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main.yml
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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