[ci] ensure correct R version is used on GitHub Actions (fixes #5640) #7378
Workflow file for this run
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| name: R-package | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| - release/* | |
| # automatically cancel in-progress builds if another commit is pushed | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| # hack to get around this: | |
| # https://stat.ethz.ch/pipermail/r-package-devel/2020q3/005930.html | |
| _R_CHECK_SYSTEM_CLOCK_: 0 | |
| # ignore R CMD CHECK NOTE checking how long it has | |
| # been since the last submission | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: 0 | |
| # CRAN ignores the "installed size is too large" NOTE, | |
| # so our CI can too. Setting to a large value here just | |
| # to catch extreme problems | |
| _R_CHECK_PKG_SIZES_THRESHOLD_: 100 | |
| jobs: | |
| test: | |
| name: ${{ matrix.task }} (${{ matrix.os }}, ${{ matrix.compiler }}, R ${{ matrix.r_version }}, ${{ matrix.build_type }}) | |
| runs-on: ${{ matrix.os }} | |
| container: ${{ matrix.container }} | |
| timeout-minutes: 60 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| ################ | |
| # CMake builds # | |
| ################ | |
| - os: ubuntu-latest | |
| task: r-package | |
| compiler: gcc | |
| r_version: 3.6 | |
| build_type: cmake | |
| container: 'ubuntu:18.04' | |
| - os: ubuntu-latest | |
| task: r-package | |
| compiler: gcc | |
| r_version: 4.3 | |
| build_type: cmake | |
| container: 'ubuntu:22.04' | |
| - os: ubuntu-latest | |
| task: r-package | |
| compiler: clang | |
| r_version: 3.6 | |
| build_type: cmake | |
| container: 'ubuntu:18.04' | |
| - os: ubuntu-latest | |
| task: r-package | |
| compiler: clang | |
| r_version: 4.3 | |
| build_type: cmake | |
| container: 'ubuntu:22.04' | |
| - os: macOS-latest | |
| task: r-package | |
| compiler: gcc | |
| r_version: 4.3 | |
| build_type: cmake | |
| container: null | |
| - os: macOS-latest | |
| task: r-package | |
| compiler: clang | |
| r_version: 4.3 | |
| build_type: cmake | |
| container: null | |
| - os: windows-latest | |
| task: r-package | |
| compiler: MINGW | |
| toolchain: MINGW | |
| r_version: 3.6 | |
| build_type: cmake | |
| container: null | |
| - os: windows-latest | |
| task: r-package | |
| compiler: MINGW | |
| toolchain: MSYS | |
| r_version: 4.2 | |
| build_type: cmake | |
| container: null | |
| # Visual Studio 2019 | |
| - os: windows-2019 | |
| task: r-package | |
| compiler: MSVC | |
| toolchain: MSVC | |
| r_version: 3.6 | |
| build_type: cmake | |
| container: null | |
| # Visual Studio 2022 | |
| - os: windows-2022 | |
| task: r-package | |
| compiler: MSVC | |
| toolchain: MSVC | |
| r_version: 4.2 | |
| build_type: cmake | |
| container: null | |
| ############### | |
| # CRAN builds # | |
| ############### | |
| - os: windows-latest | |
| task: r-package | |
| compiler: MINGW | |
| toolchain: MINGW | |
| r_version: 3.6 | |
| build_type: cran | |
| container: null | |
| - os: windows-latest | |
| task: r-package | |
| compiler: MINGW | |
| toolchain: MSYS | |
| r_version: 4.2 | |
| build_type: cran | |
| container: null | |
| - os: ubuntu-latest | |
| task: r-package | |
| compiler: gcc | |
| r_version: 4.3 | |
| build_type: cran | |
| container: 'ubuntu:22.04' | |
| - os: macOS-latest | |
| task: r-package | |
| compiler: clang | |
| r_version: 4.3 | |
| build_type: cran | |
| container: null | |
| ################ | |
