unused argument #317
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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 | |
| name: R-CMD-check | |
| on: | |
| pull_request: | |
| branches: | |
| - "*" | |
| push: | |
| branches: | |
| - "master" | |
| env: | |
| cache-version: "cache-v1" | |
| jobs: | |
| R-CMD-check: | |
| strategy: | |
| matrix: | |
| config: | |
| - { os: ubuntu-latest } | |
| - { os: macos-latest } # disabling until https://github.com/r-lib/actions/issues/950 is resolved | |
| - { os: windows-latest } | |
| runs-on: ${{ matrix.config.os }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup R and Bioconductor | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| id: install-r | |
| with: | |
| bioc-version: devel | |
| - name: Install ubuntu dependencies | |
| if: ${{ matrix.config.os == 'ubuntu-latest' }} | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y libgsl-dev | |
| - name: Install macos dependencies | |
| if: ${{ matrix.config.os == 'macos-latest' }} | |
| run: | | |
| brew install gsl | |
| - name: Get R version | |
| id: R | |
| run: | | |
| R --version > VERSION | |
| echo "version=$(head -1 VERSION | awk '{print $3}')" >> $GITHUB_OUTPUT | |
| rm VERSION | |
| shell: bash -l {0} | |
| - name: Get Bioconductor version | |
| id: BIOC | |
| run: | | |
| echo "version=$R_BIOC_VERSION" >> $GITHUB_OUTPUT | |
| shell: bash -l {0} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Cache R packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: /home/runner/work/_temp/Library | |
| key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ steps.BIOC.outputs.version}}-r-${{ steps.R.outputs.version}}-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-${{ steps.BIOC.outputs.version}}-r-${{ steps.R.outputs.version}}- | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| - uses: r-lib/actions/check-r-package@v2 | |
| - name: Check if actor has permission | |
| if: matrix.config.os == 'ubuntu-latest' | |
| id: check_permissions | |
| run: | | |
| # Define allowed actors | |
| ALLOWED_ACTORS=("zktuong" "Jiawei-Yu10") # Replace these with the actual GitHub usernames | |
| if [[ " ${ALLOWED_ACTORS[@]} " =~ " ${GITHUB_ACTOR} " ]]; then | |
| echo "has_permission=true" >> $GITHUB_OUTPUT | |
| else | |
| echo "has_permission=false" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Debug permissions output | |
| run: | | |
| echo "Has permission: ${{ steps.check_permissions.outputs.has_permission }}" | |
| - name: Setup to test coverage | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| if: steps.check_permissions.outputs.has_permission == 'true' && matrix.config.os == 'ubuntu-latest' | |
| with: | |
| packages: covr | |
| - name: Test coverage | |
| if: steps.check_permissions.outputs.has_permission == 'true' && matrix.config.os == 'ubuntu-latest' | |
| run: | | |
| Rscript -e 'covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")' | |
| shell: bash -l {0} |