make copying files more robust

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '158648'
+ValidationKey: '178524'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'piamPlotComparison: Create comparison plots for your model results'
-version: 0.0.8
-date-released: '2024-04-18'
+version: 0.0.9
+date-released: '2024-04-23'
 abstract: A frameworks to create comparison plots for your model results.
 authors:
 - family-names: Benke

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: piamPlotComparison
 Title: Create comparison plots for your model results
-Version: 0.0.8
-Date: 2024-04-18
+Version: 0.0.9
+Date: 2024-04-23
 Authors@R: c(
     person("Falk", "Benke", , "[email protected]", role = c("aut", "cre")),
     person("Christof", "Schoetz", role = "aut")

NAMESPACE

@@ -15,6 +15,7 @@ importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(dplyr,summarize)
+importFrom(piamutils,getSystemFile)
 importFrom(rlang,.data)
 importFrom(rlang,.env)
 importFrom(tidyr,pivot_wider)

R/compareScenarios.R

@@ -29,6 +29,7 @@
 #'   an preprocess data in your global environment during development.
 #' @param quiet \code{logical(1)}. Suppress printing during rendering?
 #' @param ... YAML parameters, see below.
+#' @importFrom piamutils getSystemFile
 #' @return The value returned by \code{\link[rmarkdown:render]{rmarkdown::render()}}.
 #' @section YAML Parameters:
 #' \describe{
@@ -124,14 +125,14 @@
 #' }
 #' @export
 compareScenarios <- function(
-  mifScen, mifHist,
-  projectLibrary = NULL,
-  outputDir = getwd(),
-  outputFile = "CompareScenarios",
-  outputFormat = "PDF",
-  envir = new.env(),
-  quiet = FALSE,
-  ...
+    mifScen, mifHist,
+    projectLibrary = NULL,
+    outputDir = getwd(),
+    outputFile = "CompareScenarios",
+    outputFormat = "PDF",
+    envir = new.env(),
+    quiet = FALSE,
+    ...
 ) {
   # Set yaml parameters and convert relative to absolute paths.
   yamlParams <- c(
@@ -162,11 +163,11 @@ compareScenarios <- function(
   # copy the template directory from the package to the outputDir because
   # rmarkdown writes to the folder containing the template.
   templateInOutputDir <- file.path(outputDir, "compareScenarios", "cs_main.Rmd")
-  file.copy(system.file("compareScenarios", package = "piamPlotComparison"),
+  file.copy(piamutils::getSystemFile("compareScenarios", package = "piamPlotComparison"),
             outputDir, recursive = TRUE)
 
   if (!is.null(projectLibrary)) {
-    file.copy(system.file("compareScenarios", package = projectLibrary),
+    file.copy(piamutils::getSystemFile("compareScenarios", package = projectLibrary),
               outputDir, recursive = TRUE)
   }
 
@@ -187,7 +188,7 @@ compareScenarios <- function(
 # Copies the CompareScenarios-Rmds to the specified location and modifies
 # their YAML header according to \code{yamlParams}.
 .compareScenarios2Rmd <- function(projectLibrary, yamlParams, outputDir, outputFile) {
-  pathMain <- system.file("compareScenarios/cs_main.Rmd", package = "piamPlotComparison")
+  pathMain <- piamutils::getSystemFile("compareScenarios/cs_main.Rmd", package = "piamPlotComparison")
   linesMain <- readLines(pathMain)
   delimiters <- grep("^(---|\\.\\.\\.)\\s*$", linesMain)
   headerMain <- linesMain[(delimiters[1]):(delimiters[2])]
@@ -211,10 +212,10 @@ compareScenarios <- function(
 
   if (!dir.exists(pathDir)) dir.create(pathDir)
 
-  dirFiles <- dir(system.file("compareScenarios", package = "piamPlotComparison"), full.names = TRUE)
+  dirFiles <- dir(piamutils::getSystemFile("compareScenarios", package = "piamPlotComparison"), full.names = TRUE)
 
   if (!is.null(projectLibrary)) {
-    dirFiles <- c(dirFiles, dir(system.file("compareScenarios", package = projectLibrary), full.names = TRUE))
+    dirFiles <- c(dirFiles, dir(piamutils::getSystemFile("compareScenarios", package = projectLibrary), full.names = TRUE))
   }
 
   rmdDirFiles <- grep(
@@ -227,7 +228,7 @@ compareScenarios <- function(
   ymlthis::use_rmarkdown(
     newYaml,
     path = file.path(pathDir, "cs_main.Rmd"),
-    template = system.file(
+    template = piamutils::getSystemFile(
       "compareScenarios/cs_main.Rmd",
       package = "piamPlotComparison"),
     include_yaml = FALSE)

README.md

@@ -1,6 +1,6 @@
 # Create comparison plots for your model results
 
-R package **piamPlotComparison**, version **0.0.8**
+R package **piamPlotComparison**, version **0.0.9**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/piamPlotComparison)](https://cran.r-project.org/package=piamPlotComparison)  [![R build status](https://github.com/pik-piam/piamPlotComparison/workflows/check/badge.svg)](https://github.com/pik-piam/piamPlotComparison/actions) [![codecov](https://codecov.io/gh/pik-piam/piamPlotComparison/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/piamPlotComparison) [![r-universe](https://pik-piam.r-universe.dev/badges/piamPlotComparison)](https://pik-piam.r-universe.dev/builds)
 
@@ -46,7 +46,7 @@ In case of questions / problems please contact Falk Benke <[email protected]>
 
 To cite package **piamPlotComparison** in publications use:
 
-Benke F, Schoetz C (2024). _piamPlotComparison: Create comparison plots for your model results_. R package version 0.0.8, <https://github.com/pik-piam/piamPlotComparison>.
+Benke F, Schoetz C (2024). _piamPlotComparison: Create comparison plots for your model results_. R package version 0.0.9, <https://github.com/pik-piam/piamPlotComparison>.
 
 A BibTeX entry for LaTeX users is
 
@@ -55,7 +55,7 @@ A BibTeX entry for LaTeX users is
   title = {piamPlotComparison: Create comparison plots for your model results},
   author = {Falk Benke and Christof Schoetz},
   year = {2024},
-  note = {R package version 0.0.8},
+  note = {R package version 0.0.9},
   url = {https://github.com/pik-piam/piamPlotComparison},
 }
 ```

inst/compareScenarios/cs_main.Rmd

@@ -83,7 +83,6 @@ if (interactive()) {
 # may cause "Undefined control sequence" errors in LaTeX.
 try(unloadNamespace("kableExtra"), silent = TRUE)
 
-library(piamPlotComparison)
 suppressMessages(library(gridExtra))
 options(tidyverse.quiet = TRUE)
 library(tidyverse)