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]
  pull_request:
    branches: [main]

name: R-CMD-check

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

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

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest,   r: 'release'}
#          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
          - {os: ubuntu-latest,   r: 'release'}
          - {os: ubuntu-latest,   r: 'oldrel-1'}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      SYNAPSE_USERNAME: ${{ secrets.SYNAPSE_USERNAME }}
      SYNAPSE_PASSWORD: ${{ secrets.SYNAPSE_PASSWORD }}
      CBIOPORTAL_TOKEN: ${{ secrets.CBIOPORTAL_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.config.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}
          use-public-rspm: true

      - uses: grimbough/bioc-actions/setup-bioc@v1
        with:
          bioc-version: release
          bioc-mirror: https://ftp.gwdg.de/pub/misc/bioconductor

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: rcmdcheck

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