R-CMD-check.yaml

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on: [push, pull_request]

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ubuntu-latest
    container: bioconductor/bioconductor_docker:devel

    steps:
      - uses: actions/checkout@v1
      - name: Install system dependencies
        run: |
          wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
          /bin/bash ~/miniconda.sh -b -p /opt/conda && \
          rm ~/miniconda.sh && \
          ln -s /opt/conda/bin/conda /usr/local/bin/
      - name: Fix blas bug
        run: |
          ARCH=$(uname -m)
          update-alternatives --set "libblas.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/blas/libblas.so.3"
          update-alternatives --set "liblapack.so.3-${ARCH}-linux-gnu" "/usr/lib/${ARCH}-linux-gnu/lapack/liblapack.so.3"
      - name: Install dependencies
        run: |
          BiocManager::install("AnVIL")
          BiocManager::install(c("remotes", "rcmdcheck", "basilisk", "reticulate", "S4Vectors", "ExperimentHub", "AnnotationHub"))
          remotes::install_deps(dependencies = TRUE)
        shell: Rscript {0}
      - name: Check
        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
        shell: Rscript {0}