + -* checking whether package ‘robmedExtra’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/robmedExtra/new/robmedExtra.Rcheck/00install.out’ for details. - ``` -## Installation + +``` +# RplotterPkg + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/RplotterPkg +* Number of recursive dependencies: 123 + +Run `revdepcheck::cloud_details(, "RplotterPkg")` for more info + +
+ +## 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’ + + + + ``` ### 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’ + + + + ``` @@ -9389,10 +9768,10 @@ ERROR: lazy loading failed for package ‘RPPanalyzer’
-* Version: 1.3.0 +* Version: 1.3.2 * GitHub: NA * Source code: https://github.com/cran/RQdeltaCT -* Date/Publication: 2024-04-17 15:50:02 UTC +* Date/Publication: 2025-02-13 12:02:01 UTC * Number of recursive dependencies: 163 Run `revdepcheck::cloud_details(, "RQdeltaCT")` for more info @@ -9483,6 +9862,84 @@ Run `revdepcheck::cloud_details(, "RRPP")` for more info +``` +# rshift + +
+ +* Version: 3.1.2 +* GitHub: https://github.com/alexhroom/rshift +* Source code: https://github.com/cran/rshift +* Date/Publication: 2025-04-06 18:40:02 UTC +* Number of recursive dependencies: 37 + +Run `revdepcheck::cloud_details(, "rshift")` for more info + +
+ +## In both + +* checking whether package ‘rshift’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/rshift/new/rshift.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘rshift’ ... +** package ‘rshift’ successfully unpacked and MD5 sums checked +** using staged installation +Using cargo 1.75.0 +Using rustc 1.75.0 (82e1608df 2023-12-21) (built from a source tarball) +Building for CRAN. +Writing `src/Makevars`. +`tools/config.R` has finished. +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +... +export CARGO_HOME=/tmp/workdir/rshift/new/rshift.Rcheck/00_pkg_src/rshift/src/.cargo && \ +export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/root/.cargo/bin" && \ +RUSTFLAGS=" --print=native-static-libs" cargo build -j 2 --offline --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target +error: failed to parse lock file at: /tmp/workdir/rshift/new/rshift.Rcheck/00_pkg_src/rshift/src/rust/Cargo.lock + +Caused by: + lock file version 4 requires `-Znext-lockfile-bump` +make: *** [Makevars:28: rust/target/release/librshift.a] Error 101 +ERROR: compilation failed for package ‘rshift’ +* removing ‘/tmp/workdir/rshift/new/rshift.Rcheck/rshift’ + + +``` +### CRAN + +``` +* installing *source* package ‘rshift’ ... +** package ‘rshift’ successfully unpacked and MD5 sums checked +** using staged installation +Using cargo 1.75.0 +Using rustc 1.75.0 (82e1608df 2023-12-21) (built from a source tarball) +Building for CRAN. +Writing `src/Makevars`. +`tools/config.R` has finished. +** libs +using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ +... +export CARGO_HOME=/tmp/workdir/rshift/old/rshift.Rcheck/00_pkg_src/rshift/src/.cargo && \ +export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/root/.cargo/bin" && \ +RUSTFLAGS=" --print=native-static-libs" cargo build -j 2 --offline --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target +error: failed to parse lock file at: /tmp/workdir/rshift/old/rshift.Rcheck/00_pkg_src/rshift/src/rust/Cargo.lock + +Caused by: + lock file version 4 requires `-Znext-lockfile-bump` +make: *** [Makevars:28: rust/target/release/librshift.a] Error 101 +ERROR: compilation failed for package ‘rshift’ +* removing ‘/tmp/workdir/rshift/old/rshift.Rcheck/rshift’ + + ``` # rstanarm @@ -9492,7 +9949,7 @@ 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: 140 +* Number of recursive dependencies: 141 Run `revdepcheck::cloud_details(, "rstanarm")` for more info @@ -9566,11 +10023,11 @@ ERROR: compilation failed for package ‘rstanarm’
-* Version: 1.3.0 +* Version: 1.4.0 * GitHub: https://github.com/aidanmorales/rTwig * Source code: https://github.com/cran/rTwig -* Date/Publication: 2024-11-21 21:30:02 UTC -* Number of recursive dependencies: 141 +* Date/Publication: 2025-03-03 17:10:09 UTC +* Number of recursive dependencies: 143 Run `revdepcheck::cloud_details(, "rTwig")` for more info @@ -9648,7 +10105,7 @@ 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: 210 +* Number of recursive dependencies: 211 Run `revdepcheck::cloud_details(, "RVA")` for more info @@ -9724,7 +10181,7 @@ Status: 1 ERROR * GitHub: NA * Source code: https://github.com/cran/S4DM * Date/Publication: 2025-01-10 21:00:02 UTC -* Number of recursive dependencies: 138 +* Number of recursive dependencies: 134 Run `revdepcheck::cloud_details(, "S4DM")` for more info @@ -10121,10 +10578,10 @@ ERROR: lazy loading failed for package ‘scMappR’
-* Version: 2.2.6 +* Version: 3.0.0 * GitHub: NA * Source code: https://github.com/cran/scpi -* Date/Publication: 2024-11-11 23:40:02 UTC +* Date/Publication: 2025-01-31 19:40:02 UTC * Number of recursive dependencies: 96 Run `revdepcheck::cloud_details(, "scpi")` for more info @@ -10275,11 +10732,11 @@ Status: 2 NOTEs
-* Version: 0.1.1 +* Version: 0.1.1.1 * GitHub: NA * Source code: https://github.com/cran/scRNAstat -* Date/Publication: 2021-09-22 08:10:02 UTC -* Number of recursive dependencies: 156 +* Date/Publication: 2025-03-08 08:58:55 UTC +* Number of recursive dependencies: 157 Run `revdepcheck::cloud_details(, "scRNAstat")` for more info @@ -10304,14 +10761,6 @@ Run `revdepcheck::cloud_details(, "scRNAstat")` for more info ** 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’ -... -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 @@ -10331,14 +10780,6 @@ ERROR: lazy loading failed for package ‘scRNAstat’ ** 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’ -... -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 @@ -10690,6 +11131,66 @@ ERROR: lazy loading failed for package ‘Seurat’ * removing ‘/tmp/workdir/Seurat/old/Seurat.Rcheck/Seurat’ +``` +# SeuratExplorer + +
+ +* Version: 0.1.0 +* GitHub: NA +* Source code: https://github.com/cran/SeuratExplorer +* Date/Publication: 2025-03-13 13:10:05 UTC +* Number of recursive dependencies: 236 + +Run `revdepcheck::cloud_details(, "SeuratExplorer")` for more info + +
+ +## In both + +* checking whether package ‘SeuratExplorer’ can be installed ... ERROR + ``` + Installation failed. + See ‘/tmp/workdir/SeuratExplorer/new/SeuratExplorer.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘SeuratExplorer’ ... +** package ‘SeuratExplorer’ 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 >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SeuratExplorer’ +* removing ‘/tmp/workdir/SeuratExplorer/new/SeuratExplorer.Rcheck/SeuratExplorer’ + + +``` +### CRAN + +``` +* installing *source* package ‘SeuratExplorer’ ... +** package ‘SeuratExplorer’ 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 >= 1.6.4 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace +Execution halted +ERROR: lazy loading failed for package ‘SeuratExplorer’ +* removing ‘/tmp/workdir/SeuratExplorer/old/SeuratExplorer.Rcheck/SeuratExplorer’ + + ``` # shinyTempSignal @@ -10857,136 +11358,45 @@ g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I' 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 ‘SiFINeT’ -* removing ‘/tmp/workdir/SiFINeT/new/SiFINeT.Rcheck/SiFINeT’ - - -``` -### CRAN - -``` -* 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/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 ‘SiFINeT’ -* removing ‘/tmp/workdir/SiFINeT/old/SiFINeT.Rcheck/SiFINeT’ - - -``` -# 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: 212 - -Run `revdepcheck::cloud_details(, "sigminer")` for more info - -
- -## 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 - -``` -* 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 +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 ... -** data -*** moving datasets to lazyload DB +installing to /tmp/workdir/SiFINeT/new/SiFINeT.Rcheck/00LOCK-SiFINeT/00new/SiFINeT/libs +** 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) +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.0 is required +Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace Execution halted -ERROR: lazy loading failed for package ‘sigminer’ -* removing ‘/tmp/workdir/sigminer/new/sigminer.Rcheck/sigminer’ +ERROR: lazy loading failed for package ‘SiFINeT’ +* removing ‘/tmp/workdir/SiFINeT/new/SiFINeT.Rcheck/SiFINeT’ ``` ### CRAN ``` -* installing *source* package ‘sigminer’ ... -** package ‘sigminer’ 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 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 +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 ... -** 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) +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 ‘SiFINeT’ +* removing ‘/tmp/workdir/SiFINeT/old/SiFINeT.Rcheck/SiFINeT’ ``` @@ -11072,10 +11482,10 @@ ERROR: lazy loading failed for package ‘Signac’
-* Version: 0.2.0 +* Version: 0.2.1 * GitHub: https://github.com/arcaldwell49/SimplyAgree * Source code: https://github.com/cran/SimplyAgree -* Date/Publication: 2024-03-21 14:20:06 UTC +* Date/Publication: 2025-02-24 16:40:11 UTC * Number of recursive dependencies: 118 Run `revdepcheck::cloud_details(, "SimplyAgree")` for more info @@ -11540,78 +11950,6 @@ ERROR: lazy loading failed for package ‘sparsereg’ * removing ‘/tmp/workdir/sparsereg/old/sparsereg.Rcheck/sparsereg’ -``` -# spectralAnalysis - -
- -* 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(, "spectralAnalysis")` for more info - -
- -## Newly broken - -* checking whether package ‘spectralAnalysis’ can be installed ... ERROR - ``` - Installation failed. - See ‘/tmp/workdir/spectralAnalysis/new/spectralAnalysis.Rcheck/00install.out’ for details. - ``` - -## Newly fixed - -* 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 - -``` -* 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) - - ``` # spikeSlabGAM @@ -11693,7 +12031,7 @@ ERROR: lazy loading failed for package ‘spikeSlabGAM’ * GitHub: NA * Source code: https://github.com/cran/stabiliser * Date/Publication: 2023-05-17 11:00:05 UTC -* Number of recursive dependencies: 151 +* Number of recursive dependencies: 153 Run `revdepcheck::cloud_details(, "stabiliser")` for more info @@ -11891,7 +12229,7 @@ Status: 1 ERROR * 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 +* Number of recursive dependencies: 183 Run `revdepcheck::cloud_details(, "survex")` for more info @@ -11963,10 +12301,10 @@ Status: 1 ERROR, 1 NOTE
-* Version: 2.0.2 +* Version: 2.0.3 * GitHub: https://github.com/giabaio/survHE * Source code: https://github.com/cran/survHE -* Date/Publication: 2024-10-04 09:50:02 UTC +* Date/Publication: 2025-03-03 17:40:02 UTC * Number of recursive dependencies: 129 Run `revdepcheck::cloud_details(, "survHE")` for more info @@ -12108,6 +12446,82 @@ ERROR: lazy loading failed for package ‘survidm’ * removing ‘/tmp/workdir/survidm/old/survidm.Rcheck/survidm’ +``` +# SurvMetrics + +
+ +* Version: 0.5.1 +* GitHub: https://github.com/whcsu/SurvMetrics +* Source code: https://github.com/cran/SurvMetrics +* Date/Publication: 2025-02-05 11:50:28 UTC +* Number of recursive dependencies: 194 + +Run `revdepcheck::cloud_details(, "SurvMetrics")` for more info + +
+ +## Error before installation + +### Devel + +``` +* using log directory ‘/tmp/workdir/SurvMetrics/new/SurvMetrics.Rcheck’ +* 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 ‘SurvMetrics/DESCRIPTION’ ... OK +... + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 38 ] + 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 + ‘SurvMetrics-vignette.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR + + + + + +``` +### CRAN + +``` +* using log directory ‘/tmp/workdir/SurvMetrics/old/SurvMetrics.Rcheck’ +* 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 ‘SurvMetrics/DESCRIPTION’ ... OK +... + [ FAIL 4 | WARN 0 | SKIP 0 | PASS 38 ] + 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 + ‘SurvMetrics-vignette.Rmd’ using ‘UTF-8’... OK +* checking re-building of vignette outputs ... OK +* DONE +Status: 1 ERROR + + + + + ``` # tempted @@ -12179,7 +12593,7 @@ ERROR: lazy loading failed for package ‘tempted’ * GitHub: https://github.com/jiangyouxiang/TestAnaAPP * Source code: https://github.com/cran/TestAnaAPP * Date/Publication: 2024-11-09 04:00:02 UTC -* Number of recursive dependencies: 255 +* Number of recursive dependencies: 254 Run `revdepcheck::cloud_details(, "TestAnaAPP")` for more info @@ -12246,68 +12660,6 @@ Status: 1 ERROR -``` -# 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 - -``` -* 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) - - ``` # tidyEdSurvey @@ -12383,7 +12735,7 @@ 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: 196 +* Number of recursive dependencies: 197 Run `revdepcheck::cloud_details(, "tidyseurat")` for more info @@ -12445,7 +12797,7 @@ ERROR: lazy loading failed for package ‘tidyseurat’ * 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 +* Number of recursive dependencies: 181 Run `revdepcheck::cloud_details(, "tidyvpc")` for more info @@ -12505,11 +12857,11 @@ ERROR: lazy loading failed for package ‘tidyvpc’
-* Version: 2.4.2 +* Version: 2.4.3 * 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 +* Date/Publication: 2025-03-05 13:20:02 UTC +* Number of recursive dependencies: 251 Run `revdepcheck::cloud_details(, "tinyarray")` for more info @@ -12531,7 +12883,7 @@ Run `revdepcheck::cloud_details(, "tinyarray")` for more info * using option ‘--no-manual’ * checking for file ‘tinyarray/DESCRIPTION’ ... OK ... -* this is package ‘tinyarray’ version ‘2.4.2’ +* this is package ‘tinyarray’ version ‘2.4.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -12561,7 +12913,7 @@ Status: 1 ERROR * using option ‘--no-manual’ * checking for file ‘tinyarray/DESCRIPTION’ ... OK ... -* this is package ‘tinyarray’ version ‘2.4.2’ +* this is package ‘tinyarray’ version ‘2.4.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR @@ -12858,6 +13210,41 @@ ERROR: lazy loading failed for package ‘twang’ * removing ‘/tmp/workdir/twang/old/twang.Rcheck/twang’ +``` +# ubair + +
