Fix long standing issue with cmd check failed because of example

Author: Rafnuss

CITATION.cff

@@ -121,17 +121,6 @@ references:
     address: Vienna, Austria
   year: '2024'
   version: '>= 4.1.0'
-- type: software
-  title: assertthat
-  abstract: 'assertthat: Easy Pre and Post Assertions'
-  notes: Imports
-  repository: https://CRAN.R-project.org/package=assertthat
-  authors:
-  - family-names: Wickham
-    given-names: Hadley
-    email: hadley@rstudio.com
-  year: '2024'
-  doi: 10.32614/CRAN.package.assertthat
 - type: software
   title: cli
   abstract: 'cli: Helpers for Developing Command Line Interfaces'
@@ -167,9 +156,9 @@ references:
     given-names: Koen
     email: koen.hufkens@gmail.com
     orcid: https://orcid.org/0000-0002-5070-8109
+  year: '2024'
   doi: 10.32614/CRAN.package.ecmwfr
   version: '>= 2.0.0'
-  year: '2024'
 - type: software
   title: EBImage
   abstract: 'EBImage: Image processing and analysis toolbox for R'
@@ -296,7 +285,7 @@ references:
   authors:
   - family-names: Ooms
     given-names: Jeroen
-    email: jeroen@berkeley.edu
+    email: jeroenooms@gmail.com
     orcid: https://orcid.org/0000-0002-4035-0289
   year: '2024'
   doi: 10.32614/CRAN.package.jsonlite
@@ -322,6 +311,22 @@ references:
   year: '2024'
   doi: 10.32614/CRAN.package.leaflet
   version: '>= 2.2.0'
+- type: software
+  title: lifecycle
+  abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
+  notes: Imports
+  url: https://lifecycle.r-lib.org/
+  repository: https://CRAN.R-project.org/package=lifecycle
+  authors:
+  - family-names: Henry
+    given-names: Lionel
+    email: lionel@posit.co
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+    orcid: https://orcid.org/0000-0003-4757-117X
+  year: '2024'
+  doi: 10.32614/CRAN.package.lifecycle
 - type: software
   title: Matrix
   abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
@@ -468,21 +473,16 @@ references:
     address: Vienna, Austria
   year: '2024'
 - type: software
-  title: lifecycle
-  abstract: 'lifecycle: Manage the Life Cycle of your Package Functions'
-  notes: Imports
-  url: https://lifecycle.r-lib.org/
-  repository: https://CRAN.R-project.org/package=lifecycle
+  title: assertthat
+  abstract: 'assertthat: Easy Pre and Post Assertions'
+  notes: Suggests
+  repository: https://CRAN.R-project.org/package=assertthat
   authors:
-  - family-names: Henry
-    given-names: Lionel
-    email: lionel@posit.co
   - family-names: Wickham
     given-names: Hadley
-    email: hadley@posit.co
-    orcid: https://orcid.org/0000-0003-4757-117X
+    email: hadley@rstudio.com
   year: '2024'
-  doi: 10.32614/CRAN.package.lifecycle
+  doi: 10.32614/CRAN.package.assertthat
 - type: software
   title: BiocManager
   abstract: 'BiocManager: Access the Bioconductor Project Package Repository'
@@ -668,4 +668,29 @@ references:
   year: '2024'
   doi: 10.32614/CRAN.package.testthat
   version: '>= 3.0.0'
+- type: software
+  title: withr
+  abstract: 'withr: Run Code ''With'' Temporarily Modified Global State'
+  notes: Suggests
+  url: https://withr.r-lib.org
+  repository: https://CRAN.R-project.org/package=withr
+  authors:
+  - family-names: Hester
+    given-names: Jim
+  - family-names: Henry
+    given-names: Lionel
+    email: lionel@posit.co
+  - family-names: Müller
+    given-names: Kirill
+    email: krlmlr+r@mailbox.org
+  - family-names: Ushey
+    given-names: Kevin
+    email: kevinushey@gmail.com
+  - family-names: Wickham
+    given-names: Hadley
+    email: hadley@posit.co
+  - family-names: Chang
+    given-names: Winston
+  year: '2024'
+  doi: 10.32614/CRAN.package.withr
 

