R-CMD-check.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.os }}

    name: ${{ matrix.os }} (${{ matrix.r }})

    strategy:
      fail-fast: false
      matrix:
        os: ['macOS-latest', 'windows-latest', 'ubuntu-latest']
        r: ['release', 'devel']
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes

    steps:
      - uses: actions/checkout@v2

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.r }}
          use-public-rspm: true
     
      - name: Install system dependencies
        if: runner.os == 'macOS'
        run: brew install hdf5
        
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck, SeuratData=?ignore

      - name: Install SeuratData
        if: always()
        run: Rscript -e "install.packages('remotes', repos = 'http://cran.us.r-project.org'); remotes:::install_github('satijalab/seurat-data')"
        shell: bash

      - uses: r-lib/actions/check-r-package@v2

      - name: Show testthat output
        if: always()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: ${{ runner.os }}-r${{ matrix.r }}-results
          path: check