R-CMD-check #268
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| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| 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.r }} - ${{ matrix.config.bioc }} - ${{ matrix.config.image }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-latest, r: '4.1'} | |
| - { os: macOS-latest, r: '4.1'} | |
| - { os: ubuntu-16.04, r: '4.1', cran: "https://packagemanager.rstudio.com/all/__linux__/xenial/latest"} | |
| # - { os: ubuntu-20.04, r: 'devel', cran: "https://packagemanager.rstudio.com/all/__linux__/focal/latest"} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| CRAN: ${{ matrix.config.cran }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Install system libraries | |
| if: ${{ runner.os == 'Linux' }} | |
| run: | | |
| sudo apt-get install libcurl4-openssl-dev libglpk-dev | |
| - uses: actions/checkout@v2 | |
| - uses: r-lib/actions/setup-r@master | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@master | |
| - name: Install remotes | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-1- | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c('BiocManager', 'rcmdcheck', 'covr')) | |
| BiocManager::install(ask = FALSE, update = TRUE) | |
| toInstall <- remotes::dev_package_deps(dependencies = TRUE)[,'package'] | |
| toInstall <- setdiff(toInstall, installed.packages()[,'Package']) | |
| if(length(toInstall)) { BiocManager::install(toInstall, ask = FALSE) } | |
| 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: Check | |
| run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: BiocCheck | |
| run: | | |
| BiocManager::install("BiocCheck") | |
| BiocCheck::BiocCheck(".") | |
| shell: Rscript {0} | |
| - 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: ${{ runner.os }}-r${{ matrix.config.r }}-bioc-${{ matrix.config.bioc }}-results | |
| path: check | |
| - name: Test coverage | |
| if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'release' | |
| run: | | |
| install.packages("covr") | |
| covr::codecov(type = "all", token = "${{secrets.CODECOV_TOKEN}}") | |
| shell: Rscript {0} |