steup bioc devel in rprofile with ubuntu-r-devel #39
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| # | |
| # NOTE: This workflow is overkill for most R packages and | |
| # check-standard.yaml is likely a better choice. | |
| # usethis::use_github_action("check-standard") will install it. | |
| on: | |
| push: | |
| branches: [main, master, develop] | |
| pull_request: | |
| branches: [main, master, develop] | |
| name: R-CMD-check.yaml | |
| permissions: read-all | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # - {os: macos-latest, r: 'release'} | |
| # - {os: windows-latest, r: 'release'} | |
| # use 4.0 or 4.1 to check with rtools40's older compiler | |
| # - {os: windows-latest, r: 'oldrel-4'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| # - {os: ubuntu-latest, r: 'release'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| # Some packages might unavailable on the older versions, so let's ignore xref warnings | |
| _R_CHECK_RD_XREFS_: false | |
| # Runs vdiffr test only on the latest version of R | |
| VDIFFR_RUN_TESTS: ${{ matrix.config.r == 'release' }} | |
| VDIFFR_LOG_PATH: "../vdiffr.Rout.fail" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: use Bioconductor devel only for r-devel | |
| if: matrix.config.r == 'devel' | |
| run: | | |
| Rscript -e 'install.packages("BiocManager", repos = "https://cran.r-project.org")' | |
| Rscript -e 'cat("options(repos = BiocManager::repositories(version = \"devel\"))\n", file = ".Rprofile", append = TRUE)' | |
| Rscript -e 'BiocManager::version(); print(BiocManager::repositories())' | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 3 | |
| extra-packages: > | |
| any::rcmdcheck | |
| any::Hmisc | |
| any::quantreg | |
| bioc::IRanges | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| build_args: 'c("--no-build-vignettes","--no-manual")' | |
| args: 'c("--ignore-vignettes","--no-manual")' |