r-cmd-check.yaml

on:
  push:
    branches:
      - master
  pull_request:

name: R CMD check

jobs:
  check:
    name: R CMD check
    runs-on: ubuntu-latest
    container: bioconductor/bioconductor_docker:devel

    steps:
      - uses: actions/checkout@v3

      - name: Set directories
        run: |
          echo "R_PKG_DIR=${R_HOME}/site-library" >> $GITHUB_ENV

      - name: Restore the package directory
        uses: actions/cache@v3
        with:
          path: ${{ env.R_PKG_DIR }}
          key: check-packages

      - name: Install dependencies
        shell: Rscript {0}
        run: |
          stuff <- read.dcf("DESCRIPTION")
          stuff <- stuff[,intersect(colnames(stuff), c("Imports", "LinkingTo", "Suggests", "Depends"))]
          deps <- sub(" .*", "", unlist(strsplit(stuff, ",\\s*"), use.names=FALSE))
          BiocManager::install(deps)

      - name: Build the package
        run: R CMD build .
  
      - name: Check the package
        run: |
          tarball=$(ls *.tar.gz)
          R CMD check --no-manual $tarball