+ +* Version: NA +* GitHub: NA +* Source code: https://github.com/cran/ubair +* Number of recursive dependencies: 111 + +Run `revdepcheck::cloud_details(, "ubair")` for more info + +
+ +## Error before installation + +### Devel + +``` + + + + + + +``` +### CRAN + +``` + + + + + + ``` # vdg @@ -12970,11 +13357,11 @@ Run `revdepcheck::cloud_details(, "VecDep")` for more info
-* Version: 0.1.0 +* Version: 1.0.0 * 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: 139 +* Date/Publication: 2025-03-19 19:50:02 UTC +* Number of recursive dependencies: 144 Run `revdepcheck::cloud_details(, "visa")` for more info @@ -13037,7 +13424,7 @@ ERROR: lazy loading failed for package ‘visa’ * Version: NA * GitHub: NA * Source code: https://github.com/cran/VisualizeSimon2Stage -* Number of recursive dependencies: 36 +* Number of recursive dependencies: 75 Run `revdepcheck::cloud_details(, "VisualizeSimon2Stage")` for more info @@ -13064,69 +13451,6 @@ 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 @@ -13136,7 +13460,7 @@ ERROR: lazy loading failed for package ‘wppExplorer’ * 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: 139 +* Number of recursive dependencies: 141 Run `revdepcheck::cloud_details(, "WRTDStidal")` for more info diff --git a/revdep/problems.md b/revdep/problems.md index f698c10792..91d50e75bf 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,76 +1,39 @@ -# ABHgenotypeR +# CNAIM
-* 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 +* Version: 2.1.4 +* GitHub: https://github.com/Utiligize/CNAIM +* Source code: https://github.com/cran/CNAIM +* Date/Publication: 2022-08-31 08:40:22 UTC +* Number of recursive dependencies: 81 -Run `revdepcheck::cloud_details(, "ABHgenotypeR")` for more info +Run `revdepcheck::cloud_details(, "CNAIM")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ABHgenotypeR-vignette.Rmd’ - ... - + "preprefall025TestData.csv", package = "ABHgenotypeR"), nameA = "NB", - + nameB = "OL ..." ... [TRUNCATED] - - > plotGenos(genotypes) - - 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 - - ‘ABHgenotypeR-vignette.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- 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 LazyData ... NOTE +* checking installed package size ... NOTE ``` - 'LazyData' is specified without a 'data' directory + installed size is 5.3Mb + sub-directories of 1Mb or more: + R 1.6Mb + data 1.1Mb + help 1.6Mb ``` -# actxps +# covidcast
-* Version: 1.6.0 -* GitHub: https://github.com/mattheaphy/actxps -* Source code: https://github.com/cran/actxps -* Date/Publication: 2025-01-07 13:00:02 UTC -* Number of recursive dependencies: 130 +* 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: 92 -Run `revdepcheck::cloud_details(, "actxps")` for more info +Run `revdepcheck::cloud_details(, "covidcast")` for more info
@@ -79,258 +42,96 @@ Run `revdepcheck::cloud_details(, "actxps")` for more info * checking running R code from vignettes ... ERROR ``` Errors in running code in vignettes: - when running code in ‘actxps.Rmd’ + when running code in ‘plotting-signals.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. - - ... + > cprop <- covidcast_signal(data_source = "jhu-csse", + + signal = "confirmed_cumulative_prop", start_day = "2020-07-01", + + end_day = "2020-07 ..." ... [TRUNCATED] - When sourcing ‘transactions.R’: - Error: Internal error: adjust_color() expects an input of length 1 + When sourcing ‘plotting-signals.R’: + 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 - ‘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 + ‘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 ‘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. + --- re-building ‘correlation-utils.Rmd’ using rmarkdown + --- finished re-building ‘correlation-utils.Rmd’ - 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’ + --- re-building ‘covidcast.Rmd’ using rmarkdown - SUMMARY: processing the following files failed: - ‘actxps.Rmd’ ‘misc.Rmd’ ‘transactions.Rmd’ + Quitting from covidcast.Rmd:37-45 [unnamed-chunk-1] + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + NULL + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Error: Vignette re-building failed. - Execution halted - ``` - -# adklakedata - -
- -* 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(, "adklakedata")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘adklakedata-Ex.R’ failed - The error most likely occurred in: + 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 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 ‘covidcast.Rmd’ - > ### Name: adk_lake_shapes - > ### Title: Return path to Lake Polygons Shapefile - > ### Aliases: adk_lake_shapes - > - > ### ** Examples - > - > 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 + --- re-building ‘external-data.Rmd’ using rmarkdown ``` ## In both -* checking LazyData ... NOTE - ``` - '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 ‘Introduction.Rmd’ - ... - - > tavg <- data.frame(lon = runif(100, min = 110, max = 117), - + lat = runif(100, min = 31, max = 37), value = runif(100, - + min = 20, max .... [TRUNCATED] - - > hmap <- getMap(name = "河南省", returnClass = "sf") - - When sourcing ‘Introduction.R’: - Error: package tibble not available: install first? - Execution halted - - ‘Introduction.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE +* checking data for non-ASCII characters ... NOTE ``` - Error(s) in re-building vignettes: - ... - --- 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 + Note: found 20 marked UTF-8 strings ``` -# AeRobiology +# embryogrowth
-* Version: 2.0.1 +* Version: 9.5 * GitHub: NA -* Source code: https://github.com/cran/AeRobiology -* Date/Publication: 2019-06-03 06:20:03 UTC -* Number of recursive dependencies: 97 +* Source code: https://github.com/cran/embryogrowth +* Date/Publication: 2024-08-23 07:20:02 UTC +* Number of recursive dependencies: 105 -Run `revdepcheck::cloud_details(, "AeRobiology")` for more info +Run `revdepcheck::cloud_details(, "embryogrowth")` for more info
## Newly broken -* checking running R code from vignettes ... ERROR +* checking installed package size ... NOTE ``` - 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 + installed size is 7.8Mb + sub-directories of 1Mb or more: + data 7.0Mb ``` -* checking re-building of vignette outputs ... NOTE +## In both + +* checking data for non-ASCII characters ... NOTE ``` - Error(s) in re-building vignettes: - --- re-building ‘my-vignette.Rmd’ using rmarkdown + Note: found 7267 marked UTF-8 strings ``` -# agricolaeplotr +# infer
-* Version: 0.6.0 -* GitHub: https://github.com/jensharbers/agricolaeplotr -* Source code: https://github.com/cran/agricolaeplotr -* Date/Publication: 2025-01-22 13:20:02 UTC -* Number of recursive dependencies: 143 +* 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(, "agricolaeplotr")` for more info +Run `revdepcheck::cloud_details(, "infer")` for more info
@@ -341,218 +142,61 @@ Run `revdepcheck::cloud_details(, "agricolaeplotr")` for more info 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' - + > # 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 ... - `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 ] + • visualize/viz-assume-z-p-val-left.svg + • visualize/viz-assume-z-p-val-right.svg + • visualize/viz-assume-z.svg + • visualize/viz-fit-conf-int.svg + • visualize/viz-fit-no-h0.svg + • visualize/viz-fit-p-val-both.svg + • visualize/viz-fit-p-val-left.svg + • visualize/viz-fit-p-val-right.svg Error: Test failures Execution halted ``` -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘FielDHub.Rmd’ - ... - 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 - - > plt <- plot(rcbd2) - - When sourcing ‘FielDHub.R’: - Error: unused argument (dn) - Execution halted - - ‘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 ‘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 - ``` - -# agridat - -
- -* 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(, "agridat")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘agridat-Ex.R’ failed - The error most likely occurred in: - - > ### Name: connolly.potato - > ### Title: Potato yields in single-drill plots - > ### Aliases: connolly.potato - > ### Keywords: datasets - > - > ### ** Examples - > - ... - > dat <- connolly.potato - > - > # 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 - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘agridat_graphical_gems.Rmd’ - ... - - > dat <- gomez.stripsplitplot - - > 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 - - ‘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 - -
- -* 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 +# PSCBS
-* 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 +* Version: 0.67.0 +* GitHub: https://github.com/HenrikBengtsson/PSCBS +* Source code: https://github.com/cran/PSCBS +* Date/Publication: 2024-02-17 19:10:02 UTC +* Number of recursive dependencies: 44 -Run `revdepcheck::cloud_details(, "animbook")` for more info +Run `revdepcheck::cloud_details(, "PSCBS")` for more info
## Newly broken -* checking examples ... ERROR +* checking installed package size ... NOTE ``` - 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 + installed size is 5.4Mb + sub-directories of 1Mb or more: + R 1.5Mb + data-ex 2.6Mb ``` -# ANN2 +# SimNPH
-* 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: 51 +* Version: 0.5.6 +* GitHub: https://github.com/SimNPH/SimNPH +* Source code: https://github.com/cran/SimNPH +* Date/Publication: 2025-02-20 12:20:10 UTC +* Number of recursive dependencies: 133 -Run `revdepcheck::cloud_details(, "ANN2")` for more info +Run `revdepcheck::cloud_details(, "SimNPH")` for more info
@@ -564,21273 +208,22 @@ Run `revdepcheck::cloud_details(, "ANN2")` for more info Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) - > library(ANN2) + > library(SimNPH) + Loading required package: SimDesign + Loading required package: survival > - > # Only test if not on mac - > if (tolower(Sys.info()[["sysname"]]) != "darwin") { - + test_check("ANN2") - + } + > test_check("SimNPH") + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 413 ] ... - ── 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 + ══ Failed tests ════════════════════════════════════════════════════════════════ + ── Failure ('test-report_plots.R:13:5'): if labs_from_labels works ───────────── + ggplot2::get_labs(gg)[c("x", "y")] (`actual`) not equal to list(x = "weight", y = "mpg") (`expected`). - [ FAIL 5 | WARN 1 | SKIP 4 | PASS 143 ] + `actual$x`: "wt" + `expected$x`: "weight" + + [ FAIL 1 | WARN 0 | SKIP 0 | PASS 413 ] 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 48.8Mb - sub-directories of 1Mb or more: - cereal 1.4Mb - libs 47.2Mb - ``` - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# 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: 77 - -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) - ... - -0.330681588 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 - ``` - -# APCtools - -
- -* 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(, "APCtools")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘APCtools-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_densityMatrix - > ### Title: Create a matrix of density plots - > ### Aliases: plot_densityMatrix - > - > ### ** Examples - > - > library(APCtools) - ... - 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 - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > 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... - ... - ▆ - 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 2 | WARN 51 | SKIP 0 | PASS 84 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘main_functionality.Rmd’ - ... - - > 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 ‘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 - - ‘main_functionality.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘main_functionality.Rmd’ using rmarkdown - ``` - -# 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 - - 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`). - - `actual` is NULL - `expected` is a character vector ('percentile') - - [ FAIL 3 | WARN 0 | SKIP 22 | PASS 90 ] - Error: Test failures - Execution halted - ``` - -# 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 - ``` - 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() - ... - dbl (5): IDSensor, IDStation, Altitude, Latitude, Longitude - date (2): DateStart, DateStop - - 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 whether package ‘ARPALData’ can be installed ... WARNING - ``` - 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 R code for possible problems ... NOTE - ``` - 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")) - ``` - -# arulesViz - -
- -* 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(, "arulesViz")` for more info - -
- -## Newly broken - -* checking whether package ‘arulesViz’ can be installed ... WARNING - ``` - 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. - ``` - -# asremlPlus - -
- -* 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(, "asremlPlus")` for more info - -
- -## Newly broken - -* checking whether package ‘asremlPlus’ can be installed ... WARNING - ``` - 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’. - ``` - -* checking R code for possible problems ... NOTE - ``` - 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]]) - ``` - -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘asremlPlus-Ex.R’ failed - The error most likely occurred in: - - > ### Name: LSD.frame - > ### Title: Description of an LSD frame - > ### Aliases: LSD.frame - > ### Keywords: asreml htest - > - > ### ** Examples - > - ... - + } - 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 package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘asreml’ - ``` - -# 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: 73 - -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: 87 - -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 - > - ... - > p <- autoplotly(prcomp(iris[c(1, 2, 3, 4)]), data = iris, - + colour = 'Species', label = TRUE, label.size = 3, frame = 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 . - Error in pm[[2]] : subscript out of bounds - Calls: autoplotly ... autoplotly.default -> 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(autoplotly) - > - > test_check("autoplotly") - [ FAIL 3 | WARN 1 | SKIP 0 | PASS 1 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - ▆ - 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 1 | SKIP 0 | PASS 1 ] - Error: Test failures - Execution halted - ``` - -# autoTS - -
