[r] Improve error printing in call_peaks_macs
#87
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| name: Build and test R package | |
| on: | |
| pull_request: | |
| branches: | |
| - "main" | |
| jobs: | |
| build: | |
| name: ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| # Include macos-13 to get an intel mac | |
| os: [ubuntu-latest, windows-latest, macos-latest, macos-13] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install binary dependencies on ubuntu | |
| if: ${{ matrix.os == 'ubuntu-latest' }} | |
| run: sudo apt-get update && sudo apt-get install -y libhdf5-dev | |
| - name: Install binary dependencies on mac | |
| if: ${{ matrix.os == 'macos-latest' || matrix.os == 'macos-13' }} | |
| run: brew install hdf5 | |
| # R compilation options: | |
| # - Use 3 cores for compilation to speed it up | |
| # - Use lightly optimized build so Windows mingw doesn't segfault from unaligned loads of vector args with non-inlined functions | |
| # see: https://github.com/google/highway/issues/332 | |
| # - Keep NDEBUG undefined so that we only do a (fast) single-architecture build for bitpacking kernels rather than all architectures | |
| - name: Set R compilation options | |
| run: bash -c 'echo -e "MAKEFLAGS=--jobs=3\nCXXFLAGS += -O1 -UNDEBUG" > "$GITHUB_WORKSPACE/Makevars.user" && echo "R_MAKEVARS_USER=$GITHUB_WORKSPACE/Makevars.user" >> "$GITHUB_ENV"' | |
| # This is to fix assembler errors like 'file too big' or 'too many sections' on Windows | |
| # See: https://github.com/bnprks/BPCells/actions/runs/11412970445/job/31759842649?pr=141 | |
| # Solution from: https://digitalkarabela.com/mingw-w64-how-to-fix-file-too-big-too-many-sections/ and https://github.com/apache/arrow/issues/24442 | |
| - name: Handle Windows big object files | |
| if: ${{ matrix.os == 'windows-latest' }} | |
| run: bash -c 'echo "CXXFLAGS += -Wa,-mbig-obj" >> "$GITHUB_WORKSPACE/Makevars.user"' | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| Ncpus: '3' | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 1 | |
| extra-packages: | | |
| any::testthat | |
| any::decor | |
| working-directory: 'r' | |
| # Do a normal install rather than a pkgbuild-mediated install so we can control compilation flags via Makevars file | |
| - name: Install BPCells | |
| run: Rscript -e 'install.packages("r", repos=NULL, type="source")' | |
| - name: Run testthat | |
| run: Rscript -e 'testthat::test_dir("r/tests/testthat", package="BPCells", load_package="installed")' |