R-CMD-check.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
#
# NOTE: This workflow is overkill for most R packages and
# check-standard.yaml is likely a better choice.
# usethis::use_github_action("check-standard") will install it.
on:
  push:
    branches:
      - main
      - master
      - release
      - next
      - cran-*
  pull_request:
    branches:
      - main
      - master
  workflow_dispatch:
    inputs:
      ref:
        description: "Branch, tag, or commit to check out"
        required: false
        default: "main"
      versions-matrix:
        description: "Create a matrix of R versions"
        type: boolean
        default: false
      dep-suggests-matrix:
        description: "Create a matrix of suggested dependencies"
        type: boolean
        default: false
      run-rcc-full:
        description: "Run rcc-full job"
        type: boolean
        default: false
      run-rcc-suggests:
        description: "Run rcc-suggests job"
        type: boolean
        default: false
  # SECURITY: a merge-queue run executes the queued pull request's code with
  # the base repository's token and secrets, unlike `pull_request`, where a
  # fork only ever gets a read-only token and no secrets. Adding a fork's pull
  # request to the queue is therefore as much of a trust decision as merging
  # it; keep "Require merge queue" paired with a branch rule that only lets
  # maintainers enqueue.
  merge_group:
    types:
      - checks_requested
  schedule:
    - cron: "10 1 * * *"

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}-${{ inputs.ref || github.head_ref || github.sha }}-${{ github.base_ref || '' }}
  cancel-in-progress: true

name: rcc

# Read-only by default; every job opts back into what it actually needs.
# Note that for a pull request from a fork GitHub caps the token at read-only
# regardless of what is requested here.
permissions:
  contents: read

jobs:
  rcc-smoke:
    # Deliberately amd64. The smoke test is the gate that also styles,
    # roxygenizes, updates snapshots, commits back and deploys pkgdown, so it
    # must run on the most stable and available runner. The ubuntu-26.04-arm
    # image is still in public preview (actions/runner-images#14226 -- possible
    # instability and queueing), so arm64 is exercised in the full version matrix
    # (rcc-full) instead, where fail-fast: false isolates failures and jobs don't
    # mutate the repo. Revisit once the arm image is generally available.
    runs-on: ubuntu-26.04

    outputs:
      sha: ${{ steps.commit.outputs.sha }}
      versions-matrix: ${{ steps.versions-matrix.outputs.matrix }}
      dep-suggests-matrix: ${{ steps.dep-suggests-matrix.outputs.matrix }}

    name: "Smoke test: stock R"

    permissions:
      contents: write
      statuses: write
      pull-requests: write
      actions: write

    steps:
      - uses: actions/checkout@v6
        with:
          ref: ${{ inputs.ref }}

      - name: Update status for rcc (pending)
        if: github.actor != 'Copilot' && (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository)
        uses: ./.github/workflows/commit-status
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          state: pending
          sha: ${{ inputs.ref }}

      - name: Report the GitHub API rate limit
        uses: ./.github/workflows/rate-limit
        with:
          token: ${{ secrets.GITHUB_TOKEN }}

      - name: Configure the Git identity
        uses: ./.github/workflows/git-identity

      - name: Run the repository-specific before-install steps
        uses: ./.github/workflows/custom/before-install
        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''

      - name: Install R and the package dependencies
        uses: ./.github/workflows/install
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          cache-version: rcc-smoke-2
          needs: build, check, website, roxygen2
          # Beware of using dev pkgdown here, has brought in dev dependencies in the past
          extra-packages: any::rcmdcheck r-lib/roxygen2 any::decor r-lib/pkgdown deps::.