- -* 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(, "autoTS")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... NOTE - ``` - 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 ‘autoTS_vignette.Rmd’ - ... - Warning in unzip(zipfile = "../inst/extdata/namq_10_gdp.zip", exdir = tmp_dir) : - error 1 in extracting from zip file - - > 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 ‘autoTS_vignette.R’: - Error: cannot open the connection - Execution halted - - ‘autoTS_vignette.Rmd’ using ‘UTF-8’... failed - ``` - -* checking dependencies in R code ... NOTE - ``` - 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 - ``` - -# backShift - -
- -* 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(, "backShift")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘backShift-Ex.R’ failed - The error most likely occurred in: - - > ### Name: metricsThreshold - > ### Title: Performance metrics for estimate of connectiviy matrix A. - > ### Aliases: metricsThreshold - > - > ### ** Examples - > - > # true A - ... - > 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$diff) - Calls: metricsThreshold -> unlist -> metrics - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘exampleBackShift.Rmd’ - ... - - > plotGraphEdgeAttr(estimate = Ahat.structure, plotStabSelec = TRUE, - + labels = colnames(A), thres.point = thres.pe, edgeWeights = Ahat, - + t .... [TRUNCATED] - - > metricsThresholdedA <- metricsThreshold(A, Ahat, thres = thres.pe) - - When sourcing ‘exampleBackShift.R’: - Error: unused argument (errs$diff) - Execution halted - - ‘exampleBackShift.Rmd’ using ‘UTF-8’... failed - ``` - -* checking whether package ‘backShift’ can be installed ... WARNING - ``` - 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’. - ``` - -* 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 re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘exampleBackShift.Rmd’ using rmarkdown - ``` - -## In both - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’ - ``` - -# 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) - - -``` -# 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: 73 - -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 - ``` - -# bayesforecast - -
- -* 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(, "bayesforecast")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - 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 - - > 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 whether package ‘bayesforecast’ can be installed ... WARNING - ``` - 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’. - ``` - -* checking R code for possible problems ... NOTE - ``` - mcmc_plot.varstan: possible error in is.element(NA, code): unused - argument (code) - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘ARIMA.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 163.5Mb - sub-directories of 1Mb or more: - libs 162.0Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘RcppParallel’ ‘StanHeaders’ ‘astsa’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# 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, "#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 - ``` - -* 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 82.3Mb - sub-directories of 1Mb or more: - data 1.5Mb - libs 80.1Mb - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. - ``` - -# BayesianMCPMod - -
- -* 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(, "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: - > # 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 - ... - 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 ‘Simulation_Example.Rmd’ - ... - > 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 ‘analysis_normal.R’: - Error: unused argument (c("emax", "quadratic", "exponential")) - Execution halted - - ‘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 ‘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 - ``` - -# 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: 106 - -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") - - Attaching package: 'ggplot2' - - ... - `names(expected)` is absent - ── Failure ('test-PPV_heatmap.R:1097:3'): Plot with line overlay ─────────────── - vapply(p$result$layers, function(x) class(x$geom)[1], "") (`actual`) not identical to c("GeomTile", "GeomSegment", "GeomPoint", "GeomMarkRect") (`expected`). - - `names(actual)` is a character vector ('geom_tile', 'annotate', 'annotate...3', 'geom_mark_rect') - `names(expected)` is absent - - [ FAIL 8 | WARN 56 | SKIP 4 | PASS 115 ] - Error: Test failures - Execution halted - ``` - -# BayesMallows - -
- -* Version: 2.2.3 -* GitHub: https://github.com/ocbe-uio/BayesMallows -* Source code: https://github.com/cran/BayesMallows -* Date/Publication: 2025-01-14 11:30:02 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::cloud_details(, "BayesMallows")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview - > # * https://testthat.r-lib.org/articles/special-files.html - ... - `expected` is a character vector ('interaction(chain, cluster)') - ── Failure ('test-assess_convergence.R:217:3'): assess_convergence.BayesMallowsMixtures works ── - p$labels$colour (`actual`) not equal to "cluster" (`expected`). - - `actual` is NULL - `expected` is a character vector ('cluster') - - [ FAIL 10 | WARN 0 | SKIP 10 | PASS 363 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 23.6Mb - sub-directories of 1Mb or more: - doc 2.7Mb - libs 20.0Mb - ``` - -# 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: 128 - -Run `revdepcheck::cloud_details(, "bayesplot")` for more info - -
- -## Newly broken - -* 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 - ... - ══ 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 1 | WARN 1 | SKIP 73 | PASS 1024 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - 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)) - - > 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’... OK - ‘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 - ``` - -# BCEA - -
- -* Version: 2.4.7 -* GitHub: https://github.com/n8thangreen/BCEA -* Source code: https://github.com/cran/BCEA -* Date/Publication: 2025-01-14 12:30:08 UTC -* Number of recursive dependencies: 124 - -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: bcea - > ### Title: Create Bayesian Cost-Effectiveness Analysis Object - > ### Aliases: bcea bcea.default bcea.rjags bcea.rstan bcea.bugs - > ### Keywords: manip - > - > ### ** Examples - > - ... - + # 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 - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(BCEA) - Registered S3 method overwritten by 'BCEA': - method from - plot.evppi voi - The BCEA version loaded is: 2.4.7 - - ... - 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 3 | WARN 0 | SKIP 3 | PASS 89 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘bcea.Rmd’ - ... - is.element - - - > library(purrr) - - > plot(bcea_smoke) - - ... - - ‘CEriskav.Rmd’ using ‘UTF-8’... OK - ‘bcea.Rmd’ using ‘UTF-8’... failed - ‘ceac.Rmd’ using ‘UTF-8’... OK - ‘ceef.Rmd’ using ‘UTF-8’... OK - ‘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 whether package ‘BCEA’ can be installed ... WARNING - ``` - 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$k) - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘CEriskav.Rmd’ using rmarkdown - ``` - -# BEAMR - -
- -* Version: 1.1.0 -* GitHub: https://github.com/annaSeffernick/BEAMR -* Source code: https://github.com/cran/BEAMR -* Date/Publication: 2024-07-27 16:00:06 UTC -* Number of recursive dependencies: 152 - -Run `revdepcheck::cloud_details(, "BEAMR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘BEAMR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: check_beam_specs - > ### Title: Check that beam.specs satisfies all necessary conditions - > ### Aliases: check_beam_specs - > - > ### ** Examples - > - > data(beam_dat) - > data(beam_specs) - > test_specs <- check_beam_specs(beam_specs, names(beam_dat$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 - -
- -* 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: 99 - -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, "#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 - ‘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 - ``` - -# biclust - -
- -* 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(, "biclust")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘biclust-Ex.R’ failed - The error most likely occurred in: - - > ### 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 - > - > #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 - ``` - -* checking whether package ‘biclust’ can be installed ... WARNING - ``` - 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) - ``` - -# 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: 83 - -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 - - 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$P)) + 0.5. - Classes differ: 'mapped_discrete'/'numeric' is not 'numeric' - ── Failure ('test-autoplot_biclustermd.R:7:3'): autoplot_biclustermd() correctly plots cluster lines ── - ap$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: 118 - -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 - ``` - -# 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: 90 - -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 - ``` - -# 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: 103 - -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 - ``` - -# 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: 101 - -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 - ``` - -# 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. - ``` - -# 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: 76 - -Run `revdepcheck::cloud_details(, "CausalImpact")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘CausalImpact-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CausalImpact - > ### Title: Inferring causal impact using structural time-series models - > ### Aliases: CausalImpact - > - > ### ** Examples - > - > # Example 1 - ... - > 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 ‘CausalImpact_import_test.R’ - Running the tests in ‘tests/CausalImpact_import_test.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 - > # - > # 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 ‘CausalImpact.Rmd’ - ... - - > pre.period <- c(1, 70) - - > post.period <- c(71, 100) - - > impact <- CausalImpact(data, pre.period, post.period) - - When sourcing ‘CausalImpact.R’: - Error: unused argument (c("B", "M", "K")) - Execution halted - - ‘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 ‘CausalImpact.Rmd’ using rmarkdown - ``` - -# celltrackR - -
- -* 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(, "celltrackR")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... NOTE - ``` - 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() - 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: 0.76 -* GitHub: NA -* Source code: https://github.com/cran/chillR -* Date/Publication: 2024-11-14 09:40:02 UTC -* Number of recursive dependencies: 137 - -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: interpolate_gaps_hourly - > ### Title: Interpolate gaps in hourly temperature records - > ### Aliases: interpolate_gaps_hourly - > ### Keywords: utility - > - > ### ** Examples - > - > - > - > 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 - -
- -* 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: 145 - -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. - ``` - -# cjoint - -
- -* Version: 2.1.1 -* GitHub: NA -* 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(, "cjoint")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘cjoint-Ex.R’ failed - The error most likely occurred in: - - > ### Name: japan2014conjoint - > ### Title: Japan 2014 Conjoint Experiment Dataset from Horiuchi et. al. - > ### (2014) - > ### Aliases: japan2014conjoint - > ### Keywords: datasets - > - > ### ** Examples - ... - > # 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 tests ... ERROR - ``` - 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 whether package ‘cjoint’ can be installed ... WARNING - ``` - 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 data for non-ASCII characters ... NOTE - ``` - Note: found 29 marked UTF-8 strings - ``` - -# clickstream - -
- -* 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(, "clickstream")` for more info - -
- -## Newly broken - -* checking whether package ‘clickstream’ can be installed ... WARNING - ``` - 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. - ``` - -# 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: 120 - -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 pm[[2]] : subscript out of bounds - Calls: scatterplotClinData -> 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(clinDataReview) - > - > test_check("clinDataReview") - adding: report.html (deflated 63%) - adding: report_dependencies16a96c1c4532/ (stored 0%) - adding: report_dependencies16a96c1c4532/file16a9248230f.html (deflated 8%) - ... - 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 31 | WARN 0 | SKIP 31 | PASS 466 ] - 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: - subscript out of bounds - ... - --- 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 - ``` - -# 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 - -
- -* 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: 110 - -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 - ``` - -# CLONETv2 - -
- -* 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(, "CLONETv2")` for more info - -