DESCRIPTION

@@ -15,7 +15,6 @@ BugReports: https://github.com/Rafnuss/GeoPressureR/issues
 Depends: 
     R (>= 4.1.0)
 Imports: 
-    assertthat,
     cli,
     config,
     ecmwfr (>= 2.0.0),
@@ -27,6 +26,7 @@ Imports:
     httr2 (>= 1.0.0),
     jsonlite,
     leaflet (>= 2.2.0),
+    lifecycle,
     Matrix,
     methods,
     ncdf4,
@@ -36,9 +36,9 @@ Imports:
     stats,
     suntools,
     terra,
-    utils,
-    lifecycle
+    utils
 Suggests: 
+    assertthat,
     BiocManager,
     covr,
     knitr,
@@ -49,7 +49,8 @@ Suggests:
     shiny,
     shinyjs,
     shinyWidgets,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    withr
 biocViews:
 Config/testthat/edition: 3
 Encoding: UTF-8

R/edge_add_wind.R

@@ -16,10 +16,9 @@
 #' @param pressure pressure measurement of the associated `tag` data used to estimate the pressure
 #' level (i.e., altitude) of the bird during the flights. This data.frame needs to contain `date` as
 #' POSIXt and `value` in hPa.
-#' @param variable list of the variables to extract from [the ERA5 pressure level](
-#' https://confluence.ecmwf.int/display/CKB/ERA5%3A+data+documentation#ERA5:datadocumentation-Table9) # nolint
-#' using the `shortName` notation: `"u"`, `"v"`,  `"t"`, `"cc"`, `"r"`, , `"w"`, `"ciwc"`, `"clwc"`,
-#'  `"q"`, `"cswc"`, `"d"`, `"z"`, `"o3"`, `"pv"`, `'vo"`.
+#' @param variable list of the variables to extract from [the ERA5 pressure level
+#' ](https://bit.ly/3BrwLBM) using the `shortName` notation: `"u"`, `"v"`,  `"t"`, `"cc"`, `"r"`,
+#' `"w"`, `"ciwc"`, `"clwc"`, `"q"`, `"cswc"`, `"d"`, `"z"`, `"o3"`, `"pv"`, `'vo"`.
 #' @param rounding_interval temporal resolution on which to query the variable (min). Default is to
 #' macth ERA5 native resolution (1hr).
 #' @param interp_spatial_linear logical to interpolate the variable linearly over space, if `FALSE`
@@ -173,7 +172,9 @@ edge_add_wind <- function(
       # Read data from netCDF file and convert the time of data to posixt
       # Fix to use the correct time variable ("time" until the new CDS, then "valid_time")
       if ("time" %in% names(nc$dim)) {
-        time <- as.POSIXct(ncdf4::ncvar_get(nc, "time") * 60 * 60, origin = "1900-01-01", tz = "UTC")
+        time <- as.POSIXct(ncdf4::ncvar_get(nc, "time") * 60 * 60,
+          origin = "1900-01-01", tz = "UTC"
+        )
       } else if ("valid_time" %in% names(nc$dim)) {
         time <- as.POSIXct(ncdf4::ncvar_get(nc, "valid_time"), origin = "1970-01-01", tz = "UTC")
       } else {
@@ -472,7 +473,9 @@ edge_add_wind_check <- function(
 
       # Check that the time is matching
       if ("time" %in% names(nc$dim)) {
-        time <- as.POSIXct(ncdf4::ncvar_get(nc, "time") * 60 * 60, origin = "1900-01-01", tz = "UTC")
+        time <- as.POSIXct(ncdf4::ncvar_get(nc, "time") * 60 * 60,
+          origin = "1900-01-01", tz = "UTC"
+        )
       } else if ("valid_time" %in% names(nc$dim)) {
         time <- as.POSIXct(ncdf4::ncvar_get(nc, "valid_time"), origin = "1970-01-01", tz = "UTC")
       } else {