      - name: Run the repository-specific after-install steps
        uses: ./.github/workflows/custom/after-install
        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

      # Must come after the custom after-install workflow
      - name: Install package
        run: |
          _R_SHLIB_STRIP_=true R CMD INSTALL .
        shell: bash

      # From here on, every step is marked `continue-on-error: true` so that a
      # failing check doesn't hide the results of all the checks that follow.
      # The "Summarize checks" step at the end fails the job if any of them
      # did not succeed.
      - name: Collect the R versions into a matrix
        id: versions-matrix
        continue-on-error: true
        # Only run for:
        # - pull requests if the base repo is different from the head repo
        # - pull requests if the branch name starts with "cran-"
        # Do not run for:
        # - workflow_dispatch if not requested
        # Always run for other events.
        if: (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.repository || startsWith(github.head_ref, 'cran-')) && (github.event_name != 'workflow_dispatch' || inputs.versions-matrix)
        uses: ./.github/workflows/versions-matrix

      - name: Collect the suggested dependencies into a matrix
        id: dep-suggests-matrix
        continue-on-error: true
        # Not for workflow_dispatch if not requested, always run for other events
        if: github.event_name != 'workflow_dispatch' || inputs.dep-suggests-matrix
        uses: ./.github/workflows/dep-suggests-matrix

      - name: Determine repository state
        id: repo-state
        uses: ./.github/workflows/repo-state

      # Styling on foreign PRs works through the format-suggest workflow
      - name: Style the R sources
        id: style
        continue-on-error: true
        uses: ./.github/workflows/style
        if: steps.repo-state.outputs.foreign != 'true' || steps.repo-state.outputs.is_pr != 'true'

      # Snapshot tests can't work in a way similar to format-suggests
      # because it requires running code which is a security risk on pull_request_target workflows
      - name: Update the testthat snapshots
        id: snapshots
        continue-on-error: true
        uses: ./.github/workflows/update-snapshots
        with:
          base: ${{ inputs.ref || github.head_ref }}

      - name: Roxygenize the documentation
        id: roxygenize
        continue-on-error: true
        uses: ./.github/workflows/roxygenize

      - name: Remove config files from previous iteration
        run: |
          rm -f .github/dep-suggests-matrix.json .github/versions-matrix.json
        shell: bash

      - name: Commit and push the generated changes
        id: commit
        continue-on-error: true
        uses: ./.github/workflows/commit
        with:
          token: ${{ secrets.GITHUB_TOKEN }}

      - name: Run R CMD check
        id: check
        continue-on-error: true
        uses: ./.github/workflows/check
        with:
          results: ${{ runner.os }}-smoke-test

      - name: Build the pkgdown website
        id: pkgdown-build
        continue-on-error: true
        uses: ./.github/workflows/pkgdown-build
        if: github.event_name != 'push'

      # Deliberately deploy only on push
      # Deployment on schedule adds too much noise.
      # Deployment on pull_request is not possible because it requires a token with write permissions, which is not available in pull_request workflows for security reasons.
      # Deployment on workflow_dispatch is available via the pkgdown workflow
      # Deploying a broken package's website is worse than not deploying at all,
      # hence this is the one step that is still gated on a check.
      - name: Build and deploy the pkgdown website
        id: pkgdown-deploy
        continue-on-error: true
        uses: ./.github/workflows/pkgdown-deploy
        if: github.event_name == 'push' && steps.check.outcome == 'success'

      # Upload sha as artifact
      - name: Record the commit SHA reached by the smoke test
        run: |
          echo -n "${{ steps.commit.outputs.sha }}" > rcc-smoke-sha.txt
        shell: bash

      - name: Upload the commit SHA reached by the smoke test
        uses: actions/upload-artifact@v5
        with:
          name: rcc-smoke-sha
          path: rcc-smoke-sha.txt

      # This is the step that fails the job if any of the checks above failed
      - name: Summarize checks
        if: always()
        run: |
          ## -- Summarize checks --
          status=0

          report() {
            outcome="${2:-skipped}"
            case "${outcome}" in
              success) icon="✅" ;;
              skipped) icon="⏭️" ;;
              *) icon="❌" ; status=1 ;;
            esac
            echo "| ${1} | ${icon} ${outcome} |" >> "${GITHUB_STEP_SUMMARY}"
          }

