Fixed bugs in GitHub action R-CMD-check

- by adding JAGS installation to action
- by installing libgsl-dev and libgsl27 on Linux

Author: stephaniereinders

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,106 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: windows-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+      
+      - name: Install system dependencies (Ubuntu)
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgsl-dev libgsl27
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+      
+      - name: Install JAGS (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install jags
+          echo "JAGS_HOME=$(brew --prefix jags)" >> $GITHUB_ENV
+      
+      - name: Install JAGS (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          # Create a temporary directory for the installer
+          $tempDir = Join-Path $env:RUNNER_TEMP "jags-installer"
+          New-Item -ItemType Directory -Path $tempDir -Force
+          
+          # Download JAGS to the temporary directory
+          $installerPath = Join-Path $tempDir "JAGS-4.3.1.exe"
+          curl -LO https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.1.exe
+          Move-Item -Path "JAGS-4.3.1.exe" -Destination $installerPath
+          
+          # Install JAGS
+          Start-Process -FilePath $installerPath -ArgumentList "/S" -NoNewWindow -Wait
+          
+          # Set environment variable
+          echo "JAGS_HOME=C:/Program Files/JAGS/JAGS-4.3.1" >> $env:GITHUB_ENV
+          
+          # Clean up the installer
+          Remove-Item -Path $tempDir -Recurse -Force
+        shell: pwsh
+      
+      - name: Set up JAGS environment (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          echo "JAGS_LIB=$JAGS_HOME/lib" >> $GITHUB_ENV
+          echo "PKG_CONFIG_PATH=$JAGS_HOME/lib/pkgconfig:$PKG_CONFIG_PATH" >> $GITHUB_ENV
+          echo "LDFLAGS=-L$JAGS_HOME/lib" >> $GITHUB_ENV
+          echo "CPPFLAGS=-I$JAGS_HOME/include" >> $GITHUB_ENV
+          echo "LD_LIBRARY_PATH=$JAGS_HOME/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
+          echo "DYLD_LIBRARY_PATH=$JAGS_HOME/lib:$DYLD_LIBRARY_PATH" >> $GITHUB_ENV
+          # Create symbolic links for JAGS modules
+          sudo mkdir -p /usr/local/lib/JAGS/modules-4
+          for module in basemod bugs terminal; do
+            sudo ln -sf "$JAGS_HOME/lib/JAGS/modules-4/${module}.so" "/usr/local/lib/JAGS/modules-4/${module}.so"
+          done
+      
+      - name: Set up JAGS environment (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          echo "PATH=C:/Program Files/JAGS/JAGS-4.3.1/bin;${env:PATH}" >> $env:GITHUB_ENV
+        shell: pwsh
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

README.md

@@ -1,9 +1,7 @@
 # handwriterRF
 
 <!-- badges: start -->
-[![R-CMD-check MacOS](https://github.com/CSAFE-ISU/handwriterRF/actions/workflows/R-CMD-check-macos.yaml/badge.svg)](https://github.com/CSAFE-ISU/handwriterRF/actions/workflows/R-CMD-check-macos.yaml)
-[![R-CMD-check Ubuntu](https://github.com/CSAFE-ISU/handwriterRF/actions/workflows/R-CMD-check-ubuntu.yaml/badge.svg)](https://github.com/CSAFE-ISU/handwriterRF/actions/workflows/R-CMD-check-ubuntu.yaml)
-[![R-CMD-check Windows](https://github.com/CSAFE-ISU/handwriterRF/actions/workflows/R-CMD-check-windows.yaml/badge.svg)](https://github.com/CSAFE-ISU/handwriterRF/actions/workflows/R-CMD-check-windows.yaml)
+[![R-CMD-check](https://github.com/CSAFE-ISU/handwriterRF/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CSAFE-ISU/handwriterRF/actions/workflows/R-CMD-check.yaml)
 [![Codecov test coverage](https://codecov.io/gh/CSAFE-ISU/handwriterRF/graph/badge.svg)](https://app.codecov.io/gh/CSAFE-ISU/handwriterRF)
 <!-- badges: end -->