Merge pull request #184 from BIMSBbioinfo/dev #13
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| on: | |
| push: | |
| pull_request: | |
| name: R-CMD-check | |
| jobs: | |
| check: | |
| runs-on: ${{ matrix.config.os }} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| _R_CHECK_TESTS_NLINES_: 0 | |
| NOT_CRAN: true | |
| HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK: true | |
| _R_CHECK_FORCE_SUGGESTS_: false #TODO: drop this for now! | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macos-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release', rtools-version: '44'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-24.04, r: 'release'} | |
| steps: | |
| ## Most of these steps are the same as the ones in | |
| ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | |
| ## If they update their steps, we will also need to update ours. | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| ## pandoc | |
| - name: Setup pandoc from r-lib | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| ## R is already included in the Bioconductor docker images | |
| - name: Setup R from r-lib | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| rtools-version: ${{ matrix.config.rtools-version }} | |
| ## Windows dependencies | |
| - name: Install Windows system dependencies | |
| if: runner.os == 'Windows' | |
| run: | | |
| ## Edit below if you have any Windows system dependencies | |
| shell: Rscript {0} | |
| ## linux dependencies | |
| - name: Install linux system dependencies | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install -y libgdal-dev | |
| sudo apt-get install -y libfftw3-dev | |
| sudo apt-get install -y libmagick++-dev | |
| sudo apt-get install -y cmake | |
| sudo apt-get install -y libhdf5-dev | |
| sudo apt-get install -y git | |
| sudo apt-get install -y libopencv-dev | |
| sudo apt-get install -y libopencv-features2d-dev | |
| sudo apt-get install -y libssl-dev | |
| sudo apt-get install -y libcurl4-openssl-dev | |
| sudo apt-get install -y libgit2-dev | |
| sudo apt-get install -y libxml2-dev | |
| sudo apt-get install -y libfontconfig1-dev | |
| sudo apt-get install -y libharfbuzz-dev | |
| sudo apt-get install -y libfribidi-dev | |
| sudo apt-get install -y libfreetype6-dev | |
| sudo apt-get install -y libpng-dev | |
| sudo apt-get install -y libtiff5-dev | |
| sudo apt-get install -y libjpeg-dev | |
| sudo apt-get install -y libz-dev | |
| ## macOS dependencies | |
| - name: Install macOS system dependencies | |
| if: runner.os == 'macOS' | |
| run: | | |
| ## Enable installing XML from source if needed | |
| brew install libxml2 | |
| echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV | |
| ## Required to install magick as noted at | |
| ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | |
| brew install imagemagick@6 | |
| ## For textshaping, required by ragg, and required by pkgdown | |
| brew install harfbuzz fribidi | |
| ## For installing usethis's dependency gert | |
| brew install libgit2 | |
| ## hdf5 | |
| brew install hdf5 | |
| ## Required for tcltk | |
| brew install xquartz --cask | |
| ## remotes, devtools | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| install.packages('devtools') | |
| shell: Rscript {0} | |
| ## BiocManager | |
| - name: Install BiocManager | |
| run: | | |
| remotes::install_cran("BiocManager") | |
| shell: Rscript {0} | |
| # All Other dependencies | |
| - name: Install dependencies | |
| run: | | |
| ## Try installing the package dependencies in steps. First the local | |
| ## dependencies, then any remaining dependencies to avoid the | |
| ## issues described at | |
| ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html | |
| ## https://github.com/r-lib/remotes/issues/296 | |
| ## Ideally, all dependencies should get installed in the first pass. | |
| install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories()) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | |
| shell: Rscript {0} | |
| ## Linux dependencies for OpenCV | |
| - name: Install OpenCV for linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| ## Edit below if you have any ubuntu/linux dependencies, e.g. OpenCV | |
| git clone https://github.com/opencv/opencv.git | |
| git clone https://github.com/opencv/opencv_contrib.git | |
| mkdir build | |
| cd build | |
| cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local -D INSTALL_C_EXAMPLES=ON -D INSTALL_PYTHON_EXAMPLES=ON -D OPENCV_GENERATE_PKGCONFIG=ON -D OPENCV_EXTRA_MODULES_PATH=../opencv_contrib/modules/ -D BUILD_opencv_xfeatures2d=ON ../opencv/ | |
| make -j5 | |
| sudo make install | |
| sudo sh -c 'echo "/usr/local/lib" > /etc/ld.so.conf.d/opencv.conf' | |
| sudo ldconfig | |
| cd / | |
| # All Other dependencies | |
| - name: Install Suggested dependencies | |
| run: | | |
| BiocManager::install(c('DelayedArray')) | |
| BiocManager::install(c('HDF5Array')) | |
| remotes::install_github('bnprks/BPCells/r@v0.3.0') | |
| devtools::install_github('BIMSBbioinfo/ImageArray') | |
| devtools::install_github('BIMSBbioinfo/HDF5DataFrame') | |
| devtools::install_github('BIMSBbioinfo/ZarrDataFrame') | |
| shell: Rscript {0} | |
| ## R CMD Check | |
| - name: Run CMD check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| DISPLAY: 99.0 | |
| run: | | |
| options(crayon.enabled = TRUE) | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--no-vignettes", "--timings"), | |
| build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), | |
| error_on = "error", | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} |