          {
            echo "## Smoke test summary"
            echo
            echo "| Check | Result |"
            echo "| --- | --- |"
          } >> "${GITHUB_STEP_SUMMARY}"

          report "R versions matrix" "${{ steps.versions-matrix.outcome }}"
          report "Suggested dependencies matrix" "${{ steps.dep-suggests-matrix.outcome }}"
          report "Style" "${{ steps.style.outcome }}"
          report "Snapshots" "${{ steps.snapshots.outcome }}"
          report "Roxygenize" "${{ steps.roxygenize.outcome }}"
          report "Commit" "${{ steps.commit.outcome }}"
          report "R CMD check" "${{ steps.check.outcome }}"
          report "pkgdown build" "${{ steps.pkgdown-build.outcome }}"
          report "pkgdown deploy" "${{ steps.pkgdown-deploy.outcome }}"

          if [ "${status}" -ne 0 ]; then
            printf '\nAt least one check failed, see the log for details.\n' >> "${GITHUB_STEP_SUMMARY}"
          fi

          exit "${status}"
        shell: bash

      - name: Update status for rcc (final)
        if: always() && (github.actor != 'Copilot') && (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository)
        uses: ./.github/workflows/commit-status
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          state: ${{ job.status }}
          # The commit that the commit-back step created, if there was one
          sha: ${{ steps.commit.outputs.sha || inputs.ref }}

      - name: Update status for rcc (Copilot)
        # Update status directly when triggered by Copilot or bots, since they can't dispatch workflows
        if: always() && (github.actor == 'Copilot')
        uses: ./.github/workflows/commit-status
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          state: ${{ job.status }}
          sha: ${{ inputs.ref }}

  rcc-smoke-check-matrix:
    runs-on: ubuntu-26.04

    name: "Check matrix"

    needs:
      - rcc-smoke

    permissions:
      contents: read

    steps:
      - uses: actions/checkout@v6
        with:
          ref: ${{ needs.rcc-smoke.outputs.sha }}

      - name: Show the R versions matrix
        uses: ./.github/workflows/matrix-check
        with:
          matrix: ${{ needs.rcc-smoke.outputs.versions-matrix }}

      - name: Show the suggested dependencies matrix
        uses: ./.github/workflows/matrix-check
        with:
          matrix: ${{ needs.rcc-smoke.outputs.dep-suggests-matrix }}

  rcc-full:
    needs:
      - rcc-smoke

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

    if: ${{ needs.rcc-smoke.outputs.versions-matrix != '' }}

    name: 'rcc: ${{ matrix.os }} (${{ matrix.r }}) ${{ matrix.desc }}'

    permissions:
      # Both required by the update-snapshots action, which opens a pull
      # request with refreshed snapshots. It is skipped for forks, where the
      # token is read-only anyway.
      contents: write
      pull-requests: write

    strategy:
      fail-fast: false
      matrix: ${{fromJson(needs.rcc-smoke.outputs.versions-matrix)}}

    steps:
      - uses: actions/checkout@v6
        with:
          ref: ${{ needs.rcc-smoke.outputs.sha }}

      - name: Apply environment variables from the test matrix
        # Generic: matrix entries defined in .github/versions-matrix.R can
        # carry an "env" field (one KEY=VALUE per line).
        # Write it to $GITHUB_ENV here, in the workflow,
        # because composite actions cannot read the matrix context.
        # The variables then reach every subsequent step,
        # including the custom before-install and after-install actions,
        # without requiring repos to implement any plumbing of their own.
        if: matrix.env != ''
        env:
          MATRIX_ENV: ${{ matrix.env }}
        run: |
          printf '%s\n' "$MATRIX_ENV" | tee -a "$GITHUB_ENV"
        shell: bash

      - name: Run the repository-specific before-install steps
        uses: ./.github/workflows/custom/before-install
        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''

      - name: Install R and the package dependencies
        uses: ./.github/workflows/install
        with:
          r-version: ${{ matrix.r }}
          cache-version: rcc-full-1
          token: ${{ secrets.GITHUB_TOKEN }}
          needs: build, check

      - name: Run the repository-specific after-install steps
        uses: ./.github/workflows/custom/after-install
        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

