ci: Ignore errors when removing pkg-config on macOS (#2257) #4816
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| # 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 | |
| - 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 | |
| merge_group: | |
| types: | |
| - checks_requested | |
| schedule: | |
| - cron: "10 0 * * *" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ inputs.ref || github.head_ref || github.sha }}-${{ github.base_ref || '' }} | |
| cancel-in-progress: true | |
| name: rcc | |
| jobs: | |
| rcc-smoke: | |
| runs-on: ubuntu-24.04 | |
| 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" | |
| # Begin custom: services | |
| # End custom: services | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ inputs.ref }} | |
| - name: Update status for rcc | |
| # FIXME: Wrap into action | |
| if: github.event_name == 'workflow_dispatch' | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| # Check status of this workflow | |
| state="pending" | |
| sha=${{ inputs.ref }} | |
| if [ -z "${sha}" ]; then | |
| sha=${{ github.head_ref }} | |
| fi | |
| if [ -z "${sha}" ]; then | |
| sha=${{ github.sha }} | |
| fi | |
| sha=$(git rev-parse ${sha}) | |
| html_url=$(gh api \ | |
| -H "Accept: application/vnd.github+json" \ | |
| -H "X-GitHub-Api-Version: 2022-11-28" \ | |
| repos/${{ github.repository }}/actions/runs/${{ github.run_id }} | jq -r .html_url) | |
| description="${{ github.workflow }} / ${{ github.job }}" | |
| gh api \ | |
| --method POST \ | |
| -H "Accept: application/vnd.github+json" \ | |
| -H "X-GitHub-Api-Version: 2022-11-28" \ | |
| repos/${{ github.repository }}/statuses/${sha} \ | |
| -f "state=${state}" -f "target_url=${html_url}" -f "description=${description}" -f "context=rcc" | |
| shell: bash | |
| - uses: ./.github/workflows/rate-limit | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: ./.github/workflows/git-identity | |
| - uses: ./.github/workflows/custom/before-install | |
| if: hashFiles('.github/workflows/custom/before-install/action.yml') != '' | |
| - uses: ./.github/workflows/install | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| cache-version: rcc-smoke-2 | |
| needs: check, website | |
| # 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/styler r-lib/pkgdown deps::. | |
| - name: Install package | |
| run: | | |
| _R_SHLIB_STRIP_=true R CMD INSTALL . | |
| shell: bash | |
| - uses: ./.github/workflows/custom/after-install | |
| if: hashFiles('.github/workflows/custom/after-install/action.yml') != '' | |
| - id: versions-matrix | |
| # Only run for pull requests if the base repo is different from the head repo, not 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) && (github.event_name != 'workflow_dispatch' || inputs.versions-matrix) | |
| uses: ./.github/workflows/versions-matrix | |
| - id: dep-suggests-matrix | |
| # 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 | |
| - uses: ./.github/workflows/update-snapshots | |
| with: | |
| base: ${{ inputs.ref || github.head_ref }} | |
| - uses: ./.github/workflows/style | |
| - 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 | |
| - id: commit | |
| uses: ./.github/workflows/commit | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - uses: ./.github/workflows/check | |
| with: | |
| results: ${{ runner.os }}-smoke-test | |
| - uses: ./.github/workflows/pkgdown-build | |
| if: github.event_name != 'push' | |
| - uses: ./.github/workflows/pkgdown-deploy | |
| if: github.event_name == 'push' | |
| # Upload sha as artifact | |
| - run: | | |
| echo -n "${{ steps.commit.outputs.sha }}" > rcc-smoke-sha.txt | |
| shell: bash | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: rcc-smoke-sha | |
| path: rcc-smoke-sha.txt | |
| - name: Update status for rcc | |
| # FIXME: Wrap into action | |
| if: always() && github.event_name == 'workflow_dispatch' | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| # Check status of this workflow | |
| if [ "${{ job.status }}" == "success" ]; then | |
| state="success" | |
| else | |
| state="failure" | |
| fi | |
| sha=${{ steps.commit.outputs.sha }} | |
| if [ -z "${sha}" ]; then | |
| sha=${{ inputs.ref }} | |
| fi | |
| if [ -z "${sha}" ]; then | |
| sha=${{ github.head_ref }} | |
| fi | |
| if [ -z "${sha}" ]; then | |
| sha=${{ github.sha }} | |
| fi | |
| sha=$(git rev-parse ${sha}) | |
| html_url=$(gh api \ | |
| -H "Accept: application/vnd.github+json" \ | |
| -H "X-GitHub-Api-Version: 2022-11-28" \ | |
| repos/${{ github.repository }}/actions/runs/${{ github.run_id }} | jq -r .html_url) | |
| description="${{ github.workflow }} / ${{ github.job }}" | |
| gh api \ | |
| --method POST \ | |
| -H "Accept: application/vnd.github+json" \ | |
