Merge branch 'main' into copilot/fix-559

Author: rempsyc

.github/copilot-instructions.md

@@ -100,14 +100,14 @@ if (!requireNamespace("lintr", quietly = TRUE)) {
   # Based on testing with whitelisted r-lib.r-universe.dev and cdn.r-universe.dev: both r-universe and remotes work successfully
   tryCatch({
     # FIRST PRIORITY: Try r-universe installation
-    install.packages("lintr", lib = .libPaths()[1], repos="https://r-lib.r-universe.dev")
+    install.packages("lintr", lib = .libPaths()[1], repos=c("https://r-lib.r-universe.dev", "https://cloud.r-project.org"))
     cat("SUCCESS: r-universe installation worked\n")
   }, error = function(e1) {
     cat("r-universe installation failed, trying remotes...\n")
     tryCatch({
       # FALLBACK: Use remotes for development lintr installation
       if (!requireNamespace("remotes", quietly = TRUE)) {
-        install.packages("remotes", lib = .libPaths()[1], repos="https://r-universe.dev")
+        install.packages("remotes", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
       }
       remotes::install_github("r-lib/lintr")
       cat("SUCCESS: remotes installation worked\n")
@@ -125,7 +125,7 @@ if (!requireNamespace("lintr", quietly = TRUE)) {
 }'
 
 # Install reprex (ESSENTIAL for creating reproducible examples in PRs)
-sudo apt install -y r-cran-reprex || R --no-restore --no-save -e 'install.packages("reprex", lib = .libPaths()[1], repos="https://r-universe.dev")'
+sudo apt install -y r-cran-reprex || R --no-restore --no-save -e 'install.packages("reprex", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 
 # Install other essential development packages via system packages when possible
 sudo apt install -y r-cran-devtools r-cran-roxygen2 r-cran-styler || echo "Some packages not available via apt, will install via R"
@@ -136,7 +136,7 @@ packages_needed <- c("styler", "roxygen2", "devtools")
 packages_installed <- rownames(installed.packages())
 packages_to_install <- setdiff(packages_needed, packages_installed)
 if (length(packages_to_install) > 0) {
-  install.packages(packages_to_install, lib = .libPaths()[1], repos="https://r-universe.dev")
+  install.packages(packages_to_install, lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
 }
 '
 ```
@@ -172,20 +172,20 @@ if (length(missing_packages) > 0) {
 ```bash
 # Step 1: Install required dependencies for reprex
 sudo apt install -y pandoc
-R --no-restore --no-save -e 'install.packages(c("knitr", "rmarkdown"), lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages(c("knitr", "rmarkdown"), lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 
 # Step 2: Install reprex package
 R --no-restore --no-save -e '
 if (!requireNamespace("reprex", quietly = TRUE)) {
   # Try multiple installation methods
   tryCatch({
-    install.packages("reprex", lib = .libPaths()[1], repos="https://r-universe.dev")
+    install.packages("reprex", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
   }, error = function(e1) {
     tryCatch({
-      install.packages("reprex", lib = .libPaths()[1], repos="https://r-universe.dev")
+      install.packages("reprex", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
     }, error = function(e2) {
       if (!requireNamespace("remotes", quietly = TRUE)) {
-        install.packages("remotes", lib = .libPaths()[1], repos="https://r-universe.dev")
+        install.packages("remotes", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
       }
       remotes::install_github("tidyverse/reprex")
     })
@@ -233,13 +233,13 @@ grep -A2 -B2 "requireNamespace\|check_installed" R/[your_function_file].R
 ```bash
 # Step 2: Install ONLY the packages found in Step 1
 # Example: If working on report.lm(), you might need modelbased and effectsize
-R --no-restore --no-save -e 'install.packages(c("modelbased", "effectsize"), lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages(c("modelbased", "effectsize"), lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 
 # Example: If working on report.lavaan(), you might need lavaan  
-R --no-restore --no-save -e 'install.packages("lavaan", lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages("lavaan", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 
 # Example: If working on report.brmsfit(), you need brms and related packages
-R --no-restore --no-save -e 'install.packages(c("brms", "rstanarm"), lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages(c("brms", "rstanarm"), lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 ```
 
 #### Use report's Built-in Utilities (After Building Package)
@@ -256,7 +256,7 @@ if (file.exists("DESCRIPTION")) {
 # Load report and install only specific packages for your function
 library(report)
 # ONLY install packages needed for your specific function:
-# install.packages("your_specific_package", lib = .libPaths()[1], repos="https://r-universe.dev")
+# install.packages("your_specific_package", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
 '
 ```
 
@@ -569,13 +569,13 @@ Many functions require optional packages. The package uses `requireNamespace()`
 
 ```bash
 # ALWAYS install reprex first (essential for PR creation):
-sudo apt install -y r-cran-reprex || R --no-restore --no-save -e 'install.packages("reprex", lib = .libPaths()[1], repos="https://r-universe.dev")'
+sudo apt install -y r-cran-reprex || R --no-restore --no-save -e 'install.packages("reprex", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 
 # Via system packages (recommended for individual packages):
 sudo apt install -y r-cran-[package-name]
 
 # Via R (using r-universe for latest packages including development versions):
-R --no-restore --no-save -e 'install.packages("[package-name]", lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages("[package-name]", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 
 # Alternative sources when r-universe is not available:
 # Via CRAN mirror (FALLBACK PRIORITY):
@@ -613,16 +613,16 @@ grep -A2 -B2 "requireNamespace\|@importFrom" R/[function_file].R
 #### Targeted Installation Examples
 ```bash
 # Example 1: Working on report.lm() function
-R --no-restore --no-save -e 'install.packages(c("modelbased", "effectsize"), lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages(c("modelbased", "effectsize"), lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 
 # Example 2: Working on report.lavaan() function  
-R --no-restore --no-save -e 'install.packages("lavaan", lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages("lavaan", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 
 # Example 3: Working on report.brmsfit() function
-R --no-restore --no-save -e 'install.packages(c("brms", "rstanarm"), lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages(c("brms", "rstanarm"), lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 
 # Example 4: Working on report.BFBayesFactor() function
-R --no-restore --no-save -e 'install.packages("BayesFactor", lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages("BayesFactor", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 ```
 
