r.yml

# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.
#
# See https://github.com/r-lib/actions/tree/master/examples#readme for
# additional example workflows available for the R community.

# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.
#
# See https://github.com/r-lib/actions/tree/master/examples#readme for
# additional example workflows available for the R community.


name: R
on:
  push:
    branches: [ "master" ]
  pull_request:
    branches: [ "master" ]
permissions:
  contents: read
jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}
    strategy:
      matrix:
        config:
          - { os: ubuntu-22.04, r: 'devel' }
          - { os: ubuntu-22.04, r: 'release' }
          - { os: macOS-latest, r: 'next' }
          - { os: windows-latest, r: 'release' }
    steps:
    - name: Checkout code
      uses: actions/checkout@v3
      
    # Use the latest version of setup-r that includes the fix for pkgconf
    - name: Set up R (latest version)
      uses: r-lib/actions/setup-r@v2.11.1
      with:
        r-version: ${{ matrix.config.r }}
        
    # Install system dependencies for Ubuntu
    - name: Install system dependencies (Ubuntu)
      if: startsWith(matrix.config.os, 'ubuntu')
      run: |
        sudo apt-get update -y
        sudo apt-get install -y pandoc
        
    - name: Suppress Transition Warnings
      if: startsWith(matrix.config.os, 'ubuntu')
      run: echo "Suppressing Ubuntu transition warnings"
      
    # Debug Installed Tools for Ubuntu
    - name: Debug Installed Tools (Ubuntu)
      if: startsWith(matrix.config.os, 'ubuntu')
      run: |
        echo "R version:"
        Rscript -e "R.version"
        echo "Checking pkg-config installation:"
        which pkg-config || echo 'pkg-config not found'
        pkg-config --version || echo 'pkg-config version issue'
        
    # Install system dependencies for macOS
    - name: Install system dependencies (macOS)
      if: matrix.config.os == 'macOS-latest'
      run: |
        brew update
        brew install pandoc
        echo "pkgconf version:"
        pkg-config --version
        
    # Debug Installed Tools for macOS
    - name: Debug Installed Tools (macOS)
      if: matrix.config.os == 'macOS-latest'
      run: |
        echo "R version:"
        Rscript -e "R.version"
        echo "Checking pkg-config installation:"
        which pkg-config || echo 'pkg-config not found'
        pkg-config --version || echo 'pkg-config version issue'
        
    # Install Pandoc for Windows
    - name: Install Pandoc for Windows
      if: matrix.config.os == 'windows-latest'
      run: |
        choco install pandoc -y
        
    # Install R dependencies
    - name: Install R dependencies
      run: |
        Rscript -e "if (!requireNamespace('remotes', quietly = TRUE)) install.packages('remotes')"
        Rscript -e "remotes::install_deps(dependencies = TRUE)"
        
    # Run R tests
    - name: Run R tests
      run: |
        Rscript -e "testthat::test_file('tests/testthat/test-counts.R')"
        Rscript -e "testthat::test_file('tests/testthat/test-reordering.R')"
        
    # Build the package for Linux/macOS
    - name: Build the package (Linux/macOS)
      if: matrix.config.os != 'windows-latest'
      run: |
        R CMD build .
        
    # Build the package for Windows
    - name: Build the package (Windows)
      if: matrix.config.os == 'windows-latest'
      shell: cmd
      run: |
        R CMD build .
        
    # Check the package for Linux/macOS
    - name: Check the package (Linux/macOS)
      if: matrix.config.os != 'windows-latest'
      run: |
        echo "Running R CMD build"
        R CMD build .
        echo "Running R CMD check"
        PKG_TAR=$(ls *.tar.gz)
        R CMD check "$PKG_TAR" --no-manual --as-cran
        
    # Debug Build Output for Windows
    - name: Debug Build Output (Windows)
      if: matrix.config.os == 'windows-latest'
      shell: cmd
      run: |
        dir /b *.tar.gz || echo "No .tar.gz file found after build"
        
    # Check the package for Windows
    - name: Check the package (Windows)
      if: matrix.config.os == 'windows-latest'
      shell: cmd
      run: |
        dir /b *.tar.gz > tarball.txt
        set /p PKG_TAR=<tarball.txt
        echo Checking package %PKG_TAR%
        R CMD check %PKG_TAR% --no-manual --as-cran