R/geolight_map.R

@@ -18,7 +18,7 @@
 #'
 #' Instead of calibrating the twilight errors in terms of duration, we directly model the zenith
 #' angle error. We use a kernel distribution to fit the zenith angle during the known stationary
-#' period(s). The `twl_calib_adjust` parameter allows to manually adjust how smooth you want the
+#' period(s). The `twl_calib_adjust` parameter allows to mararnually adjust how smooth you want the
 #' fit of the zenith angle to be. Because the zenith angle error model is fitted with data from the
 #' calibration site only, and we are using it for all locations of the bird’s journey, it is safer
 #' to assume a broader/smoother distribution.
@@ -33,25 +33,26 @@
 #' @return a `tag` with the likelihood of light as `tag$map_light`
 #'
 #' @examples
-#' setwd(system.file("extdata", package = "GeoPressureR"))
-#' # Read geolocator data and build twilight
-#' tag <- tag_create("18LX", quiet = TRUE) |>
-#'   tag_label(quiet = TRUE) |>
-#'   tag_set_map(
-#'     extent = c(-16, 23, 0, 50),
-#'     scale = 10,
-#'     known = data.frame(
-#'       stap_id = 1,
-#'       known_lon = 17.05,
-#'       known_lat = 48.9
+#' withr::with_dir(system.file("extdata", package = "GeoPressureR"), {
+#'   # Read geolocator data and build twilight
+#'   tag <- tag_create("18LX", quiet = TRUE) |>
+#'     tag_label(quiet = TRUE) |>
+#'     tag_set_map(
+#'       extent = c(-16, 23, 0, 50),
+#'       scale = 10,
+#'       known = data.frame(
+#'         stap_id = 1,
+#'         known_lon = 17.05,
+#'         known_lat = 48.9
+#'       )
 #'     )
-#'   )
 #'
-#' # Compute the twilight
-#' tag <- twilight_create(tag) |> twilight_label_read()
+#'   # Compute the twilight
+#'   tag <- twilight_create(tag) |> twilight_label_read()
 #'
-#' # Compute likelihood map
-#' tag <- geolight_map(tag, quiet = TRUE)
+#'   # Compute likelihood map
+#'   tag <- geolight_map(tag, quiet = TRUE)
+#' })
 #'
 #' plot(tag, type = "map_light")
 #' @family geolight

R/geopressure_map.R

@@ -120,14 +120,14 @@
 #' datapoints used to compute the MSE.
 #'
 #' @examples
-#' owd <- setwd(system.file("extdata", package = "GeoPressureR"))
-#' tag <- tag_create("18LX", quiet = TRUE) |>
-#'   tag_label(quiet = TRUE) |>
-#'   tag_set_map(
-#'     extent = c(-16, 23, 0, 50),
-#'     scale = 4
-#'   )
-#' setwd(owd)
+#' withr::with_dir(system.file("extdata", package = "GeoPressureR"), {
+#'   tag <- tag_create("18LX", quiet = TRUE) |>
+#'     tag_label(quiet = TRUE) |>
+#'     tag_set_map(
+#'       extent = c(-16, 23, 0, 50),
+#'       scale = 4
+#'     )
+#' })
 #'
 #' tag <- geopressure_map_mismatch(tag,
 #'   max_sample = 50,

R/geopressure_map_preprocess.R

@@ -12,9 +12,9 @@
 #' @inheritParams geopressure_map
 #' @return Pressure data.frame without flight and discarded values, on a 1 hour resolution.
 #' @examples
-#' owd <- setwd(system.file("extdata", package = "GeoPressureR"))
-#' tag <- tag_create("18LX", quiet = TRUE) |> tag_label(quiet = TRUE)
-#' setwd(owd)
+#' withr::with_dir(system.file("extdata", package = "GeoPressureR"), {
+#'   tag <- tag_create("18LX", quiet = TRUE) |> tag_label(quiet = TRUE)
+#' })
 #'
 #' pressure_processed <- geopressure_map_preprocess(tag)
 #' str(pressure_processed)

R/geopressuretemplate.R

@@ -53,7 +53,7 @@
 #'     - `graph_most_likely()`: Computes the most likely path based on the movement model.
 #' 6. If `"simulation"` is in `config$geopressuretemplate$outputs`:
 #'     - `graph_simulation()`: Runs simulations to model multiple possible paths.
-#' 7. \*`save()`: Saves the computed graph and associated objects in `data/interim/{id}.Rdata`
+#' 7. `save()`: Saves the computed graph and associated objects in `data/interim/{id}.Rdata`
 #'
 #' * **Pressure Path Processing [`geopressuretemplate_pressurepath()`]**: Computes pressurepaths
 #' (`pressurepath_create`) using the content of the `Rdata` file and appending the pressurepath
@@ -75,7 +75,7 @@
 #' @examples
 #' \dontrun{
 #' # Run the complete geopressuretemplate workflow
-#' geopressuretemplate("example_id", quiet = TRUE)
+#' geopressuretemplate("18LX", quiet = TRUE)
 #' }
 #'
 #' @family geopressuretemplate

