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-latest, r: 'devel' }
          - { os: ubuntu-latest, r: 'release' }
          - { os: macOS-latest, r: 'release' }
          - { os: windows-latest, r: 'release' }
    steps:
    - name: Checkout code
      uses: actions/checkout@v3

    - name: Set up R (latest version)
      uses: r-lib/actions/setup-r@v2.3.0
      with:
        r-version: '4.4.1'
        
    # Install system dependencies required for R packages
    - name: Install system dependencies (Linux)
      if: matrix.config.os == 'ubuntu-latest'
      run: |
        sudo apt-get update -y || true
        sudo apt-get install -y pandoc

    - name: Debug Installed Tools
      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'

    - name: Install system dependencies (macOS)
      if: matrix.config.os == 'macOS-latest'
      run: |
        brew install pandoc

    - name: Install Pandoc for Windows
      if: matrix.config.os == 'windows-latest'
      run: |
        choco install pandoc -y

    - name: Install R dependencies
      run: |
        Rscript -e "if (!requireNamespace('remotes', quietly = TRUE)) install.packages('remotes')"
        Rscript -e "remotes::install_deps(dependencies = TRUE)"

    - 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 based on os
    - name: Build the package (Linux/macOS)
      if: matrix.config.os != 'windows-latest'
      run: |
        R CMD build .

    - name: Build the package (Windows)
      if: matrix.config.os == 'windows-latest'
      shell: cmd
      run: |
        R CMD build .

     #Check the package
    - 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

    - name: Check the package (Windows)
      if: matrix.config.os == 'windows-latest'
      shell: cmd
      run: |
        FOR /F "tokens=*" %%i IN ('dir /b *.tar.gz') DO SET PKG_TAR=%%i && R CMD check "%%PKG_TAR%" --no-manual --as-cran