Removed internal seed setting #40
Workflow file for this run
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ## 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 }} |