Fix test which had an unbalanced number of PROTECT/UNPROTECT #18
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| name: test-coverage.yaml | |
| permissions: | |
| contents: read | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr, any::xml2 | |
| needs: coverage | |
| - name: Test coverage | |
| run: | | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| print(cov) | |
| covr::to_cobertura(cov) | |
| shell: Rscript {0} | |
| - name: Ensure Codecov dependencies exist | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y bash curl git gawk grep gpg coreutils findutils gzip | |
| - name: Verify coverage file exists | |
| run: | | |
| ls -lah ./cobertura.xml | |
| test -s ./cobertura.xml | |
| - name: Debug Codecov context | |
| run: | | |
| echo "repo=$GITHUB_REPOSITORY" | |
| echo "sha=$GITHUB_SHA" | |
| echo "ref=$GITHUB_REF" | |
| echo "run_id=$GITHUB_RUN_ID" | |
| echo "actor=$GITHUB_ACTOR" | |
| git --no-pager log -1 --oneline | |
| git remote -v | |
| test -n "${{ secrets.CODECOV_TOKEN }}" && echo "codecov_token=present" || echo "codecov_token=missing" | |
| - uses: codecov/codecov-action@v5 | |
| with: | |
| # Fail if error if not on PR, or if on PR and token is given | |
| fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }} | |
| files: ./cobertura.xml | |
| disable_search: true | |
| plugins: noop | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| - name: Debug Codecov commit status | |
| if: always() | |
| run: | | |
| set +e | |
| echo "Checking Codecov API for commit: $GITHUB_SHA" | |
| curl -sS "https://codecov.io/api/v2/github/PRL-PRG/repos/MutatoR/commits/$GITHUB_SHA" | sed -n '1,200p' | |
| echo | |
| echo "Checking branch summary" | |
| curl -sS "https://codecov.io/api/v2/github/PRL-PRG/repos/MutatoR/branches/main" | sed -n '1,120p' | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package |