Testing library contents #156
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| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - master | |
| name: R-CMD-check | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.bioc-version }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-2022, bioc-version: 'devel'} | |
| - { os: macOS-latest, bioc-version: 'devel'} | |
| - { os: ubuntu-20.04, bioc-version: 'devel', system-libs: 'libcurl4-gnutls-dev libaec-dev'} | |
| - { os: ubuntu-22.04, bioc-version: 'devel', system-libs: 'libcurl4-openssl-dev'} | |
| steps: | |
| - name: Configure git | |
| run: | | |
| git config --global core.autocrlf false | |
| - name: Install Linux system libraries | |
| if: ${{ runner.os == 'Linux' }} | |
| run: | | |
| sudo apt-get update && sudo apt-get install ${{ matrix.config.system-libs }} | |
| - name: Install Mac system libraries | |
| if: ${{ matrix.config.os == 'macOS-latest' }} | |
| run: | | |
| sudo Rscript -e 'source("https://mac.R-project.org/bin/install.R")' -e 'install.libs("openssl")' | |
| shell: bash | |
| - uses: actions/checkout@v3 | |
| - name: Setup R and Bioconductor | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| with: | |
| bioc-version: ${{ matrix.config.bioc-version }} | |
| bioc-mirror: https://ftp.gwdg.de/pub/misc/bioconductor | |
| # - name: Create Makevars | |
| # if: ${{ matrix.config.os == 'macOS-latest' }} | |
| # run: | | |
| # mkdir $HOME/.R | |
| # echo 'LDFLAGS="-L/usr/local/opt/[email protected]/lib"' > $HOME/.R/Makevars | |
| # echo 'CPPFLAGS="-I/usr/local/opt/[email protected]/include"' >> $HOME/.R/Makevars | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| ## install BiocCheck here so it is cached | |
| extra-packages: | | |
| bioc::BiocCheck | |
| - name: Bioc - Build, Install, Check | |
| id: build-install-check | |
| uses: grimbough/bioc-actions/build-install-check@v1 | |
| - name: Run BiocCheck | |
| uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
| with: | |
| error-on: 'never' | |
| arguments: '--no-check-bioc-help' | |
| - name: Session info | |
| run: | | |
| sessionInfo() | |
| shell: Rscript {0} | |
| - name: Check libhdf5 status | |
| run: | | |
| ls -l ${R_LIBS_USER}/Rhdf5lib/lib | |
| nm ${R_LIBS_USER}/Rhdf5lib/lib/libhdf5.a | grep EVP_sha256 | |
| shell: bash | |
| - name: Upload check results | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ matrix.config.os }}-results | |
| path: ${{ steps.build-install-check.outputs.check-dir }} | |
| - name: Upload check results | |
| if: ${{ failure() }} | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ matrix.config.os }}-${{ matrix.config.r }}-hdf5_config.log | |
| path: check/*.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/config.log | |
| ## upload source and binary packages | |
| - name: Upload check output | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}-pkgs | |
| path: | | |
| ${{ steps.build-install-check.outputs.source-tarball }} | |
| ${{ steps.build-install-check.outputs.package-binary }} | |