- -## Newly broken - -* checking whether package ‘CLONETv2’ can be installed ... WARNING - ``` - 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. - ``` - -# 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: 113 - -Run `revdepcheck::cloud_details(, "ClusROC")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ClusROC-Ex.R’ failed - The error most likely occurred in: - - > ### Name: clus_lme - > ### Title: Linear Mixed-Effects Models for a continuous diagnostic test or - > ### a biomarker (or a classifier). - > ### Aliases: clus_lme - > - > ### ** Examples - > - ... - 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 - ``` - -* 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: 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(, "clustcurv")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘clustcurv.Rmd’ - ... - > 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 . - - When sourcing ‘clustcurv.R’: - Error: subscript out of bounds - Execution halted - - ‘clustcurv.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘clustcurv.Rmd’ using rmarkdown - - 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 file failed: - ‘clustcurv.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# clustMD - -
- -* 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 - -
- -* 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 - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘cnmap-Ex.R’ failed - The error most likely occurred in: - - > ### Name: getMap - > ### Title: China Map Data from AutoNavi Map - > ### Aliases: getMap - > - > ### ** Examples - > - > 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 running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Introduction.Rmd’ - ... - > library(sf) - Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.4.0; sf_use_s2() is TRUE - - > library(cnmap) - - > map1 <- getMap(name = "中国") - - When sourcing ‘Introduction.R’: - Error: package tibble not available: install first? - 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 - - 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’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# 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: 66 - -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| - --- - - --- - ``` - -# codez - -
- -* Version: 1.0.0 -* GitHub: NA -* 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(, "codez")` for more info - -
- -## Newly broken - -* checking whether package ‘codez’ can be installed ... WARNING - ``` - 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 - -
- -* 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 - ``` - -# colorrepel - -
- -* 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(, "colorrepel")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘colorrepel-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggplotly_background - > ### Title: Prepare ggplot object to ggplotly-compatible layer and image - > ### layer - > ### Aliases: ggplotly_background - > - > ### ** Examples - > - > 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 - ``` - -# 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: 115 - -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: 128 - -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 - ``` - -# 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: 80 - -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’ - ... - - > 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: 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 - ``` - -* 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: 90 - -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 32 ] - - ... - 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 - ``` - -# 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: 92 - -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’ - ... - • horizontal = TRUE - ℹ Did you misspell an argument name? - - 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 - ``` - -# creditmodel - -
- -* 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(, "creditmodel")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘creditmodel-Ex.R’ failed - The error most likely occurred in: - - > ### Name: char_to_num - > ### Title: character to number - > ### Aliases: char_to_num - > - > ### ** Examples - > - > 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 - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘introduction.Rmd’ - ... - > library(creditmodel) - Package 'creditmodel' version 1.3.1 - - > 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 - - ‘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 - - 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’ - - 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 7.6Mb - sub-directories of 1Mb or more: - R 1.5Mb - data 5.5Mb - ``` - -# cricketr - -
- -* 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(, "cricketr")` for more info - -
- -## Newly broken - -* checking whether package ‘cricketr’ can be installed ... WARNING - ``` - 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) - ``` - -# 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: 116 - -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 - ``` - -# 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 - -
- -* 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: 99 - -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: 132 - -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 ‘cb6interactive.Rmd’ - ... - + ymax .... [TRUNCATED] - Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0. - ℹ Please use `linewidth` instead. - - > ts_interactive <- highlight(ggplotly(ts_static, width = 600, - + height = 300), on = "plotly_selected", opacityDim = 0.012) - - ... - 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’... OK - ‘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 - ``` - -# DAISIE - -
- -* 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(, "DAISIE")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘DAISIE-Ex.R’ failed - The error most likely occurred in: - - > ### Name: DAISIE_plot_input - > ### Title: DAISIE tree plot - > ### Aliases: DAISIE_plot_input - > - > ### ** Examples - > - > - ... - 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 - ``` - -## In both - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘doMC’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 37.6Mb - sub-directories of 1Mb or more: - libs 35.5Mb - ``` - -# DAISIEprep - -
- -* Version: 1.0.0 -* GitHub: https://github.com/joshwlambert/DAISIEprep -* Source code: https://github.com/cran/DAISIEprep -* Date/Publication: 2024-12-18 00:20:02 UTC -* Number of recursive dependencies: 148 - -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 4 | SKIP 14 | PASS 2235 ] - - ══ 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 4 | SKIP 14 | PASS 2235 ] - Error: Test failures - Execution halted - ``` - -# daltoolbox - -
- -* 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(, "daltoolbox")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘daltoolbox-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_ts_pred - > ### Title: Plot a time series chart with predictions - > ### Aliases: plot_ts_pred - > - > ### ** Examples - > - > data(sin_data) - ... - > 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$coef)) - Calls: fit -> fit.ts_arima - Execution halted - ``` - -* checking whether package ‘daltoolbox’ can be installed ... WARNING - ``` - Found the following significant warnings: - Note: possible error in 'is.element("drift", names(obj$model$coef))': unused argument (names(obj$model$coef)) - See ‘/tmp/workdir/daltoolbox/new/daltoolbox.Rcheck/00install.out’ for details. - Information on the location(s) of code generating the ‘Note’s can be - obtained by re-running with environment variable R_KEEP_PKG_SOURCE set - to ‘yes’. - ``` - -* checking R code for possible problems ... NOTE - ``` - fit.ts_arima: possible error in is.element("drift", - names(obj$model$coef)): unused argument (names(obj$model$coef)) - ``` - -# dawaR - -
- -* Version: 0.2.7 -* GitHub: https://github.com/aleksanderbl29/dawaR -* Source code: https://github.com/cran/dawaR -* Date/Publication: 2024-12-08 00:00:06 UTC -* Number of recursive dependencies: 150 - -Run `revdepcheck::cloud_details(, "dawaR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dawaR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: get_data - > ### Title: Get data from section - > ### Aliases: get_data - > - > ### ** Examples - > - > if (connection_check()) { - ... - + x <- get_data("regioner") - + head(x) - + } - ✖ Request failed: HTTP 504 Gateway Timeout. - ✖ The API returned a error. - ✖ No content will be returned - Error in do.call(rbind.data.frame, response) : - second argument must be a list - Calls: get_data -> do.call - Execution halted - ``` - -## Newly fixed - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview - > # * https://testthat.r-lib.org/articles/special-files.html - ... - ── Error ('test-get_data.R:55:5'): get_data(section = 'regioner') snapshot ───── - Error in `do.call(rbind.data.frame, response)`: second argument must be a list - Backtrace: - ▆ - 1. └─testthat::expect_snapshot(get_data(section = "regioner")) at test-get_data.R:55:5 - 2. └─rlang::cnd_signal(state$error) - - [ FAIL 1 | WARN 0 | SKIP 48 | PASS 10 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- 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 - ... - --- 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’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# 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 - ``` - 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$MaxQ) - Error in is.element("Potential.contaminant", colnames(infile)) : - unused argument (colnames(infile)) - Calls: MaxQprotein -> removeConRev - Execution halted - ``` - -* checking whether package ‘DDPNA’ can be installed ... WARNING - ``` - Found the following significant warnings: - Note: possible error in 'is.element("Potential.contaminant", ': unused argument (colnames(infile)) - Note: possible error in 'is.element("+", unique(infile$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$Reverse)) - Note: possible error in 'is.element(IDname, colname)': unused argument (colname) - Note: possible error in 'is.element(QuanCol, colname)': unused argument (colname) - See ‘/tmp/workdir/DDPNA/new/DDPNA.Rcheck/00install.out’ for details. - Information on the location(s) of code generating the ‘Note’s can be - obtained by re-running with environment variable R_KEEP_PKG_SOURCE set - to ‘yes’. - ``` - -* checking R code for possible problems ... NOTE - ``` - MaxQprotein : removeConRev: possible error in - is.element("Potential.contaminant", colnames(infile)): unused - argument (colnames(infile)) - MaxQprotein : removeConRev: possible error in is.element("+", - unique(infile$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) - ``` - -# Deducer - -
- -* 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(, "Deducer")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘Deducer-Ex.R’ failed - The error most likely occurred in: - - > ### Name: sort.data.frame - > ### Title: Sort Data - > ### Aliases: sort.data.frame - > - > ### ** Examples - > - > 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 - ``` - -* 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 R code for possible problems ... NOTE - ``` - sort.data.frame: possible error in is.element(substring(formc, 1, 1), - c("+", "-")): unused argument (c("+", "-")) - ``` - -# deeptime - -
- -* 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(, "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 ‘desplot_examples.Rmd’ - ... - > if (is.element("x", names(yates.oats))) yates.oats <- transform(yates.oats, - + col = x, row = y) - - > 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 - - ‘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 ‘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 - ``` - -# diceR - -
- -* 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(, "diceR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘diceR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: graphs - > ### Title: Graphical Displays - > ### Aliases: graphs graph_cdf graph_delta_area graph_heatmap graph_tracking - > ### graph_all - > - > ### ** Examples - > - ... - 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 ‘overview.Rmd’ - ... - > hm <- graph_heatmap(pam.4) - - 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 - - ‘overview.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- re-building ‘overview.Rmd’ using rmarkdown - - 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: - ‘overview.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# 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: 81 - -Run `revdepcheck::cloud_details(, "directlabels")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - 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: 0.5.0 -* GitHub: https://github.com/mitchelloharawild/distributional -* Source code: https://github.com/cran/distributional -* Date/Publication: 2024-09-17 06:20:02 UTC -* Number of recursive dependencies: 120 - -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: 98 - -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 - - Attaching package: 'ggplot2' - - The following object is masked from 'package:base': - ... - 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 29 | WARN 0 | SKIP 0 | PASS 252 ] - Error: Test failures - Execution halted - ``` - -# divent - -
- -* 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(, "divent")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘divent-Ex.R’ failed - The error most likely occurred in: - - > ### 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 - ... - 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 ‘divent.Rmd’ - ... - - > autoplot(paracou_6_abd[1, ]) - - 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 - - ‘divent.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - ... - --- 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 - ``` - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘dbmss’ - ``` - -# doBy - -
