Coot 13, Change arma::fill to internal_compact to avoid confusion with user declarations
#5102
Workflow file for this run
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| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| - master | |
| - main | |
| pull_request: | |
| branches: | |
| - master | |
| - main | |
| release: | |
| types: [published, created, edited] | |
| permissions: | |
| contents: read | |
| name: mlpack.mlpack | |
| jobs: | |
| jobR: | |
| name: mlpack R tarball | |
| if: ${{ github.repository == 'mlpack/mlpack' }} | |
| runs-on: ubuntu-latest | |
| outputs: | |
| r_bindings: ${{ steps.mlpack_version.outputs.mlpack_r_package }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Extract mlpack version | |
| id: mlpack_version | |
| run: | | |
| MLPACK_VERSION_MAJOR=$(grep -i ".*#define MLPACK_VERSION_MAJOR.*" src/mlpack/core/util/version.hpp | grep -o "[0-9]*") | |
| MLPACK_VERSION_MINOR=$(grep -i ".*#define MLPACK_VERSION_MINOR.*" src/mlpack/core/util/version.hpp | grep -o "[0-9]*") | |
| MLPACK_VERSION_PATCH=$(grep -i ".*#define MLPACK_VERSION_PATCH.*" src/mlpack/core/util/version.hpp | grep -o "[0-9]*") | |
| MLPACK_VERSION_VALUE=${MLPACK_VERSION_MAJOR}.${MLPACK_VERSION_MINOR}.${MLPACK_VERSION_PATCH} | |
| echo "mlpack_r_package=$(echo mlpack_"$MLPACK_VERSION_VALUE".tar.gz)" >> $GITHUB_OUTPUT | |
| # Setup Pandoc | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| # Setup R actions | |
| - uses: r-lib/actions/setup-r@v2 | |
| - name: Query dependencies | |
| run: | | |
| cp src/mlpack/bindings/R/mlpack/DESCRIPTION.in DESCRIPTION | |
| Rscript -e "install.packages('remotes')" -e "saveRDS(remotes::dev_package_deps(dependencies = TRUE), 'depends.Rds')" | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' && runner.os != 'macOS' | |
| uses: actions/cache@v3 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-release-${{ hashFiles('depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-release- | |
| - name: Install Build Dependencies | |
| run: | | |
| sudo apt-get update | |
| # We don't install cereal via apt, because the Debian packagers | |
| # split the rapidjson dependency into a separate package. We will | |
| # bundle the cereal sources with the R package, so we want them to | |
| # be exactly the upstream sources (with rapidjson included). | |
| sudo apt-get install -y --allow-unauthenticated libopenblas-dev liblapack-dev g++ libensmallen-dev libhdf5-dev libarmadillo-dev libcurl4-openssl-dev | |
| wget https://github.com/USCiLab/cereal/archive/refs/tags/v1.3.2.tar.gz | |
| tar -xvzpf v1.3.2.tar.gz | |
| # These directives cause warnings on CRAN: | |
| # https://github.com/USCiLab/cereal/blob/master/include/cereal/external/base64.hpp#L28-L31 | |
| # The command below comments them out. | |
| sed -i 's|#pragma|// #pragma|' cereal-1.3.2/include/cereal/external/base64.hpp | |
| - name: Install R-bindings dependencies | |
| run: | | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("roxygen2") | |
| remotes::install_cran("pkgbuild") | |
| shell: Rscript {0} | |
| - name: CMake | |
| run: | | |
| mkdir build | |
| cd build && cmake -DDEBUG=OFF -DPROFILE=OFF -DBUILD_CLI_EXECUTABLES=OFF -DBUILD_PYTHON_BINDINGS=OFF -DBUILD_JULIA_BINDINGS=OFF -DBUILD_GO_BINDINGS=OFF -DBUILD_R_BINDINGS=ON -DDOWNLOAD_DEPENDENCIES=ON -DBUILD_TESTS=ON -DCEREAL_INCLUDE_DIR=../cereal-1.3.2/include/ .. | |
| - name: Build | |
| run: | | |
| cd build && make | |
| - name: Run tests via ctest | |
| run: | | |
| cd build && CTEST_OUTPUT_ON_FAILURE=1 ctest -T Test . | |
| - name: Upload R packages | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: mlpack_r_tarball | |
| path: build/src/mlpack/bindings/R/${{ steps.mlpack_version.outputs.mlpack_r_package }} | |
| R-CMD-check: | |
| needs: jobR | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.name }} | |
| if: ${{ github.repository == 'mlpack/mlpack' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { os: windows-latest, r: "release", name: "Windows R" } | |
| - { os: macOS-latest, r: "release", name: "macOS R" } | |
| - { | |
| os: ubuntu-latest, | |
| r: "devel", | |
| http-user-agent: "release", | |
| name: "Linux R", | |
| } | |
| env: | |
| MAKEFLAGS: "-j 2" | |
| R_BUILD_ARGS: "--no-build-vignettes" | |
| R_CHECK_ARGS: "--no-build-vignettes" | |
| _R_CHECK_FORCE_SUGGESTS: 0 | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/download-artifact@v2 | |
| with: | |
| name: mlpack_r_tarball | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: Query dependencies | |
| run: Rscript -e "install.packages('remotes')" -e "saveRDS(remotes::dev_package_deps('${{ needs.jobR.outputs.r_bindings }}', dependencies = TRUE), 'depends.Rds')" | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' && runner.os != 'macOS' | |
| uses: actions/cache@v1 | |
| with: | |
| path: ${{ env.R_LIBS_USER }} | |
| key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }} | |
| restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}- | |
| - name: Install check dependencies | |
| if: runner.os != 'Windows' && runner.os != 'macOS' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y --allow-unauthenticated libcurl4-openssl-dev | |
| - name: Install dependencies | |
| run: | | |
| install.packages('remotes') | |
| remotes::install_deps('${{ needs.jobR.outputs.r_bindings }}', dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| remotes::install_cran("curl") | |
| shell: Rscript {0} | |
| - name: Check | |
| run: Rscript -e "rcmdcheck::rcmdcheck('${{ needs.jobR.outputs.r_bindings }}', args = c('--no-manual','--as-cran'), error_on = 'warning', check_dir = 'check')" | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: ${{ runner.os }}-r${{ matrix.config.r }}-results | |
| path: | | |
| check/mlpack.Rcheck/00check.log | |
| check/mlpack.Rcheck/00install.out |