R-CMD-check #569
This file contains 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
| on: | |
| push: | |
| pull_request: | |
| branches: | |
| - devel | |
| schedule: | |
| - cron: '0 8 * * 5' | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| container: ${{ matrix.config.image }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-latest, bioc: 'devel'} | |
| - { os: macOS-latest, bioc: 'devel', curlConfigPath: '/usr/bin/'} | |
| - { os: ubuntu-latest, bioc: 'devel'} | |
| # - { os: ubuntu-latest, bioc: 'devel', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} | |
| - { os: ubuntu-latest, image: 'bioconductor/bioconductor_docker:devel'} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| CRAN: ${{ matrix.config.cran }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CURL_CONFIG: ${{ matrix.config.curlConfigPath }}curl-config | |
| steps: | |
| - name: Check out repo | |
| uses: actions/checkout@v2 | |
| - name: Set up R and install BiocManager | |
| uses: grimbough/bioc-actions/setup-bioc@v1 | |
| if: matrix.config.image == null | |
| with: | |
| bioc-version: ${{ matrix.config.bioc }} | |
| - name: Set up pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| if: matrix.config.image == null | |
| - name: Install remotes | |
| run: | | |
| install.packages('remotes') | |
| shell: Rscript {0} | |
| - name: Query dependencies | |
| run: | | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE, repos = c(getOption('repos'), BiocManager::repositories())), 'depends.Rds', version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' && matrix.config.image == null | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}- | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| pak-version: devel | |
| - name: Install system dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install cairo | |
| brew install --cask xquartz | |
| brew install harfbuzz | |
| brew install fribidi | |
| brew install fftw | |
| # - name: Set up gfortran symlinks (macOS) | |
| # if: runner.os == 'macOS' | |
| # run: | | |
| # set -x | |
| # sudo ln -s /usr/local/Cellar/gcc@11/*/lib/gcc/11 /usr/local/gfortran/lib | |
| # gfortran --version | |
| - name: Install dependencies | |
| run: | | |
| local_deps <- remotes::local_package_deps(dependencies = TRUE) | |
| deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]], Ncpu = 2L) | |
| BiocManager::install(c("GenomeInfoDbData", "GO.db"), Ncpu = 2L) | |
| remotes::install_github("krassowski/complex-upset") | |
| remotes::install_cran('rcmdcheck', Ncpu = 2L) | |
| shell: Rscript {0} | |
| - name: Session info | |
| run: | | |
| options(width = 100) | |
| pkgs <- installed.packages()[, "Package"] | |
| sessioninfo::session_info(pkgs, include_base = TRUE) | |
| shell: Rscript {0} | |
| - name: Build, Install, Check | |
| uses: grimbough/bioc-actions/build-install-check@v1 | |
| - name: Run BiocCheck | |
| uses: grimbough/bioc-actions/run-BiocCheck@v1 | |
| with: | |
| arguments: '--no-check-bioc-views --no-check-bioc-help' | |
| error-on: 'error' | |
| # - name: Upload check results | |
| # if: failure() | |
| # uses: actions/upload-artifact@master | |
| # with: | |
| # name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| # path: check | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@master | |
| with: | |
| name: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-results | |
| path: check | |
| - name: Test coverage | |
| if: matrix.config.os == 'macOS-latest' | |
| run: | | |
| install.packages("covr") | |
| covr::codecov(token = "${{secrets.CODECOV_TOKEN}}") | |
| shell: Rscript {0} | |
| - name: Deploy | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/devel' && matrix.config.os == 'macOS-latest' | |
| run: | | |
| R CMD INSTALL . | |
| Rscript -e "remotes::install_dev('pkgdown'); pkgdown::deploy_to_branch(new_process = FALSE)" |