tweaking new BiocCheck action #2
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| # workflow derived from: https://github.com/insightsengineering/bioc-check-action | |
| on: | |
| push: | |
| branches: dev | |
| name: Bioc-check-new | |
| jobs: | |
| bioc-check: | |
| runs-on: macos-latest | |
| name: Bioc-check | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: release | |
| http-user-agent: release | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| - name: Install dependencies | |
| run: | | |
| install.packages("BiocManager") | |
| BiocManager::install("BiocCheck") | |
| shell: Rscript {0} | |
| - name: Run BiocCheck | |
| run: | | |
| bc_res <- BiocCheck::BiocCheck() | |
| print(paste0("Errors: ", length(bc_res$error), "\n")) | |
| print(paste0("Warnings: ", length(bc_res$warning), "\n")) | |
| print(paste0("Notes: ", length(bc_res$note), "\n")) | |
| n_errors <- length(bc_res$error) | |
| Sys.setenv("BC_ERRORS" = n_errors) | |
| shell: Rscript {0} | |
| - name: Check BiocCheck results | |
| run: | | |
| if [[ $BC_ERRORS -gt 0 ]]; then exit 1; else echo "BiocCheck passed!"; fi | |
| shell: bash |