check-bioc.yml

name: Bioc build and check

on:
  push:
    paths:
      - 'DESCRIPTION'
      - '**.yml'
    branches:
      - devel
  pull_request:
    branches:
      - devel

jobs:
  build-check:
    runs-on: ubuntu-22.04
    container: bioconductor/bioconductor_docker:devel
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
      NOT_CRAN: true
      TZ: UTC

    steps:
      - name: Checkout Repository
        uses: actions/checkout@v3

      - name: Query dependencies
        run: |
          BiocManager::install(update = TRUE, ask = FALSE)
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
        shell: Rscript {0}

      - name: Cache R packages
        if: runner.os != 'Windows'
        uses: actions/cache@v3
        with:
          path: /usr/local/lib/R/site-library
          key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-r-1-

      - name: Install Package Dependencies
        run: |
          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
          BiocManager::install(ask = FALSE, update = TRUE)
        shell: Rscript {0}

      - name: Check Package
        id: rcmdcheck
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")
        shell: Rscript {0}