      - name: Must allow NOTEs if packages are missing, even with _R_CHECK_FORCE_SUGGESTS_
        run: |
          if (Sys.getenv("RCMDCHECK_ERROR_ON") %in% c("", "note")) {
            pkgs <- setdiff(desc::desc_get_deps()$package, "R")
            installable <- vapply(pkgs, FUN.VALUE = logical(1), requireNamespace, quietly = TRUE)
            if (any(!installable)) {
              message("Missing packages: ", paste(pkgs[!installable], collapse = ", "))
              cat('RCMDCHECK_ERROR_ON="warning"\n', file = Sys.getenv("GITHUB_ENV"), append = TRUE)
            }
          }
        shell: Rscript {0}

      - name: Update the testthat snapshots
        uses: ./.github/workflows/update-snapshots
        # Generic escape hatch: a custom action may set SKIP_UPDATE_SNAPSHOTS
        # to opt out of running the snapshot updater,
        # which runs tests directly via testthat::test_local()
        # and is difficult to disable otherwise.
        if: (github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository) && env.SKIP_UPDATE_SNAPSHOTS != 'true'
        with:
          base: ${{ github.head_ref }}

      - name: Run R CMD check
        uses: ./.github/workflows/check
        if: ${{ ! matrix.covr }}
        with:
          # Include the architecture: the matrix pairs each arm64 runner with an
          # amd64 one on the same OS and the same R version (ubuntu-26.04-arm /
          # ubuntu-26.04, windows-11-arm / windows-latest), so `runner.os` alone
          # yields duplicate artifact names, which upload-artifact rejects.
          results: ${{ runner.os }}-${{ runner.arch }}-r${{ matrix.r }}

      - name: Compute and upload the test coverage
        uses: ./.github/workflows/covr
        if: ${{ matrix.covr }}
        with:
          token: ${{ secrets.CODECOV_TOKEN }}

# The status update is taken care of by R-CMD-check-status.yaml

  rcc-suggests:
    needs:
      - rcc-smoke

    runs-on: ubuntu-26.04

    if: ${{ needs.rcc-smoke.outputs.dep-suggests-matrix != '' && (github.event_name == 'schedule' || (github.event_name == 'workflow_dispatch' && inputs.run-rcc-suggests)) }}

    name: Without ${{ matrix.package }}

    permissions:
      contents: read

    strategy:
      fail-fast: false
      matrix: ${{fromJson(needs.rcc-smoke.outputs.dep-suggests-matrix)}}

    steps:
      - uses: actions/checkout@v6

      - name: Run the repository-specific before-install steps
        uses: ./.github/workflows/custom/before-install
        if: hashFiles('.github/workflows/custom/before-install/action.yml') != ''

      - name: Install R and the package dependencies
        uses: ./.github/workflows/install
        with:
          cache-version: rcc-dev-${{ matrix.package }}-1
          needs: build, check
          extra-packages: "any::rcmdcheck any::remotes ."
          token: ${{ secrets.GITHUB_TOKEN }}

      - name: Remove ${{ matrix.package }} and all strong dependencies
        run: |
          pkg <- "${{ matrix.package }}"
          pkgs <- tools::package_dependencies(pkg, reverse = TRUE)[[1]]
          installed <- rownames(utils::installed.packages())
          to_remove <- c(pkg, intersect(pkgs, installed))
          print(to_remove)
          remove.packages(to_remove)
        shell: Rscript {0}

      - name: Session info
        run: |
          options(width = 100)
          if (!requireNamespace("sessioninfo", quietly = TRUE)) install.packages("sessioninfo")
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}

      - name: Run the repository-specific after-install steps
        uses: ./.github/workflows/custom/after-install
        if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

      - name: Must allow NOTEs, even with _R_CHECK_FORCE_SUGGESTS_
        run: |
          if (Sys.getenv("RCMDCHECK_ERROR_ON") %in% c("", "note")) {
            cat('RCMDCHECK_ERROR_ON="warning"\n', file = Sys.getenv("GITHUB_ENV"), append = TRUE)
          }
        shell: Rscript {0}

      - name: Check env vars
        run: |
          print(Sys.getenv('_R_CHECK_FORCE_SUGGESTS_'))
          print(Sys.getenv('RCMDCHECK_ERROR_ON'))
        shell: Rscript {0}

      - name: Run R CMD check
        uses: ./.github/workflows/check
        with:
          results: ${{ matrix.package }}

# The status update is taken care of by R-CMD-check-status.yaml