- -* 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(, "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 ‘doBy-Ex.R’ failed - The error most likely occurred in: - - > ### Name: by-order - > ### Title: Ordering (sorting) rows of a data frame - > ### Aliases: by-order order_by orderBy - > ### Keywords: utilities - > - > ### ** Examples - > - > - > orderBy(~ conc + Treatment, CO2) - Error in is.element(substring(formc, 1, 1), c("+", "-")) : - unused argument (c("+", "-")) - Calls: orderBy - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘doby.rmd’ - ... - > myfun1 <- function(x) { - + c(m = mean(x), s = sd(x)) - + } - - > summaryBy(cbind(mpg, cyl, lh = log(hp)) ~ vs, data = mtcars, - + FUN = myfun1) - - ... - > 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 - - ‘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 8.2Mb - sub-directories of 1Mb or more: - 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 - ``` - -# DoseFinding - -
- -* 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(, "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 ‘testgFit.R’ - Running the tests in ‘tests/testgFit.R’ failed. - Complete output: - > 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 - ``` - -* checking running R code from vignettes ... ERROR - ``` - 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 - - ‘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 whether package ‘DoseFinding’ can be installed ... WARNING - ``` - 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 re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘analysis_normal.Rmd’ using rmarkdown - ``` - -# dotsViolin - -
- -* 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(, "dotsViolin")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - 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 - > - ... - 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 - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 2 marked UTF-8 strings - ``` - -# dr4pl - -
- -* 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(, "dr4pl")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘dr4pl-Ex.R’ failed - The error most likely occurred in: - - > ### Name: IC - > ### Title: Obtain Inhibitory Concentrations (IC) of a dose-response curve - > ### Aliases: IC - > - > ### ** Examples - > - > 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 ‘walk_through_in_R.Rmd’ - ... - + }, 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 ‘walk_through_in_R.R’: - Error: unused argument (types.method.init) - Execution halted - - ‘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 ‘dr4pl_derivatives.Rmd’ using rmarkdown - --- finished re-building ‘dr4pl_derivatives.Rmd’ - - --- 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: \& - ``` - -# DRomics - -
- -* 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(, "DRomics")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘DRomics-Ex.R’ failed - The error most likely occurred in: - - > ### Name: bmdfilter - > ### Title: Filtering BMDs according to estimation quality - > ### Aliases: bmdfilter - > - > ### ** Examples - > - > - ... - > - > ### (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 5.8Mb - sub-directories of 1Mb or more: - doc 2.5Mb - ``` - -# drpop - -
- -* 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(, "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 - -
- -## 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 - ``` - -# dymo - -
- -* 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(, "dymo")` for more info - -
- -## Newly broken - -* checking whether package ‘dymo’ can be installed ... WARNING - ``` - 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 Rd files ... WARNING - ``` - 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 installed package size ... NOTE - ``` - 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 ‘linearSDE.Rmd’ using rmarkdown - --- finished re-building ‘linearSDE.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. - - ... - {bm}%bm^^M - ! ==> Fatal error occurred, no output PDF file produced! - --- failed re-building ‘NonlinearContinuousTimeModels.Rnw’ - - SUMMARY: processing the following files failed: - ‘InstallationForDevelopers.Rnw’ ‘InstallationForUsers.Rnw’ - ‘LinearDiscreteTimeModels.Rnw’ ‘NonlinearContinuousTimeModels.Rnw’ - - Error: Vignette re-building failed. - 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: 155 - -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 - ``` - -# 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$x (`actual`) not equal to "sample" (`expected`). - - `actual` is NULL - `expected` is a character vector ('sample') - - [ FAIL 1 | WARN 0 | SKIP 19 | PASS 43 ] - Error: Test failures - Execution halted - ``` - -# entropart - -
- -* Version: 1.6-15 -* GitHub: https://github.com/EricMarcon/entropart -* Source code: https://github.com/cran/entropart -* Date/Publication: 2024-08-26 19:30:09 UTC -* Number of recursive dependencies: 128 - -Run `revdepcheck::cloud_details(, "entropart")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘entropart-Ex.R’ failed - The error most likely occurred in: - - > ### Name: Accumulation - > ### Title: Diversity accumulation. - > ### Aliases: DivAC EntAC as.AccumCurve is.AccumCurve autoplot.AccumCurve - > ### plot.AccumCurve - > - > ### ** Examples - > - ... - 11. │ └─base::withCallingHandlers(...) - 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) - 13. └─l$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 - ``` - -# 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: 129 - -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: 0.5.0 -* GitHub: NA -* Source code: https://github.com/cran/EQUALSTATS -* Date/Publication: 2024-09-23 08:30:02 UTC -* Number of recursive dependencies: 131 - -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’ - ``` - -# esci - -
- -* 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(, "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$interaction, - + effect_size = "mean" - + ) - Warning: Using size for a discrete variable is not advised. - Warning: Using alpha for a discrete variable is not advised. - Error in use_defaults(..., self = self) : - unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, 90, NULL, c(0, 2.75, 0, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, NULL, 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, - Calls: ... -> -> compute_geom_2 -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(esci) - > - > test_check("esci") - [1] "WARNING: ratio-scale scores cannot be negative" - [1] "WARNING: ratio-scale scores cannot be negative" - [1] "WARNING: ratio-scale scores cannot be negative" - ... - 17. │ └─self$geom$use_defaults(...) - 18. └─base::.handleSimpleError(...) - 19. └─rlang (local) h(simpleError(msg, call)) - 20. └─handlers[[1L]](cnd) - 21. └─cli::cli_abort(...) - 22. └─rlang::abort(...) - - [ FAIL 3 | WARN 0 | SKIP 52 | PASS 2889 ] - 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: 166 - -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: 100 - -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$ymax (`actual`) not equal to "ci_upper" (`expected`). - - `actual` is NULL - `expected` is a character vector ('ci_upper') - - [ FAIL 6 | WARN 0 | SKIP 0 | PASS 258 ] - Error: Test failures - Execution halted - ``` - -# expirest - -
- -* Version: 0.1.6 -* GitHub: https://github.com/piusdahinden/expirest -* Source code: https://github.com/cran/expirest -* Date/Publication: 2024-03-25 16:30:02 UTC -* Number of recursive dependencies: 45 - -Run `revdepcheck::cloud_details(, "expirest")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(expirest) - > - > test_check("expirest") - [ FAIL 9 | WARN 0 | SKIP 0 | PASS 1122 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - ── Failure ('test-plot_expirest_wisle.R:260:3'): plot_expirest_wisle_succeeds ── - tmp4l2[["Graph"]]$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: 1.0.2 -* GitHub: https://github.com/PERSIMUNE/explainer -* Source code: https://github.com/cran/explainer -* Date/Publication: 2024-09-30 17:30:02 UTC -* Number of recursive dependencies: 186 - -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. - ``` - -# 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: 79 - -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 - ``` - -# 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: 113 - -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] 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, "#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 - ``` - -* 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: 0.5.0 -* GitHub: https://github.com/tidyverts/fabletools -* Source code: https://github.com/cran/fabletools -* Date/Publication: 2024-09-17 07:30:02 UTC -* Number of recursive dependencies: 107 - -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, "#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 - ``` - -* 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 266 ] - Error: Test failures - 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: 86 - -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 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 2 | SKIP 0 | PASS 312 ] - Error: Test failures - Execution halted - ``` - -# FCPS - -
- -* 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(, "FCPS")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘FCPS-Ex.R’ failed - The error most likely occurred in: - - > ### Name: SOTAclustering - > ### Title: SOTA Clustering - > ### Aliases: SOTAclustering sotaClustering - > ### Keywords: SOTAclustering - > - > ### ** Examples - > - > #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 11.1Mb - sub-directories of 1Mb or more: - data 6.5Mb - doc 3.9Mb - ``` - -# fdANOVA - -
- -* 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(, "fdANOVA")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘fdANOVA-Ex.R’ failed - The error most likely occurred in: - - > ### 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))) - > - > # 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 - ``` - -# 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: 92 - -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: 0.4.1 -* GitHub: https://github.com/tidyverts/feasts -* Source code: https://github.com/cran/feasts -* Date/Publication: 2024-09-25 23:40:02 UTC -* Number of recursive dependencies: 100 - -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 100 ] - - ... - ── 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 100 ] - Error: Test failures - 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: 106 - -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, "#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 - ``` - -# 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: 133 - -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$X) - > plot(fit, par="Lambda") - Scale for colour is already present. - Adding another scale for colour, which will replace the existing scale. - Error in use_defaults(..., self = self) : - unused argument (theme = list(list("black", 0.5, 1, "butt", FALSE, "black", TRUE), list("white", "black", 0.5, 1, TRUE), list("", "plain", "black", 11, 0.5, 0.5, 0, 0.9, c(0, 0, 0, 0), FALSE, TRUE), list(NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list("black", "white", "#3366FF", 0.5, 0.5, 1, 1, "", 3.86605783866058, 1.5, 19, TRUE), 5.5, c(5.5, 5.5, 5.5, 5.5), NULL, NULL, list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.75, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, - NULL, 0, NULL, NULL, c(0, 0, 2.75, 0), NULL, TRUE), NULL, list(), NULL, list(NULL, NULL, NULL, NULL, NULL, 1, -90, NULL, c(0, 0, 0, 2.75), NULL, TRUE), list(NULL, NULL, "#4D4D4DFF", 0.8, NULL, NULL, NULL, NULL, NULL, NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 1, NULL, NULL, c(2.2, 0, 0, 0), NULL, TRUE), list(NULL, NULL, NULL, NULL, NULL, 0, NULL, NULL, c(0, 0, 2.2, 0), NULL, TRUE), NULL, list(NULL, NULL, NULL, NULL, 1, NULL, NULL, NULL, c(0, 2.2, 0, 0), NULL, TRUE), N - Calls: ... -> -> compute_geom_2 -> - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(fido) - > - > #Sys.setenv(KMP_DUPLICATE_LIB_OK="TRUE") - > test_check("fido") - [1] 0.27980164 -0.69169550 -0.53205652 0.11488451 -0.42419872 2.20261388 - [7] -1.62190133 -0.90893172 0.07891428 0.75060681 0.43593605 0.26819442 - ... - 21. └─base::Map(...) - 22. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE) - 23. └─ggplot2 (local) ``(layer = dots[[1L]][[1L]], df = dots[[2L]][[1L]]) - 24. └─layer$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 106.6Mb - sub-directories of 1Mb or more: - data 4.0Mb - libs 100.8Mb - ``` - -* 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 - ``` - -# FielDHub - -
- -* 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(, "FielDHub")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - 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) - - ... - - ‘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 re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘RCBD_augmented.Rmd’ using rmarkdown - - 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’ - - --- re-building ‘alpha_lattice.Rmd’ using rmarkdown - - ... - --- 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’ - - 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: - R 1.5Mb - doc 1.8Mb - help 1.1Mb - ``` - -# figuRes2 - -
- -* 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(, "figuRes2")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘figuRes2-Ex.R’ failed - The error most likely occurred in: - - > ### 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 - > - ... - ▆ - 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 - -
