Merge pull request #18 from ecohealthalliance/fix #72
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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 | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| workflow_dispatch: | |
| inputs: | |
| ssh_debug: | |
| description: Launch shell for interactive debugging? | |
| type: boolean | |
| required: true | |
| default: false | |
| name: R-CMD-check | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| R-CMD-check-base: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Do a pre-emptive apt-update | |
| run: sudo apt-get update -qq | |
| if: ${{ !env.ACT }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: release | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::sessioninfo, any::rcmdcheck, any::pkgdepends, any::covr, any::riskmetric, github::ropensci-review-tools/pkgcheck, | |
| needs: check | |
| - name: Run just package tests and record test coverage | |
| run: | | |
| cat("LOGNAME=", Sys.info()[["user"]], "\n", sep = "", file = Sys.getenv("GITHUB_ENV"), append = TRUE) | |
| cat("check-dir-path=", file.path(getwd(), ("check")), "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) | |
| coverage <- covr::package_coverage(code = "saveRDS(testthat::capture_output(testthat::test_package('relic', reporter = 'Progress')), file.path('check', 'test_results.rds'))", install_path = "check", clean=FALSE) | |
| saveRDS(coverage, file.path("check", "coverage.rds")) | |
| cat(readRDS(file.path('check', 'test_results.rds'))) | |
| shell: Rscript {0} | |
| - name: Run R-CMD-check without tests | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| cat("LOGNAME=", Sys.info()[["user"]], "\n", sep = "", file = Sys.getenv("GITHUB_ENV"), append = TRUE) | |
| if (Sys.getenv("_R_CHECK_FORCE_SUGGESTS_", "") == "") Sys.setenv("_R_CHECK_FORCE_SUGGESTS_" = "false") | |
| if (Sys.getenv("_R_CHECK_CRAN_INCOMING_", "") == "") Sys.setenv("_R_CHECK_CRAN_INCOMING_" = "false") | |
| cat("check-dir-path=", file.path(getwd(), ("check")), "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE) | |
| rcmdcheck::rcmdcheck(args = c("--no-tests", "--no-manual"), error_on = "warning", check_dir = ("check")) | |
| shell: Rscript {0} | |
| - name: Print and upload coverage | |
| run: | | |
| library(covr) | |
| coverage <- readRDS(file.path("check", "coverage.rds")) | |
| coverage | |
| covr::codecov(coverage = coverage) | |
| shell: Rscript {0} | |
| continue-on-error: true | |
| - name: Additional diagnostics | |
| run: | | |
| pkc <- pkgcheck::pkgcheck(goodpractice = FALSE) | |
| gp <- goodpractice::goodpractice(checks = goodpractice::all_checks()[grep("(rcmdcheck|covr)", goodpractice::all_checks(), invert = TRUE)]) | |
| pkc | |
| gp | |
| shell: Rscript {0} | |
| continue-on-error: true | |
| - name: Launch a temporary interactive debugging session | |
| uses: mxschmitt/[email protected] | |
| if: always() && inputs.ssh_debug | |
| with: | |
| detached: true | |
| # - uses: r-lib/actions/check-r-package@v2 | |
| # with: | |
| # upload-snapshots: true | |
| R-CMD-check-grid: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| needs: R-CMD-check-base | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macos-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| #- {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install libgit2 on macOS | |
| run: | | |
| if [ "$RUNNER_OS" == "macOS" ]; then | |
| brew install libgit2 | |
| fi | |
| shell: bash | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::sessioninfo, any::rcmdcheck, any::pkgdepends | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| - name: Launch a temporary interactive debugging session | |
| uses: mxschmitt/[email protected] | |
| if: always() && inputs.ssh_debug | |
| with: | |
| detached: true |