BiocCheck.yaml

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}