- -* 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: 150 - -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’ - ... - - > kmsurvplot <- ggsurvplot(km) - - > kmsurvplot + xlab("Time from diagnosis (years)") - Warning in eval(ei, envir) : - Incompatible methods ("+.ggsurv", "+.gg") for "+" - - When sourcing ‘standsurv.R’: - Error: non-numeric argument to binary operator - 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: - non-numeric argument to binary operator - --- 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: 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 11.2Mb - sub-directories of 1Mb or more: - doc 9.1Mb - libs 1.4Mb - ``` - -# forestmodel - -
- -* Version: 0.6.2 -* GitHub: NA -* 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(, "forestmodel")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘forestmodel-Ex.R’ failed - The error most likely occurred in: - - > ### Name: forest_rma - > ### Title: Generate a forest plot from a meta-analysis - > ### Aliases: forest_rma - > - > ### ** Examples - > - > if (require("metafor")) { - ... - Loading required package: metadat - Loading required package: numDeriv - - Loading the 'metafor' package (version 4.6-0). For an - introduction to the package please type: help(metafor) - - 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 - ``` - -* checking whether package ‘forestmodel’ can be installed ... WARNING - ``` - 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 LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# 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 - - 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 - ``` - -# gapmap - -
- -* 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(, "gapmap")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gapmap-Ex.R’ failed - The error most likely occurred in: - - > ### Name: gapmap - > ### Title: Function to draw a gapped cluster heatmap - > ### Aliases: gapmap - > - > ### ** Examples - > - > set.seed(1234) - ... - 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 - ``` - -* checking running R code from vignettes ... ERROR - ``` - 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 - . - - When sourcing ‘simple_example.R’: - Error: The `panel.margin` argument of `theme()` was deprecated in ggplot2 2.2.0 - ... - . - - 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 - - ‘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 ‘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’ - ... - 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 files failed: - ‘simple_example.Rmd’ ‘tcga_example.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# gapminder - -
- -* 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(, "gapminder")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘gapminder-Ex.R’ failed - The error most likely occurred in: - - > ### Name: country_colors - > ### Title: Gapminder color schemes. - > ### Aliases: country_colors continent_colors - > ### Keywords: datasets - > - > ### ** Examples - > - ... - 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 ‘gapminder.Rmd’ - ... - - > head(continent_colors) - Africa Americas Asia Europe Oceania - "#7F3B08" "#A50026" "#40004B" "#276419" "#313695" - - > knitr::include_graphics("../man/figures/gapminder-color-scheme-ggplot2.png") - - When sourcing ‘gapminder.R’: - Error: Cannot find the file(s): "../man/figures/gapminder-color-scheme-ggplot2.png" - Execution halted - - ‘gapminder.Rmd’ using ‘UTF-8’... failed - ``` - -# GEInter - -
- -* 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(, "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 ‘GEInter-Ex.R’ failed - The error most likely occurred in: - - > ### 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 - ... - > - > ##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 - -
- -* 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: 105 - -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: 0.1.5 -* GitHub: https://github.com/AllanCameron/geomtextpath -* Source code: https://github.com/cran/geomtextpath -* Date/Publication: 2025-01-14 17:40:02 UTC -* Number of recursive dependencies: 93 - -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(...) - 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 - - 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 ──────────────── - 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 - ``` - -# ggalign - -
- -* 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(, "ggalign")` for more info - -
- -## Newly broken - -* checking for code/documentation mismatches ... WARNING - ``` - 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 Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘ComplexHeatmap’, ‘pheatmap’ - ``` - -# 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: 145 - -Run `revdepcheck::cloud_details(, "GGally")` for more info - -
- -## Newly broken - -* 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") - + } - ... - `expected` is a character vector ('tip') - ── Failure ('test-ggsurv.R:26:3'): multiple ──────────────────────────────────── - !is.null(a$labels$group) is not TRUE - - `actual`: FALSE - `expected`: TRUE - - [ FAIL 3 | WARN 1 | SKIP 26 | PASS 477 ] - 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: 96 - -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 - - 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) - 5. └─args$renderer(frames_vars$frame_source, args$fps) - 6. └─gganimate:::png_dim(frames[1]) - 7. └─cli::cli_abort("Provided file ({file}) does not exist") - 8. └─rlang::abort(...) - - [ FAIL 1 | WARN 3 | SKIP 1 | PASS 5 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘gganimate.Rmd’ - ... - Theme element `panel.grid.major.y` is missing - Theme element `panel.grid.major.x` is missing - Warning: Failed to plot frame - Caused by error in `UseMethod()`: - ! no applicable method for 'element_grob' applied to an object of class "NULL" - - When sourcing ‘gganimate.R’: - Error: Provided file (/tmp/Rtmp2TPR8x/1a1142709f90/gganim_plot0001.png) does - not exist - Execution halted - - ‘gganimate.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘gganimate.Rmd’ using rmarkdown - ``` - -# ggblanket - -
- -* Version: 12.1.0 -* GitHub: https://github.com/davidhodge931/ggblanket -* Source code: https://github.com/cran/ggblanket -* Date/Publication: 2025-01-27 09:00:12 UTC -* Number of recursive dependencies: 111 - -Run `revdepcheck::cloud_details(, "ggblanket")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggblanket-Ex.R’ failed - The error most likely occurred in: - - > ### Name: annotate_axis_line - > ### Title: Replace a axis line with an annotated segment - > ### Aliases: annotate_axis_line - > - > ### ** Examples - > - > library(dplyr) - ... - 25. │ │ └─rlang::list2(...) - 26. │ └─scales::alpha(coord$colour, coord$alpha) - 27. │ └─farver::decode_colour(colour, alpha = TRUE) - 28. │ └─farver:::decode_c(...) - 29. └─base::.handleSimpleError(``, "Unknown colour name: ~", base::quote(NULL)) - 30. └─rlang (local) h(simpleError(msg, call)) - 31. └─handlers[[1L]](cnd) - 32. └─cli::cli_abort(...) - 33. └─rlang::abort(...) - Execution halted - ``` - -# ggdark - -
- -* Version: 0.2.1 -* GitHub: NA -* Source code: https://github.com/cran/ggdark -* Date/Publication: 2019-01-11 17:30:06 UTC -* Number of recursive dependencies: 45 - -Run `revdepcheck::cloud_details(, "ggdark")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggdark-Ex.R’ failed - The error most likely occurred in: - - > ### Name: dark_mode - > ### Title: Activate dark mode on a 'ggplot2' theme - > ### Aliases: dark_mode - > - > ### ** Examples - > - > library(ggplot2) - ... - > - > p1 <- ggplot(iris, aes(Sepal.Width, Sepal.Length, color = Species)) + - + geom_point() - > - > p1 # theme returned by theme_get() - > p1 + dark_mode() # activate dark mode on theme returned by theme_get() - Error in match(x, table, nomatch = 0L) : - 'match' requires vector arguments - Calls: dark_mode -> %in% - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggdark) - > - > test_check("ggdark") - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ] - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ... - ── Error ('test_dark_mode.R:10:1'): (code run outside of `test_that()`) ──────── - Error in `match(x, table, nomatch = 0L)`: 'match' requires vector arguments - Backtrace: - ▆ - 1. └─ggdark::dark_mode(light_theme) at test_dark_mode.R:10:1 - 2. └─geoms[["GeomPoint"]]$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 - ``` - -# 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 - -
- -* 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: 126 - -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, "#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 - ``` - -* 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, "#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 - ‘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 - ``` - -# 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: 94 - -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: compare - > ### Title: compare - > ### Aliases: compare - > - > ### ** Examples - > - > 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 - ``` - -# 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: 218 - -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: ggInterval_scatter - > ### Title: scatter plot for two continuous interval data - > ### Aliases: ggInterval_scatter - > - > ### ** Examples - > - > 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 - ``` - -# ggfixest - -
- -* 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(, "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) - ... - 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: 5 out of 103 tests failed - In addition: There were 11 warnings (use warnings() to see them) - Execution halted - ``` - -# 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 27.3Mb - sub-directories of 1Mb or more: - R 1.0Mb - 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: 122 - -Run `revdepcheck::cloud_details(, "ggformula")` for more info - -
- -## Newly broken - -* 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 - ``` - -## 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: 124 - -Run `revdepcheck::cloud_details(, "ggfortify")` 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) - > - > suppressWarnings(RNGversion("3.5.0")) - > set.seed(1, sample.kind = "Rejection") - > - > test_check('ggfortify') - Loading required package: ggfortify - ... - - 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 - ``` - -# ggh4x - -
- -* 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(, "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 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 - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(ggh4x) - Loading required package: ggplot2 - - Attaching package: 'ggplot2' - - 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 0 | SKIP 15 | PASS 663 ] - Error: Test failures - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘Miscellaneous.Rmd’ - ... - + aest .... [TRUNCATED] - - > ggplot(diamonds, aes(price, carat, colour = clarity)) + - + geom_point(shape = ".") + scale_colour_brewer(palette = "Dark2", - + guide = "stri ..." ... [TRUNCATED] - - 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’... failed - ‘Statistics.Rmd’ using ‘UTF-8’... OK - ‘ggh4x.Rmd’ using ‘UTF-8’... OK - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘Facets.Rmd’ using rmarkdown - ``` - -# 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 - - Attaching package: 'ggplot2' - - The following object is masked from 'package:base': - ... - 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 - ``` - -# ggiraph - -
- -* Version: 0.8.12 -* GitHub: https://github.com/davidgohel/ggiraph -* Source code: https://github.com/cran/ggiraph -* Date/Publication: 2025-01-08 11:10:02 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: geom_path_interactive - > ### Title: Create interactive observations connections - > ### Aliases: geom_path_interactive geom_line_interactive - > ### geom_step_interactive - > - > ### ** Examples - > - ... - 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 - ``` - -* 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 - Attaching package: 'ggplot2' - ... - 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 - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.1Mb - sub-directories of 1Mb or more: - R 1.5Mb - libs 5.2Mb - ``` - -# ggmap - -
- -* 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(, "ggmap")` for more info - -
- -## Newly broken - -* checking whether package ‘ggmap’ can be installed ... WARNING - ``` - 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. - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.4Mb - sub-directories of 1Mb or more: - data 7.0Mb - ``` - -# ggmcmc - -