 ## Code Quality and Best Practices
@@ -1136,11 +1136,11 @@ cat(paste(reprex_result, collapse = "\n"))
 
 ### Styler Not Available
 - **Cause**: styler package not installed
-- **Solution**: Install via R: `R --no-restore --no-save -e 'install.packages("styler", lib = .libPaths()[1], repos="https://r-universe.dev")'` or skip styling step if not critical
+- **Solution**: Install via R: `R --no-restore --no-save -e 'install.packages("styler", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'` or skip styling step if not critical
 
 ### Roxygen2 Not Available
 - **Cause**: roxygen2 package not installed
-- **Solution**: Install via R: `R --no-restore --no-save -e 'install.packages("roxygen2", lib = .libPaths()[1], repos="https://r-universe.dev")'` or use devtools: `R --no-restore --no-save -e 'devtools::document()'`
+- **Solution**: Install via R: `R --no-restore --no-save -e 'install.packages("roxygen2", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'` or use devtools: `R --no-restore --no-save -e 'devtools::document()'`
 
 ### Documentation Build Failures
 - **Cause**: Documentation not updated after changing roxygen2 comments
@@ -1169,14 +1169,14 @@ cat(paste(reprex_result, collapse = "\n"))
     # Based on testing with whitelisted r-lib.r-universe.dev and cdn.r-universe.dev: both r-universe and remotes work successfully
     tryCatch({
       # FIRST PRIORITY: Try r-universe installation
-      install.packages("lintr", lib = .libPaths()[1], repos="https://r-lib.r-universe.dev")
+      install.packages("lintr", lib = .libPaths()[1], repos=c("https://r-lib.r-universe.dev", "https://cloud.r-project.org"))
       cat("SUCCESS: r-universe installation worked\n")
     }, error = function(e1) {
       cat("r-universe installation failed, trying remotes...\n")
       tryCatch({
         # FALLBACK: Use remotes for development lintr installation
         if (!requireNamespace("remotes", quietly = TRUE)) {
-          install.packages("remotes", lib = .libPaths()[1], repos="https://r-universe.dev")
+          install.packages("remotes", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
         }
         remotes::install_github("r-lib/lintr")
         cat("SUCCESS: remotes installation worked\n")
@@ -1218,7 +1218,7 @@ cat(paste(reprex_result, collapse = "\n"))
 - **Cause**: Cannot install packages from CRAN mirrors
 - **Solutions**: 
   - Use system packages: `sudo apt install r-cran-[package]`
-  - Try R-universe (FIRST PRIORITY): `repos="https://r-universe.dev"`  
+  - Try R-universe (FIRST PRIORITY): `repos=c("https://r-universe.dev", "https://cloud.r-project.org")`  
   - Use remotes for GitHub packages (SECOND PRIORITY): `remotes::install_github("[author]/[package]")`
 
 ### reprex Package Issues and Complete Debugging Guide
@@ -1232,7 +1232,7 @@ cat(paste(reprex_result, collapse = "\n"))
 ```bash
 # Install core dependencies first
 sudo apt install -y pandoc
-R --no-restore --no-save -e 'install.packages(c("knitr", "rmarkdown"), lib = .libPaths()[1], repos="https://r-universe.dev")'
+R --no-restore --no-save -e 'install.packages(c("knitr", "rmarkdown"), lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))'
 ```
 
 #### Step 2: Install reprex Package
@@ -1241,13 +1241,13 @@ R --no-restore --no-save -e 'install.packages(c("knitr", "rmarkdown"), lib = .li
 R --no-restore --no-save -e '
 if (!requireNamespace("reprex", quietly = TRUE)) {
   tryCatch({
-    install.packages("reprex", lib = .libPaths()[1], repos="https://r-universe.dev")
+    install.packages("reprex", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
   }, error = function(e1) {
     tryCatch({
-      install.packages("reprex", lib = .libPaths()[1], repos="https://r-universe.dev")
+      install.packages("reprex", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
     }, error = function(e2) {
       if (!requireNamespace("remotes", quietly = TRUE)) {
-        install.packages("remotes", lib = .libPaths()[1], repos="https://r-universe.dev")
+        install.packages("remotes", lib = .libPaths()[1], repos=c("https://r-universe.dev", "https://cloud.r-project.org"))
       }
       remotes::install_github("tidyverse/reprex")
     })
@@ -1424,7 +1424,7 @@ These workflows run automatically on pushes and pull requests to main/master bra
 #### 3. Package Installation Strategy
 When packages can't be installed from CRAN:
 - **Primary**: Use system packages via `sudo apt install r-cran-[package]`
-- **Alternative (FIRST PRIORITY)**: Use R-universe repository: `repos="https://r-universe.dev"`
+- **Alternative (FIRST PRIORITY)**: Use R-universe repository: `repos=c("https://r-universe.dev", "https://cloud.r-project.org")`
 - **Fallback (SECOND PRIORITY)**: Use remotes for GitHub packages: `remotes::install_github("[author]/[package]")`
 
 #### 4. Pre-Commit Validation Checklist