fix: resolve Bioconductor check warnings (#383) #39
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| ## Bioconductor-style R CMD check + BiocCheck | |
| ## Mirrors the checks run on the Bioconductor build system (BBS) | |
| ## https://contributions.bioconductor.org/bioconductor-package-submissions.html | |
| name: BioC Check | |
| on: | |
| push: | |
| branches: [master, devel] | |
| pull_request: | |
| branches: [master, devel] | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| bioc-check: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 120 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # Bioconductor devel tracks the latest R release | |
| - os: ubuntu-latest | |
| r-version: "devel" | |
| bioc-version: "devel" | |
| # Bioconductor release tracks the current R release | |
| - os: ubuntu-latest | |
| r-version: "release" | |
| bioc-version: "release" | |
| - os: macos-latest | |
| r-version: "release" | |
| bioc-version: "release" | |
| - os: windows-latest | |
| r-version: "release" | |
| bioc-version: "release" | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r-version }} | |
| use-public-rspm: true | |
| - name: Setup Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| # System dependencies (Linux) | |
| - name: Install system dependencies (Linux) | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update -qq | |
| sudo apt-get install -y --no-install-recommends \ | |
| libcurl4-openssl-dev \ | |
| libssl-dev \ | |
| libxml2-dev \ | |
| libglpk-dev | |
| # Install dependencies using r-lib/actions (uses pak, handles R-devel well) | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | | |
| any::BiocCheck | |
| any::rcmdcheck | |
| # Setup Python for reticulate (cross-platform) | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.x' | |
| - name: Install Python packages | |
| run: | | |
| pip install --upgrade pip | |
| pip install numpy scipy pandas | |
| shell: bash | |
| - name: Set RETICULATE_PYTHON | |
| run: | | |
| echo "RETICULATE_PYTHON=$(python -c 'import sys; print(sys.executable)')" >> $GITHUB_ENV | |
| shell: bash | |
| # R CMD build (mirrors BBS: build step) | |
| - name: Build package | |
| run: | | |
| R CMD build . --no-build-vignettes | |
| shell: bash | |
| # R CMD check (mirrors BBS: check step with --no-vignettes) | |
| - name: R CMD check | |
| run: | | |
| pkg=$(ls -1 netZooR_*.tar.gz) | |
| R CMD check "$pkg" \ | |
| --no-manual \ | |
| --no-vignettes \ | |
| --timings \ | |
| --install-args="--build" | |
| shell: bash | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| - name: Show check results | |
| if: always() | |
| run: | | |
| cat netZooR.Rcheck/00check.log | |
| shell: bash | |
| # BiocCheck (mirrors BBS: BiocCheck step) | |
| - name: BiocCheck | |
| run: | | |
| library(BiocCheck) | |
| BiocCheck(".", `no-check-vignettes` = TRUE, `new-package` = FALSE) | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: check-results-${{ matrix.os }}-R${{ matrix.r-version }} | |
| path: netZooR.Rcheck/ | |
| # Separate test job with coverage | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "release" | |
| use-public-rspm: true | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update -qq | |
| sudo apt-get install -y --no-install-recommends \ | |
| libcurl4-openssl-dev libssl-dev libxml2-dev libglpk-dev | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | | |
| any::covr | |
| - name: Test coverage | |
| run: | | |
| covr::codecov(quiet = FALSE) | |
| shell: Rscript {0} | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |