v0.1.0: Initial release #8
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| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: R-CMD-check | |
| 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'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| 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: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - name: Install Bioconductor Suggests (optional) | |
| run: | | |
| if (!requireNamespace("BiocManager", quietly = TRUE)) | |
| install.packages("BiocManager") | |
| bioc_pkgs <- c("DESeq2", "edgeR", "limma", "ShortRead", "Biostrings", | |
| "Rsamtools", "GenomicAlignments", "GenomicFeatures", | |
| "GenomicRanges", "SummarizedExperiment", "Biobase", | |
| "ComplexHeatmap") | |
| # Only install packages that are actually in Suggests | |
| desc_suggests <- strsplit(read.dcf("DESCRIPTION")[, "Suggests"], ",\\s*")[[1]] | |
| desc_suggests <- trimws(gsub("\\s*\\(.*\\)", "", desc_suggests)) | |
| to_install <- intersect(bioc_pkgs, desc_suggests) | |
| if (length(to_install) > 0) { | |
| message("Installing Bioconductor packages: ", paste(to_install, collapse = ", ")) | |
| tryCatch( | |
| BiocManager::install(to_install, update = FALSE), | |
| error = function(e) message("Bioconductor install skipped: ", e$message) | |
| ) | |
| } else { | |
| message("No Bioconductor Suggests found — skipping.") | |
| } | |
| shell: Rscript {0} | |
| continue-on-error: true | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' |