Package build & check #248
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| # 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 | |
| # This workflow tests if the package can be installed | |
| # Trigger workflow on push to main or development, and on a daily schedule | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - devel | |
| schedule: | |
| - cron: '0 4 * * *' | |
| # Name of the workflow as shown in GitHub Actions UI | |
| name: 'Package build & check' | |
| jobs: | |
| build-check: | |
| # Run the job on each OS in the matrix (macOS, Ubuntu, Windows) | |
| runs-on: ${{ matrix.config.os }} | |
| # Show OS and R version in job name | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| # Define the matrix for cross-platform testing | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macos-latest, r: 'release'} # macOS latest with R release | |
| - {os: ubuntu-latest, r: 'release'} # Ubuntu latest with R release | |
| - {os: windows-latest, r: 'release'} # Windows latest with R release | |
| # Set environment variables for authentication and R package source retention | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| R_LIBS_USER: ${{ github.workspace }}/.Rlibrary | |
| R_BIOC_VERSION: "3.22" | |
| # Only run on push to main/development or scheduled run | |
| if: | | |
| (github.event_name == 'push' && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/devel')) || | |
| (github.event_name == 'schedule' && github.ref == 'refs/heads/devel') | |
| steps: | |
| # Checkout the repository code | |
| - uses: actions/checkout@v4 | |
| # Setup Pandoc (required for vignette and markdown rendering) | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| # Install system dependency for glpk (required by some R packages on Ubuntu) | |
| - name: Install libglpk40 | |
| if: ${{ matrix.config.os == 'ubuntu-latest' }} | |
| run: sudo apt-get install -y libglpk40 | |
| # Install XQuartz for graphics on macOS (required by some R packages) | |
| - name: Install xquartz (Mac OS) | |
| if: ${{ matrix.config.os == 'macos-latest' }} | |
| run: brew install --cask xquartz | |
| # Setup R with the specified version | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| # Set R version as environment variable (used for caching and package installation) | |
| - name: Set R version | |
| run: | | |
| Rscript -e "cat('R_VERSION=', as.character(getRversion()), '\n', file = Sys.getenv('GITHUB_ENV'), append = TRUE)" | |
| # Ensure user library directory exists (cross-platform) | |
| - name: Create user library directory | |
| run: | | |
| mkdir -p "$R_LIBS_USER" | |
| shell: bash | |
| # Cache R package installations to speed up repeated builds | |
| - name: Set up R dependency cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ env.R_VERSION }} | |
| restore-keys: | | |
| ${{ runner.os }}-r-${{ env.R_VERSION }} | |
| # Install knitr to user library (required for vignette building; fixes missing knitr error) | |
| - name: Install knitr | |
| run: Rscript -e 'install.packages("knitr", lib = Sys.getenv("R_LIBS_USER"))' | |
| - name: Install remotes | |
| run: | | |
| Rscript -e 'install.packages("remotes")' | |
| Rscript -e 'remotes::install_github("r-lib/remotes")' # see: https://github.com/r-lib/remotes/issues/798 | |
| # Install OmnipathR from Bioconductor devel | |
| - name: Install OmnipathR from Bioconductor devel | |
| run: | | |
| Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' | |
| Rscript -e 'BiocManager::install()' | |
| Rscript -e 'remotes::install_github("saezlab/OmnipathR@devel")' | |
| - name: Install EnhancedVolcano (not yet in Bioc 3.22) | |
| run: | | |
| Rscript -e 'remotes::install_github("kevinblighe/EnhancedVolcano")' | |
| # Set Bioconductor back to release and install other Bioconductor dependencies | |
| - name: Install other Bioconductor dependencies from release | |
| run: | | |
| Rscript -e 'remotes::install_deps(dependencies = TRUE)' | |
| # ComplexUpset should be installed after ggplot2 to ensure compatibility, especially on Linux/Ubuntu. | |
| - name: Install latest ggplot2 | |
| run: Rscript -e 'install.packages("ggplot2", type="source")' | |
| - name: Install ComplexUpset from source | |
| run: Rscript -e 'install.packages("ComplexUpset", type="source")' | |
| # Install MetaProViz | |
| - name: Install MetaProViz from git by remotes | |
| if: github.ref == 'refs/heads/main' | |
| run: Rscript -e 'remotes::install_github("saezlab/MetaProViz", dependencies = TRUE)' #we install from GitHub as if we are a random user | |
| # Build and check the package using bash shell (required for Windows compatibility) | |
| - name: Build and check package | |
| shell: bash | |
| run: | | |
| R CMD build . | |
| R CMD check *.tar.gz --no-manual | |
| - name: Run BiocCheck | |
| run: | | |
| Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' | |
| Rscript -e 'BiocManager::install("BiocCheck")' | |
| Rscript -e 'BiocCheck::BiocCheck(list.files(pattern = "*.tar.gz"))' |