WIP: [R-package] require lgb.Dataset, remove support for passing 'colnames' and 'categorical_feature' for lgb.train() and lgb.cv() #9384
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| name: R-package | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| # automatically cancel in-progress builds if another commit is pushed | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| # in CMake-driven builds, parallelize compilation | |
| CMAKE_BUILD_PARALLEL_LEVEL: 4 | |
| # on Debian-based images, avoid interactive prompts | |
| DEBIAN_FRONTEND: noninteractive | |
| # parallelize compilation (extra important for Linux, where CRAN doesn't supply pre-compiled binaries) | |
| MAKEFLAGS: "-j4" | |
| # 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: 4.3 | |
| build_type: cmake | |
| container: 'ubuntu:22.04' | |
| - os: ubuntu-latest | |
| task: r-package | |
| compiler: clang | |
| r_version: 4.3 | |
| build_type: cmake | |
| container: 'ubuntu:22.04' | |
| - os: macos-13 | |
| task: r-package | |
| compiler: gcc | |
| r_version: 4.3 | |
| build_type: cmake | |
| container: null | |
| - os: macos-13 | |
| 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: 4.3 | |
| 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: 4.3 | |
| 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: 4.3 | |
| 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-13 | |
| task: r-package | |
| compiler: clang | |
| r_version: 4.3 | |
| build_type: cran | |
| container: null | |
| # macos-14 = arm64 | |
| - os: macos-14 | |
| task: r-package | |
| compiler: clang | |
| r_version: 4.3 | |
| build_type: cran | |
| container: null | |
| 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@v4 | |
| 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: startsWith(matrix.os, 'macos') || startsWith(matrix.os, 'ubuntu') | |
| shell: bash | |
| run: | | |
| export TASK="${{ matrix.task }}" | |
| export COMPILER="${{ matrix.compiler }}" | |
| if [[ "${{ matrix.os }}" =~ ^macos ]]; then | |
| export OS_NAME="macos" | |
| elif [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then | |
| export OS_NAME="linux" | |
| export IN_UBUNTU_BASE_CONTAINER="true" | |
| 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 }}" | |
| $env:TASK = "${{ 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@v4 | |
| with: | |
| fetch-depth: 5 | |
| submodules: true | |
| - name: Install packages | |
| shell: bash | |
| run: | | |
| RDscript${{ matrix.r_customization }} -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())" | |
| sh build-cran-package.sh --r-executable=RD${{ 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 ${exit_code} | |
| test-r-extra-checks: | |
| name: r-package (${{ matrix.image }}, R-devel) | |
| timeout-minutes: 60 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| # references: | |
| # * CRAN "additional checks": https://cran.r-project.org/web/checks/check_issue_kinds.html | |
| # * images: https://r-hub.github.io/containers/containers.html | |
| image: | |
| - clang16 | |
| - clang17 | |
| - clang18 | |
| - clang19 | |
| - gcc14 | |
| - intel | |
| - rchk | |
| runs-on: ubuntu-latest | |
| container: ghcr.io/r-hub/containers/${{ matrix.image }}:latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 5 | |
| submodules: true | |
| - name: Install pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install LaTeX | |
| shell: bash | |
| run: | | |
| if type -f apt 2>&1 > /dev/null; then | |
| apt-get update | |
| apt-get install --no-install-recommends -y \ | |
| devscripts \ | |
| texinfo \ | |
| texlive-latex-extra \ | |
| texlive-latex-recommended \ | |
| texlive-fonts-recommended \ | |
| texlive-fonts-extra \ | |
| tidy \ | |
| qpdf | |
| else | |
| yum update -y | |
| yum install -y \ | |
| devscripts \ | |
| qpdf \ | |
| texinfo \ | |
| texinfo-tex \ | |
| texlive-latex \ | |
| tidy | |
| fi | |
| - name: Install packages and run tests | |
| shell: bash | |
| run: | | |
| Rscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())" | |
| sh build-cran-package.sh | |
| # 'rchk' isn't run through 'R CMD check', use the approach documented at | |
| # https://r-hub.github.io/containers/local.html | |
| if [[ "${{ matrix.image }}" =~ "rchk" ]]; then | |
| r-check "$(pwd)" \ | |
| | tee ./rchk-logs.txt 2>&1 | |
| # the '-v' exceptions below are from R/rchk itself and not LightGBM: | |
| # https://github.com/kalibera/rchk/issues/22#issuecomment-656036156 | |
| if grep -E '\[PB\]|ERROR' ./rchk-logs.txt \ | |
| | grep -v 'too many states' \ | |
| > /dev/null; \ | |
| then | |
| echo "rchk found issues" | |
| exit 1 | |
| else | |
| echo "rchk did not find any issues" | |
| exit 0 | |
| fi | |
| fi | |
| # 'testthat' is not needed by 'rchk', so avoid installing it until here | |
| Rscript -e "install.packages('testthat', repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())" | |
| if [[ "${{ matrix.image }}" =~ "clang" ]]; then | |
| # allowing the following NOTEs (produced by default in the clang images): | |
| # | |
| # * checking compilation flags used ... NOTE | |
| # Compilation used the following non-portable flag(s): | |
| # ‘-Wp,-D_FORTIFY_SOURCE=3’ | |
| # | |
| # even though CRAN itself sets that: | |
| # https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-clang | |
| # | |
| declare -i allowed_notes=1 | |
| else | |
| declare -i allowed_notes=0 | |
| fi | |
| bash .ci/run-r-cmd-check.sh \ | |
| "$(echo lightgbm_$(head -1 VERSION.txt).tar.gz)" \ | |
| "${allowed_notes}" | |
| all-r-package-jobs-successful: | |
| if: always() | |
| runs-on: ubuntu-latest | |
| needs: [test, test-r-sanitizers, test-r-extra-checks] | |
| steps: | |
| - name: Note that all tests succeeded | |
| uses: re-actors/[email protected] | |
| with: | |
| jobs: ${{ toJSON(needs) }} |