check.yaml

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

jobs:
  R-CMD-check:
    name: R CMD check (${{ matrix.os }})
    runs-on: ${{ matrix.os }}

    strategy:
      fail-fast: false
      matrix:
         os: ['ubuntu-latest']

    steps:
      - uses: actions/checkout@v4
      - name: Set up Conda env
        uses: mamba-org/provision-with-micromamba@e2b397b12d0a38069451664382b769c9456e3d6d
        with:
          cache-env: true
      - name: Install TinyTex
        shell: bash -l {0}
        run: |
          Rscript -e 'tinytex::install_tinytex()'
      - name: Install demo datasets
        shell: bash -l {0}
        run: |
          Rscript -e 'install.packages("eicu.demo", repos="https://eth-mds.github.io/physionet-demo")'
      - name: Run R CMD check
        shell: bash -l {0}
        run: |
          R CMD build . && R CMD check --no-manual --as-cran $(ls -t . | head -n1)
        env:
          _R_CHECK_CRAN_INCOMING_: false
          _R_CHECK_FORCE_SUGGESTS_: false
      # R CMD check raises a warning by qpdf that the generated docs PDF is large and
      # should be compressed. Currently we ignore this warning via the grep below.
      - name: Check for warnings
        shell: bash -l {0}
        run: |
          CHECK_LOG_FILE=ricu.Rcheck/00check.log
          CHECK_INSTALL_FILE=ricu.Rcheck/00install.out
          if ! [[ -f "$CHECK_LOG_FILE" ]]; then
            echo "Log-file not found."
            exit 1
          fi
          if cat $CHECK_LOG_FILE | grep -q "ERROR"; then
            cat $CHECK_INSTALL_FILE
            cat $CHECK_LOG_FILE
            exit 1
          fi
          if cat $CHECK_LOG_FILE | grep -q "WARNING" | grep -q -v -e "checking sizes of PDF files under ‘inst/doc’ ... WARNING"; then
            echo "Found warnings, treated as errors."
            cat $CHECK_LOG_FILE
            exit 1
          fi