- -* 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(, "ggmcmc")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggmcmc-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggs_geweke - > ### Title: Dotplot of the Geweke diagnostic, the standard Z-score - > ### Aliases: ggs_geweke - > - > ### ** Examples - > - > 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 - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘using_ggmcmc.Rmd’ - ... - - > ggs_crosscorrelation(S) - - > ggs_Rhat(S) + xlab("R_hat") - - > ggs_geweke(S) - - ... - + 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 - - ‘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 ‘using_ggmcmc.Rmd’ using rmarkdown - ``` - -# 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: 122 - -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 - - 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, "#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 - ``` - -* 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: 'ggplot2' - ... - 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: 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 - ‘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 - ``` - -# 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: 50 - -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. │ └─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 - ``` - -# 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 - ``` - -# 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 - ``` - -# 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: 91 - -Run `revdepcheck::cloud_details(, "ggpubr")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - 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': - ... - [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 - ``` - -# 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: 68 - -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) - - 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(...) - - [ 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: 0.8.5 -* 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 - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggseqplot-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ggseqtrplot - > ### Title: Sequence Transition Rate Plot - > ### Aliases: ggseqtrplot - > - > ### ** Examples - > - > # Use example data from TraMineR: biofam data set - ... - 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 - ``` - -* 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 2.2-11 (Built: 2024-12-09) - 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 16 | 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’ - ... - 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: 0.3.1 -* 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(, "ggside")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘ggside-Ex.R’ failed - The error most likely occurred in: - - > ### Name: geom_xsidebar - > ### Title: Side bar Charts - > ### Aliases: geom_xsidebar geom_*sidebar geom_ysidebar geom_xsidecol - > ### geom_ysidecol - > - > ### ** Examples - > - ... - + 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 ‘ggside_aes_mapping.Rmd’ - ... - +.gg ggplot2 - - > p <- ggplot(mpg, aes(displ, hwy, colour = class)) + - + geom_point(size = 2) + theme_bw() - - > 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 - - ‘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 ‘ggside_aes_mapping.Rmd’ using rmarkdown - - 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’ - - --- re-building ‘ggside_basic_usage.Rmd’ using rmarkdown - ``` - -# 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: 83 - -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/RtmpKyNdR5/b96ef7031e/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: 107 - -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 3.12.1, GDAL 3.8.4, PROJ 9.4.0; 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: 0.13.0 -* 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(, "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) - ... - + ggplot2::geom_rug(sides = "b") - > - > # 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 - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ggstatsplot.Rmd’ - ... - - > 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 - - ‘additional.Rmd’ using ‘UTF-8’... OK - ‘ggstatsplot.Rmd’ using ‘UTF-8’... failed - ``` - -# ggswissmaps - -
- -* 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(, "ggswissmaps")` for more info - -
- -## Newly broken - -* checking whether package ‘ggswissmaps’ can be installed ... WARNING - ``` - 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 whether the namespace can be loaded with stated dependencies ... NOTE - ``` - 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. - ``` - -# 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) - - -``` -# 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: 45 - -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: 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 ‘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 - ``` - -# 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: 89 - -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 - ``` - -# GWASinspector - -
- -* 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(, "GWASinspector")` for more info - -
- -## Newly broken - -* checking whether package ‘GWASinspector’ can be installed ... WARNING - ``` - 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$reference.data, "variants")) - validate_Inspector: possible error in is.element(population.Column, - tblFields): unused argument (tblFields) - variable_statistics_post_matching: possible error in is.element("CHR", - names(input.data)): unused argument (names(input.data)) - variantDiscrimination: possible error in is.element(EFFECT_ALL, c("A", - "G", "C", "T")): unused argument (c("A", "G", "C", "T")) - variantDiscrimination: possible error in is.element(OTHER_ALL, c("A", - "G", "C", "T")): unused argument (c("A", "G", "C", "T")) - ``` - -## In both - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘GWASinspector.Rmd’ - ... - > knitr::opts_chunk$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 - ``` - -# GWlasso - -
- -* 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(, "GWlasso")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘GWlasso-Ex.R’ failed - The error most likely occurred in: - - > ### 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 - ``` - -# harbinger - -
- -* 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(, "harbinger")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘harbinger-Ex.R’ failed - The error most likely occurred in: - - > ### Name: hanr_arima - > ### Title: Anomaly detector using ARIMA. - > ### Aliases: hanr_arima - > - > ### ** Examples - > - > library(daltoolbox) - ... - > - > # 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$coef)) - Calls: fit -> fit.hanr_arima - Execution halted - ``` - -* checking whether package ‘harbinger’ can be installed ... WARNING - ``` - Found the following significant warnings: - Note: possible error in 'is.element("drift", names(obj$model$coef))': unused argument (names(obj$model$coef)) - See ‘/tmp/workdir/harbinger/new/harbinger.Rcheck/00install.out’ for details. - Information on the location(s) of code generating the ‘Note’s can be - obtained by re-running with environment variable R_KEEP_PKG_SOURCE set - to ‘yes’. - ``` - -* checking R code for possible problems ... NOTE - ``` - fit.hanr_arima: possible error in is.element("drift", - names(obj$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)) - ``` - -# HCmodelSets - -
- -* 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(, "HCmodelSets")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘HCmodelSets-Ex.R’ failed - The error most likely occurred in: - - > ### Name: DGP - > ### Title: Data generating process used by Battey, H. S. & Cox, D. R. - > ### (2018). - > ### Aliases: DGP - > - > ### ** Examples - > - > ## 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 - ``` - -* 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 R code for possible problems ... NOTE - ``` - DGP: possible error in is.element(type.response, c("S", "N")): unused - argument (c("S", "N")) - ``` - -# 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: 0.3.1 -* 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(, "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 5.3Mb - ``` - -# 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: 110 - -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 ‘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 - ``` - -# heemod - -
- -* 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(, "heemod")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘e_probabilistic.Rmd’ - ... - Scale for colour is already present. - Adding another scale for colour, which will replace the existing scale. - - > bcea <- run_bcea(pm, plot = TRUE, Kmax = 10000) - Loading required namespace: BCEA - No reference selected. Defaulting to first intervention. - - ... - ‘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 - ``` - -# hesim - -
- -* 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(, "hesim")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(hesim) - > - > test_check("hesim") - sample = 1 - sample = 2 - [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1121 ] - ... - ── 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 4 | WARN 0 | SKIP 0 | PASS 1121 ] - Error: Test failures - Execution halted - ``` - -## 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 - ``` - -# hmsidwR - -
- -* 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 running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘hmsidwR.Rmd’ - ... - The following object is masked from ‘package: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 - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 7.2Mb - sub-directories of 1Mb or more: - data 3.0Mb - doc 4.0Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 1686 marked UTF-8 strings - ``` - -# HVT - -
- -* 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(, "HVT")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘HVT-Ex.R’ failed - The error most likely occurred in: - - > ### Name: clustHVT - > ### Title: Performing Hierarchical Clustering Analysis - > ### Aliases: clustHVT - > ### Keywords: Clustering_Analysis - > - > ### ** 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 - ``` - -* 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: 0.2.0 -* 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(, "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. - ``` - -# iCARH - -
- -* 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(, "iCARH")` for more info - -
- -## Newly broken - -* checking whether package ‘iCARH’ can be installed ... WARNING - ``` - 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’. - ``` - -* checking R code for possible problems ... NOTE - ``` - 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")) - ``` - -# ICSsmoothing - -
- -* 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(, "ICSsmoothing")` for more info - -
- -## Newly broken - -* checking tests ... ERROR - ``` - 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' - - ... - [ 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 - ``` - -# 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: 66 - -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 - ``` - -# 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 data for non-ASCII characters ... NOTE - ``` - Note: found 2 marked UTF-8 strings - ``` - -# 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: 126 - -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 - ... - 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 ‘infer.Rmd’ - ... - # A tibble: 1 × 2 - lower_ci upper_ci - - 1 40.1 42.7 - - > 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 - - ‘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 - ``` - -# inferCSN - -
- -* 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(, "inferCSN")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘inferCSN-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plot_dynamic_networks - > ### Title: Plot dynamic networks - > ### Aliases: plot_dynamic_networks - > - > ### ** Examples - > - > data("example_matrix") - ... - + ) - > - > 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 - ``` - -## In both - -* checking installed package size ... NOTE - ``` - 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 ‘model-injury-data-ii.Rmd’ - ... - 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] - Warning in eval(ei, envir) : - Incompatible methods ("+.ggsurv", "+.gg") for "+" - - When sourcing ‘model-injury-data-ii.R’: - Error: non-numeric argument to binary operator - 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 - ``` - -# 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: 112 - -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 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) - - [ 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 installed package size ... NOTE - ``` - installed size is 10.3Mb - sub-directories of 1Mb or more: - doc 9.7Mb - ``` - -# inti - -
- -* 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(, "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 ‘heritability.Rmd’ - ... - > library(inti) - - > dt <- potato - - > 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 - - ‘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 ‘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) - - -``` -# 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$layers)) - 8. └─vctrs::vec_as_names(names, repair = "check_unique") - 9. └─vctrs (local) ``() - 10. └─vctrs:::validate_unique(names = names, arg = arg, call = call) - 11. └─vctrs:::stop_names_cannot_be_empty(names, call = call) - 12. └─vctrs:::stop_names(...) - 13. └─vctrs:::stop_vctrs(...) - 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - Execution halted - ``` - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘ipv-vignette.Rmd’ - ... - Facet circle radius set to 0.211 based on the data. - cor_spacing set to 0.193 based on the data. - Relative scaling set to 3.78 based on the data. - Axis tick set to 0.1 based on the data. - dist_construct_label set to 0.5 based on the data. - - When sourcing ‘ipv-vignette.R’: - Error: Names can't be empty. - ✖ Empty name found at location 4. - Execution halted - - ‘ipv-vignette.Rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘ipv-vignette.Rmd’ using rmarkdown - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.0Mb - sub-directories of 1Mb or more: - data 7.0Mb - ``` - -# IRon - -
- -* Version: 0.1.4 -* GitHub: https://github.com/nunompmoniz/IRon -* Source code: https://github.com/cran/IRon -* Date/Publication: 2023-01-20 07:20:06 UTC -* Number of recursive dependencies: 84 - -Run `revdepcheck::cloud_details(, "IRon")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘IRon-Ex.R’ failed - The error most likely occurred in: - - > ### Name: sera - > ### Title: Squared Error-Relevance Area (SERA) - > ### Aliases: sera - > - > ### ** Examples - > - > library(IRon) - ... - 16. │ └─self$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 - ``` - -# 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: 122 - -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’: - Error: Names can't be empty. - ✖ Empty name found at location 1. - 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’... OK - ``` - -* 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 - ``` - -# jenga - -
