R-CMD-check.yaml

# NOTE: This workflow is overkill for most R packages
# check-standard.yaml is likely a better choice
# usethis::use_github_action("check-standard") will install it.
#
# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
on:
  push:
    branches:
      - main
      - master
  pull_request:
    branches:
      - main
      - master

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:
          # vdiffr & shinytest only runs on mac r-release since the results aren't cross-platform
          - {os: macOS-latest,   r: 'release', visual_tests: true, node: "14.x", shinytest: true}
          - {os: windows-latest, r: 'release'}
          - {os: windows-latest, r: '4.1'}
          - {os: windows-latest, r: '3.6'}
          - {os: ubuntu-latest,   r: 'devel'}
          - {os: ubuntu-latest,   r: 'release'}
          - {os: ubuntu-latest,   r: 'oldrel-1'}
          - {os: ubuntu-latest,   r: 'oldrel-2'}
          - {os: ubuntu-latest,   r: 'oldrel-3'}
          - {os: ubuntu-latest,   r: 'oldrel-4'}

    env:
      VISUAL_TESTS: ${{ matrix.config.visual_tests }}
      SHINYTEST: ${{ matrix.config.shinytest }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      MAPBOX_TOKEN: ${{ secrets.MAPBOX_TOKEN }}
      plotly_username: ${{ secrets.PLOTLY_USERNAME }}
      plotly_api_key: ${{ secrets.PLOTLY_API_KEY }}

    steps:
      - uses: actions/checkout@v2

      - uses: r-lib/actions/setup-r@v2
        id: install-r
        with:
          r-version: ${{ matrix.config.r }}
          use-public-rspm: true

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

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          cache-version: 3
          needs: check

      - name: Set up Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8
      
      - name: Install kaleido
        if: matrix.config.visual_tests == true
        run: |
          sudo chown -R $UID $CONDA # https://github.com/nextstrain/conda/issues/5
          Rscript -e "reticulate::install_miniconda()"
          Rscript -e "reticulate::conda_install('r-reticulate', 'python-kaleido')"
          Rscript -e "reticulate::conda_install('r-reticulate', 'plotly', channel = 'plotly')"
          Rscript -e "reticulate::use_miniconda('r-reticulate')"
        
      - name: Install shinytest deps
        if: matrix.config.shinytest == true
        run: |
          Rscript -e 'shinytest::installDependencies()'
          R CMD install .
        shell: bash
        
        # Run test() before R CMD check since, for some reason, rcmdcheck::rcmdcheck() skips vdiffr tests
      - name: Run Tests
        run: |
          options(crayon.enabled = TRUE, testthat.progress.max_fails=1000)
          res <- devtools::test()
          df <- as.data.frame(res)
          if (sum(df$failed) > 0 || any(df$error)) stop("GHA CI tests failed")
        shell: Rscript {0}
        
      # Upload the whole pkg since tests where run with devtools::test()
      - name: Upload check results
        if: always()
        uses: actions/upload-artifact@master
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: ./

      - name: Check package
        uses: r-lib/actions/check-r-package@v2
        with:
          check-dir: '"check"'
          # Run check with --no-tests since we ran them abve
          # 2023-01-03: `{purrr}` v1.0.0 had trouble on Windows without the `--no-multiarch`
          # https://github.com/plotly/plotly.R/pull/2221
          args: 'c("--no-tests", "--no-manual", "--as-cran", "--no-multiarch")'
          error-on: '"warning"'
      
      #- name: Show testthat output
      #  if: always()
      #  run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
      #  shell: bash