r-cmd-check.yml

# Download the stock synthesis executable, then Run r cmd check

# Name of the workflow, which will be what it is called under the "actions" tab
name: r-cmd-check
# on specifies the build triggers. Learn more at https://docs.github.com/en/actions/using-workflows/events-that-trigger-workflows
on:
  # The schedule build trigger runs the workflow at a scheduled time.
  schedule:
    # This should run the default branch (typically main) weekly on sunday at 2:45am UTC
    - cron: '01 3 * * 2'
  # The workflow_dispatch build trigger adds a button so that you can start workflows manually.
  workflow_dispatch:
  # The push build trigger runs jobs when new commits are pushed up to github.
  push:
    # specifying branches means the workflow will only run on pushes to the branches listed, in this case, only main
    branches:
      - main
      - r4ss_1.50.0
  # The pull_request build trigger runs jobs when a pull request is made or commits are pushed to the pull request.
  pull_request:
    # specifying branches means the workflow will only run when the pull request is to the merge into the branch listed, in this case, main.
    branches:
      - main
# jobs specifies the jobs to run. you can have multiple jobs per github actions workflow, but in this case we have only one, which is
# named run-R-CMD-check.
jobs:
  run-R-CMD-check:
    # the operating system to run on
    runs-on: 'ubuntu-latest'
    strategy:
      fail-fast: false
    # environment settings, needed for running r (first 2 settings) and downloading from github (GITHUB_PAT)
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Checkout github repository, in this case nwfscDiags
        uses: actions/checkout@v3

      - name: update linux libraries
        run: |
          sudo apt-get update
          sudo apt-get install -y libcurl4-openssl-dev
          sudo add-apt-repository ppa:ubuntu-toolchain-r/test
          sudo apt-get install --only-upgrade libstdc++6

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: 'release'

      - name: Setup pandoc, in case of vignettes in the R package
        uses: r-lib/actions/setup-pandoc@v2

      - name: Setup R packages
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck
          needs: check

      - name: Get the latest SS3 executable and move to expected location
        run: |
          wget -O ss3 https://github.com/nmfs-ost/ss3-source-code/releases/latest/download/ss3_linux
          sudo chmod a+x ss3
          cp ss3 inst/extdata/simple_small/ss3
          rm ss3

      - name: run r-cmd-check using R
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
        shell: Rscript {0}

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

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: 'linux-release-results'
          path: check