- -* Version: 1.3.0 -* GitHub: NA -* 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(, "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 - > - > - ... - 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 - ``` - -# Keyboard - -
- -* 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(, "Keyboard")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - 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 - - NOTE: no estimate is provided for the doses at which no patient was treated. - - > plot_kb(sel.comb) - Error in is.element(strpattern, c("none", names(objectPlot))) : - unused argument (c("none", names(objectPlot))) - Calls: plot_kb - Execution halted - ``` - -* checking whether package ‘Keyboard’ 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/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’. - ``` - -* checking R code for possible problems ... NOTE - ``` - plot_kb: possible error in is.element(strpattern, c("none", - names(objectPlot))): unused argument (c("none", names(objectPlot))) - ``` - -# 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: 142 - -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")$R - > proc.time() - start_time - user system elapsed - 0.018 0.000 0.017 - > # Heatmap for latent correlation matrix. - > Heatmap_R_approx = latentcor(X = X, types = "tru", method = "approx", - + showplot = TRUE)$plotR - Error in pm[[2]] : subscript out of bounds - Calls: latentcor ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -# lcars - -
- -* 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(, "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$y, : - font family '0.5' not found in PostScript font database - - When sourcing ‘lcars.R’: - Error: invalid font type - Execution halted - - ‘lcars.Rmd’ using ‘UTF-8’... failed - ``` - -# lemon - -
- -* Version: 0.5.0 -* GitHub: https://github.com/stefanedwards/lemon -* Source code: https://github.com/cran/lemon -* Date/Publication: 2024-11-10 18:20:02 UTC -* Number of recursive dependencies: 75 - -Run `revdepcheck::cloud_details(, "lemon")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lemon-Ex.R’ failed - The error most likely occurred in: - - > ### Name: annotate_y_axis - > ### Title: Annotations on the axis - > ### Aliases: annotate_y_axis annotate_x_axis - > - > ### ** Examples - > - > library(ggplot2) - ... - is.element - - > - > p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point() - > - > l <- p + annotate_y_axis('mark at', y=200, tick=TRUE) - > l - Error in identicalUnits(x) : object is not a unit - Calls: ... polylineGrob -> is.unit -> unit.c -> identicalUnits - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(lemon) - > - > - > if (TRUE) { - + test_check("lemon") - + } #else { - ... - 13. └─gtable::gtable_add_row_space(panel_table, theme$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 - ``` - -* 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: 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(, "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 rlr_knn, rlr_lls vsn_lls rlr_lls - - > Boxplot_data(yeast$rlr_knn_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 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’ - - SUMMARY: processing the following file failed: - ‘user_guide.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# lilikoi - -
- -* Version: 2.1.1 -* GitHub: NA -* 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(, "lilikoi")` for more info - -
- -## Newly broken - -* checking whether package ‘lilikoi’ can be installed ... WARNING - ``` - 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 R code for possible problems ... NOTE - ``` - 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")) - ``` - -# 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 - ``` - -# LocalCop - -
- -* 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(, "LocalCop")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... NOTE - ``` - 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 ‘LocalCop.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.R’: - Error: invalid line type: must be length 2, 4, 6 or 8 - Execution halted - - ‘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 ‘lognorm.R’: - Error: invalid hex digit in 'color' or 'lty' - Execution halted - - ‘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 ‘lognorm.Rmd’ using rmarkdown - - 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’ - - --- re-building ‘lognormalDiff.Rmd’ using rmarkdown - ``` - -# lsl - -
- -* 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(, "lsl")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘lsl-Ex.R’ failed - The error most likely occurred in: - - > ### Name: lslSEM-class - > ### Title: A Reference Class for Learning a SEM model via penalized - > ### likelihood. - > ### Aliases: lslSEM-class lslSEM - > - > ### ** Examples - > - ... - > - > 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 - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` - -# MAINT.Data - -
- -* 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(, "MAINT.Data")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MAINT.Data-Ex.R’ failed - The error most likely occurred in: - - > ### Name: ConfMat - > ### Title: Confussion Matrices for classification results - > ### Aliases: ConfMat - > ### Keywords: discriminant analysis error rates - > - > ### ** Examples - > - ... - > # 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$GeoReg) - Error in is.element(1, Config) : unused argument (Config) - Calls: lda -> lda -> .local -> IdtNmle - Execution halted - ``` - -* checking tests ... ERROR - ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > test_check("MAINT.Data") - Loading required package: MAINT.Data - Loading required package: Rcpp - - Attaching package: 'MAINT.Data' - - ... - ── Error ('test-mle.R:49:5'): mle computes correct standar errors for default Gaussian models ── - Error in `is.element(Conf, 1:4)`: unused argument (1:4) - Backtrace: - ▆ - 1. ├─MAINT.Data::mle(AbaloneIdt, CovCase = Cv) at test-mle.R:49:5 - 2. └─MAINT.Data::mle(AbaloneIdt, CovCase = Cv) - - [ FAIL 10 | WARN 24 | SKIP 0 | PASS 74 ] - Error: Test failures - Execution halted - ``` - -* checking whether package ‘MAINT.Data’ can be installed ... WARNING - ``` - Found the following significant warnings: - Note: possible error in 'is.element(4, CovCase)': unused argument (CovCase) - Note: possible error in 'is.element(model, names(x@allres$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) - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 19.3Mb - sub-directories of 1Mb or more: - R 3.5Mb - data 6.5Mb - libs 8.9Mb - ``` - -# 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 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’ - - SUMMARY: processing the following file failed: - ‘MarketMatching-Vignette.Rmd’ - - Error: Vignette re-building failed. - Execution halted - ``` - -# metacart - -
- -* 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(, "metacart")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - 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) - ... - 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 - ``` - -* 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 R code for possible problems ... NOTE - ``` - 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)) - ``` - -# MetAlyzer - -
- -* 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(, "MetAlyzer")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MetAlyzer-Ex.R’ failed - The error most likely occurred in: - - > ### Name: plotly_scatter - > ### Title: Plotly Log2FC Scatter Plot - > ### Aliases: plotly_scatter - > - > ### ** Examples - > - > - ... - Warning: Partial NA coefficients for 2 probe(s) - > - > 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$Metabolite, "\nClass: ", : - Ignoring unknown aesthetics: text - Error in pm[[2]] : subscript out of bounds - Calls: plotly_scatter -> ggplotly -> ggplotly.ggplot -> gg2list - Execution halted - ``` - -# metR - -
- -* Version: 0.17.0 -* GitHub: https://github.com/eliocamp/metR -* Source code: https://github.com/cran/metR -* Date/Publication: 2025-01-13 19:50:02 UTC -* Number of recursive dependencies: 120 - -Run `revdepcheck::cloud_details(, "metR")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘metR-Ex.R’ failed - The error most likely occurred in: - - > ### Name: geom_contour_tanaka - > ### Title: Illuminated contours - > ### Aliases: geom_contour_tanaka GeomContourTanaka - > ### Keywords: datasets - > - > ### ** Examples - > - ... - 19. │ ├─rlang::inject(self$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) - > - ... - 26. │ └─metR:::stopf(...) - 27. │ └─base::stop(e) - 28. └─rlang (local) ``(``) - 29. └─handlers[[1L]](cnd) - 30. └─cli::cli_abort(...) - 31. └─rlang::abort(...) - - [ FAIL 1 | WARN 1 | SKIP 19 | PASS 184 ] - 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 - ``` - -# mgcViz - -
- -* 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(, "mgcViz")` for more info - -
- -## Newly broken - -* checking running R code from vignettes ... ERROR - ``` - Errors in running code in vignettes: - when running code in ‘mgcviz.rmd’ - ... - > v <- getViz(b) - - > pl <- plotSlice(x = sm(v, 1), fix = list(z = seq(-2, - + 2, length.out = 3), x = c(-1, 0, 1))) - - 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 - - ‘mgcviz.rmd’ using ‘UTF-8’... failed - ``` - -* checking re-building of vignette outputs ... NOTE - ``` - Error(s) in re-building vignettes: - --- re-building ‘mgcviz.rmd’ using rmarkdown - ``` - -# 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 - ``` - 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 0 | 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 0 | 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: 129 - -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: 192 - -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: 125 - -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: 0.10.1 -* 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(, "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 - > - ... - 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 - ``` - -* 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 - - 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 - ``` - -# 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 - ``` - -# 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’ - 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 - ... - • 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 - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.5Mb - sub-directories of 1Mb or more: - help 1.8Mb - ``` - -# MLEce - -
- -* Version: 2.1.0 -* GitHub: NA -* 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(, "MLEce")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MLEce-Ex.R’ failed - The error most likely occurred in: - - > ### Name: MLEce - > ### Title: Calculating MLEces for three different distributions - > ### Aliases: MLEce - > - > ### ** Examples - > - > #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 - ``` - -* 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: 0.2.3 -* 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(, "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 1.0.7 ✔ 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: 163 - -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 - ``` - -# 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) - - > 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 - ``` - -* 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 R code for possible problems ... NOTE - ``` - 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 - ``` - -# MPTmultiverse - -
- -* 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(, "MPTmultiverse")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - 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 - ``` - -* 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: 0.1.8 -* 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(, "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") - - Attaching package: 'ggplot2' - - ... - - "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 - ``` - -# 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 - -Run `revdepcheck::cloud_details(, "mudfold")` for more info - -
- -## Newly broken - -* checking whether package ‘mudfold’ can be installed ... WARNING - ``` - 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 R code for possible problems ... NOTE - ``` - check.visitSequence: possible error in is.element(visitSequence, - names(blocks)): unused argument (names(blocks)) - ``` - -# 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$arrow) : - invalid line type: must be length 2, 4, 6 or 8 - Calls: ... drawDetails -> drawDetails.segments -> grid.Call.graphics - Execution halted - ``` - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.8Mb - sub-directories of 1Mb or more: - data 8.5Mb - ``` - -# MultiTraits - -
- -* Version: 0.2.0 -* GitHub: NA -* Source code: https://github.com/cran/MultiTraits -* Date/Publication: 2024-12-21 14:10:02 UTC -* Number of recursive dependencies: 138 - -Run `revdepcheck::cloud_details(, "MultiTraits")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in ‘MultiTraits-Ex.R’ failed - The error most likely occurred in: - - > ### Name: CSR_plot - > ### Title: Create a ternary plot of CSR strategies - > ### Aliases: CSR_plot - > - > ### ** Examples - > - > data(PFF) - ... - 3. ├─ggtern::ggplot_build(x) - 4. └─ggtern:::ggplot_build.ggplot(x) - 5. └─ggtern:::layers_add_or_remove_mask(plot) - 6. └─ggint$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 ‘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 re-building of vignette outputs ... NOTE - ``` - 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 - ``` - -# mvSLOUCH - -
- -* 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(, "mvSLOUCH")` for more info - -
- -## Newly broken - -* checking re-building of vignette outputs ... NOTE - ``` - 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 - -