| # Other checks # | |
| ################ | |
| - os: ubuntu-latest | |
| task: r-rchk | |
| compiler: gcc | |
| r_version: 4.3 | |
| build_type: cran | |
| container: 'ubuntu:22.04' | |
| steps: | |
| - name: Prevent conversion of line endings on Windows | |
| if: startsWith(matrix.os, 'windows') | |
| shell: pwsh | |
| run: git config --global core.autocrlf false | |
| - name: Install packages used by third-party actions | |
| if: startsWith(matrix.os, 'ubuntu') | |
| shell: bash | |
| run: | | |
| apt-get update -y | |
| apt-get install --no-install-recommends -y \ | |
| ca-certificates \ | |
| dirmngr \ | |
| gpg \ | |
| gpg-agent \ | |
| software-properties-common \ | |
| sudo | |
| # install newest version of git | |
| # ref: | |
| # - https://unix.stackexchange.com/a/170831/550004 | |
| # - https://git-scm.com/download/linux | |
| add-apt-repository ppa:git-core/ppa -y | |
| apt-get update -y | |
| apt-get install --no-install-recommends -y \ | |
| git | |
| - name: Trust git cloning LightGBM | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| git config --global --add safe.directory "${GITHUB_WORKSPACE}" | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 5 | |
| submodules: true | |
| - name: Install pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: install tinytex | |
| if: startsWith(matrix.os, 'windows') | |
| uses: r-lib/actions/setup-tinytex@v2 | |
| env: | |
| CTAN_MIRROR: https://ctan.math.illinois.edu/systems/win32/miktex | |
| TINYTEX_INSTALLER: TinyTeX | |
| - name: Setup and run tests on Linux and macOS | |
| if: matrix.os == 'macOS-latest' || matrix.os == 'ubuntu-latest' | |
| shell: bash | |
| run: | | |
| export TASK="${{ matrix.task }}" | |
| export COMPILER="${{ matrix.compiler }}" | |
| export GITHUB_ACTIONS="true" | |
| if [[ "${{ matrix.os }}" == "macOS-latest" ]]; then | |
| export OS_NAME="macos" | |
| elif [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then | |
| export OS_NAME="linux" | |
| export IN_UBUNTU_BASE_CONTAINER="true" | |
| # the default version of cmake provided on Ubuntu 18.04 (v3.10.2), is not supported by LightGBM | |
| # see https://github.com/microsoft/LightGBM/issues/5642 | |
| if [[ "${{ matrix.container }}" == "ubuntu:18.04" ]]; then | |
| export INSTALL_CMAKE_FROM_RELEASES="true" | |
| fi | |
| fi | |
| export BUILD_DIRECTORY="$GITHUB_WORKSPACE" | |
| export R_VERSION="${{ matrix.r_version }}" | |
| export R_BUILD_TYPE="${{ matrix.build_type }}" | |
| $GITHUB_WORKSPACE/.ci/setup.sh | |
| $GITHUB_WORKSPACE/.ci/test.sh | |
| - name: Setup and run tests on Windows | |
| if: startsWith(matrix.os, 'windows') | |
| shell: pwsh -command ". {0}" | |
| run: | | |
| $env:BUILD_SOURCESDIRECTORY = $env:GITHUB_WORKSPACE | |
| $env:LGB_VER = (Get-Content -TotalCount 1 $env:BUILD_SOURCESDIRECTORY\VERSION.txt).trim().replace('rc', '-') | |
| $env:TOOLCHAIN = "${{ matrix.toolchain }}" | |
| $env:R_VERSION = "${{ matrix.r_version }}" | |
| $env:R_BUILD_TYPE = "${{ matrix.build_type }}" | |
| $env:COMPILER = "${{ matrix.compiler }}" | |
| $env:GITHUB_ACTIONS = "true" | |
| $env:TASK = "${{ matrix.task }}" | |
| & "$env:GITHUB_WORKSPACE/.ci/test_windows.ps1" | |
| test-r-sanitizers: | |
| name: r-sanitizers (ubuntu-latest, R-devel, ${{ matrix.compiler }} ASAN/UBSAN) | |
| timeout-minutes: 60 | |
| runs-on: ubuntu-latest | |
| container: wch1/r-debug | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - r_customization: san | |
| compiler: gcc | |
