BiocCheck: only fail on errors, allow warnings #4
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| name: BiocCheck | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| jobs: | |
| BiocCheck: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev | |
| - name: Install BiocManager and BiocCheck | |
| run: | | |
| install.packages("BiocManager", repos = "https://cloud.r-project.org") | |
| BiocManager::install("BiocCheck", update = FALSE, ask = FALSE) | |
| shell: Rscript {0} | |
| - name: Install package dependencies | |
| run: | | |
| BiocManager::install(c("remotes"), update = FALSE, ask = FALSE) | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| shell: Rscript {0} | |
| - name: Run BiocCheck (warnings allowed) | |
| run: | | |
| result <- BiocCheck::BiocCheck( | |
| ".", | |
| `quit-with-status` = FALSE, | |
| `no-check-bioc-help` = TRUE | |
| ) | |
| # Print summary | |
| cat("\n\n=== BiocCheck Summary ===\n") | |
| print(result) | |
| # Only fail on ERRORs, not WARNINGs | |
| if (length(result$error) > 0) { | |
| cat("\n\nERRORS found:\n") | |
| print(result$error) | |
| quit(status = 1) | |
| } else { | |
| cat("\n\nNo critical errors. Package ready for submission.\n") | |
| } | |
| shell: Rscript {0} |