fix: integer vectors are validated before transferring them to the C … #4393
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| # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. | |
| # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions | |
| on: | |
| push: | |
| branches: | |
| - main | |
| - fix/* | |
| pull_request: | |
| branches: | |
| - main | |
| - fix/* | |
| schedule: | |
| - cron: '0 2 * * *' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }}-${{ github.head_ref || github.sha }}-${{ github.base_ref || '' }} | |
| cancel-in-progress: true | |
| name: R-CMD-check | |
| jobs: | |
| build_src_package: | |
| runs-on: ubuntu-22.04 | |
| name: Build source R package | |
| env: | |
| RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: apt update | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libarpack2-dev | |
| shell: bash | |
| - name: Cache Python virtualenv | |
| uses: actions/cache@v2 | |
| with: | |
| path: .venv | |
| key: Python-venv-jammy-${{ runner.os }}-${{ hashFiles('tools/build-requirements.txt') }} | |
| - name: Install R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| needs: build | |
| pak-version: devel | |
| - name: Create R source package | |
| run: | | |
| make igraph | |
| shell: bash | |
| - name: Commit changes | |
| if: ${{ env.GITHUB_ACTOR == env.GITHUB_REPOSITORY_OWNER }} | |
| run: | | |
| if [ -n "$(git status --porcelain)" ]; then | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "[email protected]" | |
| git fetch | |
| if [ -n "${GITHUB_HEAD_REF}" ]; then | |
| git add . | |
| git stash save | |
| git switch ${GITHUB_HEAD_REF} | |
| git stash pop | |
| fi | |
| git add . | |
| git commit -m "Automated changes" | |
| git push | |
| fi | |
| shell: bash | |
| - name: Package validation | |
| if: ${{ env.GITHUB_ACTOR != env.GITHUB_REPOSITORY_OWNER }} | |
| run: | | |
| git status --porcelain | |
| if [ -n "$(git status --porcelain)" ]; then | |
| git add . | |
| git diff --cached | |
| /bin/false | |
| fi | |
| shell: bash | |
| - name: Smoke test | |
| run: | | |
| make test | |
| shell: bash | |
| - name: Upload R source package | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: rigraph | |
| path: igraph_*.tar.gz | |
| retention-days: 5 | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| needs: build_src_package | |
| name: Check ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-latest, r: 'release'} | |
| # - {os: macOS-latest, r: 'release'} | |
| - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| # - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'oldrel-1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'oldrel-2', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'oldrel-3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| - {os: ubuntu-20.04, r: 'oldrel-4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | |
| env: | |
| RSPM: ${{ matrix.config.rspm }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| RGL_USE_NULL: true # Ensure that rgl functions correctly on macOS | |
| MAKEFLAGS: -j2 | |
| _R_CHECK_PKG_SIZES_: FALSE | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install ccache | |
| uses: hendrikmuhs/[email protected] | |
| with: | |
| max-size: 10G | |
| verbose: 1 | |
| save: false | |
| restore: false | |
| - name: apt update | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libarpack2-dev | |
| shell: bash | |
| - name: apt update | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install glpk | |
| shell: bash | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - name: Setup Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - name: Check R package | |
| uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| error-on: '"note"' | |
| coverage: | |
| runs-on: ubuntu-20.04 | |
| needs: build_src_package | |
| name: Coverage | |
| env: | |
| RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| MAKEFLAGS: -j2 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: apt update | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libarpack2-dev | |
| shell: bash | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Setup Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| needs: coverage | |
| pak-version: devel | |
| - name: Run coverage | |
| run: | | |
| line_exclusions <- fs::dir_ls(c("src/vendor"), type = "file", recurse = TRUE) | |
| cov <- covr::package_coverage( | |
| type = c("tests", "examples"), | |
| line_exclusions = as.list(names(line_exclusions)), | |
| quiet = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| covr::to_cobertura(cov) | |
| shell: Rscript {0} | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} | |
| file: ./cobertura.xml | |
| plugin: noop | |
| disable_search: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| sanitizer: | |
| runs-on: ubuntu-22.04 | |
| needs: build_src_package | |
| name: Sanitizer | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: apt update | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libarpack2-dev | |
| shell: bash | |
| - name: run sanitizer | |
| uses: addnab/docker-run-action@v3 | |
| with: | |
| image: ghcr.io/krlmlr/rigraph-san:main | |
| options: --rm --platform linux/amd64 -v ${{ github.workspace }}:/rigraph | |
| run: | | |
| set -e | |
| printenv | |
| # Memory leaks with rgl 1.3.12, https://github.com/dmurdoch/rgl/issues/439 | |
| RDcsan -e 'pak::pak("dmurdoch/rgl")' | |
| cd rigraph | |
| RDcsan CMD INSTALL . --no-byte-compile | |
| TESTTHAT_PARALLEL=false CI=true RDcsan -q -e 'testthat::test_local(reporter = c("location", "summary"), load_package = "installed")' |