R/geopressuretemplate_graph.R

@@ -91,7 +91,7 @@ geopressuretemplate_graph <- function(
 
 
   # Store the graph parameters
-  param <- graph$param
+  param <- graph$param # nolint
 
   # Initialize a list to keep track of outputs to be saved
   save_list <- c("tag", "param")
@@ -103,7 +103,7 @@ geopressuretemplate_graph <- function(
         if (!quiet) {
           cli::cli_h2("Compute marginal map")
         }
-        marginal <- graph_marginal(graph, quiet = quiet)
+        marginal <- graph_marginal(graph, quiet = quiet) # nolint
         save_list <- c(save_list, "marginal")
       }
 
@@ -113,7 +113,7 @@ geopressuretemplate_graph <- function(
           cli::cli_h2("Compute most likely path")
         }
         path_most_likely <- graph_most_likely(graph, quiet = quiet)
-        edge_most_likely <- path2edge(path_most_likely, graph)
+        edge_most_likely <- path2edge(path_most_likely, graph) # nolint
         save_list <- c(save_list, "path_most_likely", "edge_most_likely")
       }
 
@@ -127,7 +127,7 @@ geopressuretemplate_graph <- function(
           nj = config$graph_simulation$nj,
           quiet = quiet
         )
-        edge_simulation <- path2edge(path_simulation, graph)
+        edge_simulation <- path2edge(path_simulation, graph) # nolint
         save_list <- c(save_list, "path_simulation", "edge_simulation")
       }
     },

R/geopressuretemplate_pressurepath.R

@@ -2,7 +2,6 @@
 #' @family geopressuretemplate
 #' @export
 geopressuretemplate_pressurepath <- function(
-    # nolint
     id,
     config = config::get(config = id),
     quiet = FALSE,
@@ -32,7 +31,7 @@ geopressuretemplate_pressurepath <- function(
     if ("most_likely" %in% config$geopressuretemplate$pressurepath &&
       "path_most_likely" %in% save_list) {
       path_most_likely <- get("path_most_likely")
-      pressurepath_most_likely <- pressurepath_create(
+      pressurepath_most_likely <- pressurepath_create( # nolint
         tag,
         path = path_most_likely,
         variable = config$pressurepath_create$variable,
@@ -45,7 +44,7 @@ geopressuretemplate_pressurepath <- function(
     if ("geopressureviz" %in% config$geopressuretemplate$pressurepath &&
       "path_geopressureviz" %in% save_list) {
       path_geopressureviz <- get("path_geopressureviz")
-      pressurepath_geopressureviz <- pressurepath_create(
+      pressurepath_geopressureviz <- pressurepath_create( # nolint
         tag,
         path = path_geopressureviz,
         variable = config$pressurepath_create$variable,

R/graph_create.R

@@ -44,17 +44,18 @@
 #' - `param`: list of parameters including `thr_likelihood` and `thr_gs` (same as `tag$param`)
 #'
 #' @examples
-#' setwd(system.file("extdata", package = "GeoPressureR"))
-#' tag <- tag_create("18LX", quiet = TRUE) |>
-#'   tag_label(quiet = TRUE) |>
-#'   twilight_create() |>
-#'   twilight_label_read() |>
-#'   tag_set_map(
-#'     extent = c(-16, 23, 0, 50),
-#'     known = data.frame(stap_id = 1, known_lon = 17.05, known_lat = 48.9)
-#'   ) |>
-#'   geopressure_map(quiet = TRUE) |>
-#'   geolight_map(quiet = TRUE)
+#' withr::with_dir(system.file("extdata", package = "GeoPressureR"), {
+#'   tag <- tag_create("18LX", quiet = TRUE) |>
+#'     tag_label(quiet = TRUE) |>
+#'     twilight_create() |>
+#'     twilight_label_read() |>
+#'     tag_set_map(
+#'       extent = c(-16, 23, 0, 50),
+#'       known = data.frame(stap_id = 1, known_lon = 17.05, known_lat = 48.9)
+#'     ) |>
+#'     geopressure_map(quiet = TRUE) |>
+#'     geolight_map(quiet = TRUE)
+#' })
 #'
 #' # Create graph
 #' graph <- graph_create(tag, thr_likelihood = 0.95, thr_gs = 100, quiet = TRUE)