| -H "X-GitHub-Api-Version: 2022-11-28" \ | |
| repos/${{ github.repository }}/statuses/${sha} \ | |
| -f "state=${state}" -f "target_url=${html_url}" -f "description=${description}" -f "context=rcc" | |
| shell: bash | |
| rcc-smoke-check-matrix: | |
| runs-on: ubuntu-24.04 | |
| name: "Check matrix" | |
| needs: | |
| - rcc-smoke | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ needs.rcc-smoke.outputs.sha }} | |
| - uses: ./.github/workflows/matrix-check | |
| with: | |
| matrix: ${{ needs.rcc-smoke.outputs.versions-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 }}' | |
| # Begin custom: services | |
| # End custom: services | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{fromJson(needs.rcc-smoke.outputs.versions-matrix)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ needs.rcc-smoke.outputs.sha }} | |
| - uses: ./.github/workflows/custom/before-install | |
| if: hashFiles('.github/workflows/custom/before-install/action.yml') != '' | |
| - uses: ./.github/workflows/install | |
| with: | |
| r-version: ${{ matrix.r }} | |
| cache-version: rcc-full-1 | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| needs: check | |
| - uses: ./.github/workflows/custom/after-install | |
| if: hashFiles('.github/workflows/custom/after-install/action.yml') != '' | |
| - uses: ./.github/workflows/update-snapshots | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository | |
| - uses: ./.github/workflows/check | |
| with: | |
| results: ${{ runner.os }}-r${{ matrix.r }} | |
| # The status update is taken care of by R-CMD-check-status.yaml | |
| rcc-suggests: | |
| needs: | |
| - rcc-smoke | |
| runs-on: ubuntu-22.04 | |
| if: ${{ needs.rcc-smoke.outputs.dep-suggests-matrix != '' }} | |
| name: Without ${{ matrix.package }} | |
| # Begin custom: services | |
| # End custom: services | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{fromJson(needs.rcc-smoke.outputs.dep-suggests-matrix)}} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ./.github/workflows/custom/before-install | |
| if: hashFiles('.github/workflows/custom/before-install/action.yml') != '' | |
| - uses: ./.github/workflows/install | |
| with: | |
| cache-version: rcc-dev-${{ matrix.package }}-1 | |
| needs: 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} | |
| - uses: ./.github/workflows/custom/after-install | |
| if: hashFiles('.github/workflows/custom/after-install/action.yml') != '' | |
| - name: Define _R_CHECK_FORCE_SUGGESTS_ | |
| run: | | |
| cat('_R_CHECK_FORCE_SUGGESTS_=false\n', file = Sys.getenv("GITHUB_ENV"), append = TRUE) | |
| shell: Rscript {0} | |
| - 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} | |
| - uses: ./.github/workflows/check | |
| with: | |
| results: ${{ matrix.package }} | |
| # The status update is taken care of by R-CMD-check-status.yaml | |
| # FIXME: integrate with dynamic matrix creation | |
| validate: | |
| needs: | |
| - rcc-smoke | |
| runs-on: ${{ matrix.config.os }}${{ matrix.config.os-version }} | |
| name: ${{ matrix.config.os }}${{ matrix.config.os-version }} (${{ matrix.config.r }}) ${{ matrix.config.desc }} | |
| # Begin custom: services | |
| # End custom: services | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: ubuntu-, os-version: 22.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| # prevent rgl issues because no X11 display is available | |
| RGL_USE_NULL: true | |
| # Begin custom: env vars | |
| # End custom: env vars | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: ./.github/workflows/custom/before-install | |
| if: hashFiles('.github/workflows/custom/before-install/action.yml') != '' | |
| - uses: ./.github/workflows/install | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| install-r: false | |
| cache-version: rcc-smoke-1 | |
| needs: check | |
| extra-packages: any::rcmdcheck any::roxygen2 r-lib/styler | |
| - uses: ./.github/workflows/custom/after-install | |
| if: hashFiles('.github/workflows/custom/after-install/action.yml') != '' | |
| - name: Instrument R code for validation | |
| run: | | |
| if [ $(git status --porcelain | wc -l) -gt 0 ]; then | |
| echo "Fatal: git working copy not clean" | |
| fi | |
| sed -i -r '/INSTRUMENT: validate/ s/^( +)# /\1/g' R/* | |
| if [ $(git status --porcelain | wc -l) -eq 0 ]; then | |
| echo "Fatal: substitution did not change anything" | |
| fi | |
| - name: Run tests | |
| run: | | |
| testthat::test_local(reporter = testthat::ProgressReporter$new(max_failures = Inf, update_interval = Inf)) | |
| shell: Rscript {0} | |
| - name: Show test output | |
| if: always() | |
| run: | | |
| find check -name '*.Rout*' -exec head -n 1000000 '{}' \; || true | |
| shell: bash | |
| - name: Test coverage | |
| run: covr::codecov() | |
| shell: Rscript {0} |