rhub.yaml

# GitHub Action workflow for R-hub testing
#
# This file is a heavily-modified version of the generic workflow file generated by
# `rhub::rhub_setup()`. See r-hub documentation for details.
#
# The heavy modifications are to allow installation of NGCHMSupportFiles and
# NGCHMDemoData from the non-standard R-universe repository. (These packages
# are listed ans 'Enhances' and the R-universe repository is listed in the
# "Additional_repositories" field of the DESCRIPTION file.)

name: R-hub
run-name: "${{ github.sha }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"

on:
  workflow_dispatch:
    inputs:
      config:
        description: 'A comma separated list of R-hub platforms to use.'
        type: string
        default: 'linux,windows,macos'
      name:
        description: 'Run name. You can leave this empty now.'
        type: string
      id:
        description: 'Unique ID. You can leave this empty now.'
        type: string

jobs:

  setup:
    runs-on: ubuntu-latest
    outputs:
      containers: ${{ steps.rhub-setup.outputs.containers }}
      platforms: ${{ steps.rhub-setup.outputs.platforms }}
    steps:
    - uses: r-hub/actions/setup@v1
      with:
        config: ${{ github.event.inputs.config }}
      id: rhub-setup

  # In r_hub 2.0.0, the linux containers (based on ubuntu and fedora) are used
  # to run R CMD CHECK for various versions of R, compilers (e.g. gcc, clang), etc.
  linux-containers:
    needs: setup
    if: ${{ needs.setup.outputs.containers != '[]' }}
    runs-on: ubuntu-latest
    name: ${{ matrix.config.label }}
    strategy:
      fail-fast: false
      matrix:
        config: ${{ fromJson(needs.setup.outputs.containers) }}
    container:
      image: ${{ matrix.config.container }}
    steps:
      - uses: r-hub/actions/checkout@v1
      # marohrdanz tried all the 'standard' ways to configure this workflow to allow for
      # NGCHMDemoData and NGCHMSupportFiles setup from R-universe, but none of them worked here.
      # So, using a custom Rprofile to set the repos option explicitly.
      # Note (this method doesn't work on Windows, so it is not used in the 'other-platform' job below.
      #       Instead one of the 'standard' methods is used there.)
      - name: Create Rprofile with R-universe repo
        run: |
          echo 'local({
            r <- getOption("repos")
            r["CRAN"] <- "https://cloud.r-project.org/"
            r["MDA"] <- "https://md-anderson-bioinformatics.r-universe.dev"
            options(repos = r)
          })' > ~/.Rprofile
      - uses: r-hub/actions/platform-info@v1
        with:
          token: ${{ secrets.RHUB_TOKEN }}
          job-config: ${{ matrix.config.job-config }}
      - uses: r-hub/actions/setup-deps@v1
        with:
          token: ${{ secrets.RHUB_TOKEN }}
          job-config: ${{ matrix.config.job-config }}
      - uses: r-hub/actions/run-check@v1
        with:
          token: ${{ secrets.RHUB_TOKEN }}
          job-config: ${{ matrix.config.job-config }}

  # In r_hub 2.0.0, "other-platforms" are linux, macos, macos-arm64, and windows
  other-platforms:
    needs: setup
    if: ${{ needs.setup.outputs.platforms != '[]' }}
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.label }}
    strategy:
      fail-fast: false
      matrix:
        config: ${{ fromJson(needs.setup.outputs.platforms) }}

    steps:
      - uses: r-hub/actions/checkout@v1
      - uses: r-hub/actions/setup-r@v1
        with:
          job-config: ${{ matrix.config.job-config }}
          token: ${{ secrets.RHUB_TOKEN }}
      # using r-lib action instead of r-hub/actions/setup-r because of need for extra-repositories input
      - uses: r-lib/actions/setup-r@v2
        with:
          extra-repositories: "https://md-anderson-bioinformatics.r-universe.dev"
      - uses: r-hub/actions/platform-info@v1
        with:
          token: ${{ secrets.RHUB_TOKEN }}
          job-config: ${{ matrix.config.job-config }}
      # using r-lib action instead of r-hub/actions/setup-deps because of need for extra-repositories above
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck, local::.
          needs: check
      - uses: r-hub/actions/run-check@v1
        with:
          job-config: ${{ matrix.config.job-config }}
          token: ${{ secrets.RHUB_TOKEN }}