Update R-CMD-check.yaml #55
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| # Workflow derived from https://github.com/r-lib/actions/tree/master/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: R-CMD-check | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (R-${{ matrix.config.r }}), ADMIXTOOLS v${{ matrix.admixtools }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # vignette rendering is switched off though because of: | |
| # - https://github.com/tidyverse/ggplot2/issues/2252#issuecomment-1006713187 | |
| # - https://github.com/lcolladotor/biocthis/issues/27 | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: windows-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'devel'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| admixtools: ["7.0.2"] #, "6.0", "5.1"] | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install ADMIXTOOLS/admixr dependencies (Linux) | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev bedtools | |
| - name: Install ADMIXTOOLS/admixr dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: brew install openblas gsl lapack bedtools | |
| - name: Compile and install ADMIXTOOLS (Linux + macOS) | |
| # if: runner.os != 'Windows' | |
| if: runner.os == 'Linux' | |
| run: | | |
| # create a single directory for all external software | |
| mkdir -p ~/deps | |
| cd ~/deps | |
| # download and unpack the ADMIXTOOLS source code | |
| curl -LO https://github.com/DReichLab/AdmixTools/archive/v${{ matrix.admixtools }}.tar.gz | |
| tar xf v${{ matrix.admixtools }}.tar.gz | |
| cd AdmixTools-${{ matrix.admixtools }} | |
| # set compiler flags (compilation on macOS was failing unable to find | |
| # openblas library files) | |
| export LDFLAGS="-L/usr/local/opt/openblas/lib" | |
| export CPPFLAGS="-I/usr/local/opt/openblas/include" | |
| # compile ADMIXTOOLS and move binaries under bin/ | |
| cd src | |
| make clobber | |
| make LDLIBS="-llapack" all | |
| make install | |
| # download testing data for unit tests | |
| cd ../ | |
| curl -LO https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz | |
| tar xf AdmixTools_Example_Data.tar_.gz | |
| # run the Perl script with tests for the compiled binaries | |
| cd examples | |
| # fix unportable Perl shebang | |
| if [[ "$OSTYPE" == "darwin"* ]]; then | |
| sed -i '' "1s/.*/\#\!\/usr\/bin\/env perl -w/" mklog | |
| else | |
| sed -i "1s/.*/\#\!\/usr\/bin\/env perl/" mklog | |
| fi | |
| ./mklog | |
| cd ../ | |
| # we need to do this in bash because of $OSTYPE above | |
| shell: bash | |
| - name: Populate PATH with compiled binaries | |
| if: runner.os != 'Windows' | |
| run: | | |
| export PATH="$HOME/deps/AdmixTools-${{ matrix.admixtools }}/bin:$PATH" | |
| echo "PATH=$PATH" > ~/.Renviron | |
| - 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 | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: rcmdcheck | |
| - uses: r-lib/actions/check-r-package@v2 |