main_check.yml

# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.
#
# See https://github.com/r-lib/actions/tree/master/examples#readme for
# additional example workflows available for the R community.


name: R-CMD-check

on:
  pull_request:
    types: closed
    branches: [ "main" ]

permissions:
  contents: read


jobs:
  R-CMD-check:
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    runs-on: ${{ matrix.config.os }}

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

    strategy:
      fail-fast: false
      matrix:
        config: # matrix of system runners to run workflow on
          - {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'}

    steps:

      - name: Remove vignettes dir
        run: rm -rf 'vignettes/'
        shell: bash

      - name: Checkout repo for workflow access
        uses: actions/checkout@v4

      - name: Set up R environment
        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

      - name: Set up dependencies (general)
        uses: r-lib/actions/setup-r-dependencies@v2
        env:
          _R_CHECK_FORCE_SUGGESTS: false
          _R_CHECK_RD_XREFS: false
        with:
          install-pandoc: false
          dependencies: '"hard"' # do not use suggested dependencies
          extra-packages: |
            any::ggdendro
            any::ComplexHeatmap
            any::ggalluvial
            any::ggforce
            any::ggraph

      - name: Set up dependencies (GiottoData)
        run: |
          suppressWarnings({
            remotes::install_github('drieslab/GiottoData', build = FALSE)
          })
        shell: Rscript {0}

      - name: Run R CMD check
        uses: r-lib/actions/check-r-package@v2
        with:
          upload-snapshots: true
          error-on: '"error"' # workflow errors on error only, can change to include warnings

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



  # render-rmarkdown:
  #   name: Update README.Rmd
  #   runs-on: ubuntu-latest
  #   steps:
  #     - name: Checkout repo
  #       uses: actions/checkout@v3
  #       with:
  #         fetch-depth: 0
  #
  #     - uses: r-lib/actions/setup-pandoc@v2
  #
  #     - uses: r-lib/actions/setup-r@v2
  #
  #     - uses: r-lib/actions/setup-renv@v2
  #
  #     - name: Install rmarkdown
  #       run: Rscript -e 'install.packages("rmarkdown")'
  #
  #     - name: Render README
  #       run: Rscript -e 'rmarkdown::render("README.Rmd")'
  #
  #     - name: Commit results
  #       run: |
  #         git commit README.md -m 'Re-build README.Rmd' || echo "No changes to commit"
  #         git push origin || echo "No changes to commit"