check-bioc.yml

## Following the example workflow at
## https://github.com/grimbough/biocActionsExamples/blob/2205c9ff10ae2ebf04b5477028bc50397c6b61b4/.github/workflows/example-workflow.yml

on:
  push:
  pull_request:
  workflow_dispatch:

name: R-CMD-check-bioc

jobs:
  build-check:
    name: Bioc ${{ matrix.bioc-version }} (${{ matrix.os }})
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, windows-latest, macos-latest]
        bioc-version: [devel] ## Test on Bioconductor's latest devel

    runs-on: ${{ matrix.os }}

    steps:

      - name: Checkout repository
        uses: actions/checkout@v2

      - name: Setup R and Bioconductor
        uses: grimbough/bioc-actions/setup-bioc@v1
        with:
          bioc-version: ${{ matrix.bioc-version }}
          bioc-mirror: https://ftp.gwdg.de/pub/misc/bioconductor
          use-public-rspm: false

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

      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 1

      - name: Build, Install, Check
        id: build-install-check
        uses: grimbough/bioc-actions/build-install-check@v1
        with:
          package-directory: '.'

      ## Turn off the checks that we know will fail
      ## Cause the workflow to error if any new errors appear
      - name: Run BiocCheck with arguments
        uses: grimbough/bioc-actions/run-BiocCheck@v1
        with:
          package-directory: '.'
          arguments: '--no-check-bioc-help --no-check-version-num --no-check-news'
          error-on: 'warning'

      - name: Upload check output
        uses: actions/upload-artifact@v2
        with:
          name: ${{ matrix.os }}-bioc-${{ matrix.bioc-version}}
          path: |
            ${{ steps.build-install-check.outputs.check-dir }}
            ${{ steps.build-install-check.outputs.source-tarball }}
            ${{ steps.build-install-check.outputs.package-binary }}