R-CMD-check #204
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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 from github from within | |
| # a github action. | |
| on: | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| - cron: '0 4 * * *' | |
| name: R-CMD-check | |
| 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: 'release'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| if: | | |
| (github.event_name == 'push' && github.ref == 'refs/heads/main') || | |
| (github.event_name == 'schedule' && github.ref == 'refs/heads/development') | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install libglpk40 | |
| if: ${{ matrix.config.os == 'ubuntu-latest' }} | |
| run: sudo apt-get install -y libglpk40 | |
| - name: Install xquartz (Mac OS) | |
| if: ${{ matrix.config.os == 'macos-latest' }} | |
| run: brew install --cask xquartz | |
| - 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: Set R version | |
| run: | | |
| echo "R_VERSION=`R --version | head -n 1 | awk '{print $3}' | cut -b 1-3`" >> $GITHUB_ENV | |
| echo "R_LIBS_USER=`Rscript -e 'cat(.libPaths()[1L])'`" >> $GITHUB_ENV | |
| - 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 }} | |
| - 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 | |
| Rscript -e 'remotes::install_github("ctlab/fgsea")' # see: https://github.com/ctlab/fgsea/issues/165 | |
| - name: Install MetaProViz from git by remotes | |
| run: Rscript -e 'remotes::install_github("saezlab/MetaProViz", dependencies = TRUE)' #we install from GitHub as if we are a random user | |
| - name: Build and check package | |
| run: | | |
| R CMD build . | |
| R CMD check *.tar.gz --no-manual |