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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,69 @@ | ||
| # 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: devel | ||
|
|
||
| name: test-coverage | ||
|
|
||
| jobs: | ||
| test-coverage: | ||
| runs-on: ubuntu-22.04 | ||
| container: bioconductor/bioconductor_docker:devel | ||
| env: | ||
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
| CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
|
|
||
| steps: | ||
| - name: Checkout Repository | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
| BiocManager::install(c("remotes", "covr")) | ||
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Cache R packages | ||
| if: runner.os != 'Windows' | ||
| uses: actions/cache@v1 | ||
| with: | ||
| path: /usr/local/lib/R/site-library | ||
| key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ runner.os }}-r-1- | ||
|
|
||
| - name: Install Dependencies | ||
| run: | | ||
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | ||
| BiocManager::install("rcmdcheck", ask = FALSE, update = TRUE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Check Package | ||
| env: | ||
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | ||
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Test coverage | ||
| run: | | ||
| covr::codecov( | ||
| quiet = FALSE, | ||
| clean = FALSE, | ||
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | ||
| ) | ||
| shell: Rscript {0} | ||
|
|
||
| - 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@v3 | ||
| with: | ||
| name: coverage-test-failures | ||
| path: ${{ runner.temp }}/package |
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