Merge branch 'master' into GHA-sanitizers #4
Workflow file for this run
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| on: | |
| push: | |
| branches: | |
| - master | |
| - GHA-sanitizers # during development | |
| workflow_dispatch: | |
| name: R-CMD-check-sanitized | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| R-CMD-check-sanitized: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: docker://docker.io/rocker/r-devel-ubsan-clang | |
| strategy: | |
| fail-fast: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: "Environment setup" | |
| run: | | |
| RDscript -e ' | |
| # install the dependencies into a separate directory to cache them | |
| dir.create(lib <- Sys.getenv("R_LIBS_USER"), recursive = TRUE) | |
| writeLines(paste0("R_LIBS_USER=", lib), Sys.getenv("GITHUB_ENV")) | |
| # to be used as the cache key | |
| writeLines(R.version.string, ".R_version_string") | |
| ' | |
| echo "MAKEFLAGS=-j$(nproc)" >> $GITHUB_ENV | |
| # fontconfig is known to leak; add more suppressions as discovered | |
| echo "LSAN_OPTIONS=suppressions=$(realpath .github/workflows/LSan.supp)" >> $GITHUB_ENV | |
| # disable for most operations just in case | |
| echo "ASAN_OPTIONS=detect_leaks=0" >> $GITHUB_ENV | |
| # needed by udunits2, sf | |
| apt-get update && apt-get install -y libudunits2-dev libgdal-dev | |
| - name: "Restore dependency cache" | |
| id: dependency-cache | |
| uses: actions/cache/restore@v4 | |
| with: | |
| path: ${{ env.R_LIBS_USER }}/* | |
| key: r-clang-san-deps-${{hashFiles('.R_version_string')}} | |
| - name: "Install dependencies" | |
| shell: RDscript {0} | |
| run: | | |
| lib <- Sys.getenv('R_LIBS_USER') # why doesn't it work by itself? | |
| if (!requireNamespace('BiocManager')) install.packages('BiocManager', lib = lib) | |
| union( | |
| 'DESCRIPTION' |> read.dcf('Suggests') |> tools:::.split_dependencies() |> names(), | |
| 'inst/tests/other.Rraw' |> parse() |> _[[1]][[3]] |> eval() | |
| ) |> setdiff(tools::standard_package_names()$base) |> | |
| BiocManager::install(lib = lib, update = TRUE, ask = FALSE) | |
| - name: "Save dependency cache" | |
| uses: actions/cache/save@v4 | |
| with: | |
| path: ${{ env.R_LIBS_USER }}/* | |
| key: ${{ steps.dependency-cache.outputs.cache-primary-key }} | |
| - name: "Build" | |
| run: | | |
| rm .R_version_string # there's probably a better place for this | |
| RD CMD build . | |
| - name: "Check" | |
| run: | | |
| set +e # expect some things to fail and keep going | |
| echo "::group::full R CMD check output" | |
| # only use leak checking for this run | |
| ASAN_OPTIONS=detect_leaks=1 RD CMD check --no-manual data.table_*.tar.gz; res1=$? | |
| echo "::endgroup::" | |
| perl -nle '(print, $a=1) if /: runtime error: |ERROR: LeakSanitizer/../SUMMARY.*Sanitizer/ }{ exit $a' data.table.Rcheck/**/*.Rout*; res2=$? | |
| # fail if R CMD check had failed or if sanitizer output found | |
| [ $res1 -eq 0 ] && [ $res2 -eq 0 ] |