| - r_customization: csan | |
| compiler: clang | |
| steps: | |
| - name: Trust git cloning LightGBM | |
| run: | | |
| git config --global --add safe.directory "${GITHUB_WORKSPACE}" | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 5 | |
| submodules: true | |
| - name: Install packages | |
| shell: bash | |
| run: | | |
| RDscript${{ matrix.r_customization }} -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'Matrix', 'RhpcBLASctl', 'rmarkdown', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())" | |
| sh build-cran-package.sh --r-executable=RD${{ matrix.r_customization }} | |
| RD${{ matrix.r_customization }} CMD INSTALL lightgbm_*.tar.gz || exit -1 | |
| - name: Run tests with sanitizers | |
| shell: bash | |
| run: | | |
| cd R-package/tests | |
| exit_code=0 | |
| RDscript${{ matrix.r_customization }} testthat.R >> tests.log 2>&1 || exit_code=-1 | |
| cat ./tests.log | |
| exit ${exit_code} | |
| test-r-debian-clang: | |
| name: r-package (debian, R-devel, clang) | |
| timeout-minutes: 60 | |
| runs-on: ubuntu-latest | |
| container: rhub/debian-clang-devel | |
| steps: | |
| - name: Install Git before checkout | |
| shell: bash | |
| run: | | |
| apt-get update --allow-releaseinfo-change | |
| apt-get install --no-install-recommends -y git | |
| - name: Trust git cloning LightGBM | |
| run: | | |
| git config --global --add safe.directory "${GITHUB_WORKSPACE}" | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 5 | |
| submodules: true | |
| - name: update to clang 15 | |
| shell: bash | |
| run: | | |
| # remove clang stuff that comes installed in the image | |
| apt-get autoremove -y --purge \ | |
| clang-* \ | |
| libclang-* \ | |
| libunwind-* \ | |
| llvm-* | |
| # | |
| # replace it all with clang-15 | |
| apt-get update -y | |
| apt-get install --no-install-recommends -y \ | |
| gnupg \ | |
| lsb-release \ | |
| software-properties-common \ | |
| wget | |
| # | |
| wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add - | |
| # | |
| add-apt-repository "deb http://apt.llvm.org/unstable/ llvm-toolchain main" | |
| apt-get install -y --no-install-recommends \ | |
| clang-15 \ | |
| clangd-15 \ | |
| clang-format-15 \ | |
| clang-tidy-15 \ | |
| clang-tools-15 \ | |
| lldb-15 \ | |
| lld-15 \ | |
| llvm-15-dev \ | |
| llvm-15-tools \ | |
| libomp-15-dev \ | |
| libc++-15-dev \ | |
| libc++abi-15-dev \ | |
| libclang-common-15-dev \ | |
| libclang-15-dev \ | |
| libclang-cpp15-dev \ | |
| libunwind-15-dev | |
| # overwrite everything in /usr/bin with the new v15 versions | |
| cp --remove-destination /usr/lib/llvm-15/bin/* /usr/bin/ | |
| - name: Install packages and run tests | |
| shell: bash | |
| run: | | |
| export PATH=/opt/R-devel/bin/:${PATH} | |
| Rscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'Matrix', 'RhpcBLASctl', 'rmarkdown', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())" | |
| sh build-cran-package.sh | |
| R CMD check --as-cran --run-donttest lightgbm_*.tar.gz || exit -1 | |
| if grep -q -E "NOTE|WARNING|ERROR" lightgbm.Rcheck/00check.log; then | |
| echo "NOTEs, WARNINGs, or ERRORs have been found by R CMD check" | |
| exit -1 | |
| fi | |
| all-r-package-jobs-successful: | |
| if: always() | |
| runs-on: ubuntu-latest | |
| needs: [test, test-r-sanitizers, test-r-debian-clang] | |
| steps: | |
| - name: Note that all tests succeeded | |
| uses: re-actors/[email protected] | |
| with: | |
| jobs: ${{ toJSON(needs) }} |