R-CMD-check.yaml

# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
on:
  push:
    branches:
      - master
      - devel
  pull_request:
    branches:
      - master
      - devel

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          #- {os: windows-latest, r: 'devel', rglusenull: "true"}
          - {os: windows-latest, r: 'release', rglusenull: "true"}
          #- {os: windows-latest, r: '3.6', rglusenull: "true"}
          #- {os: macOS-latest, r: 'release', rglusenull: "true"}
          - {os: ubuntu-latest, r: 'release'}
          #- {os: ubuntu-latest, r: 'devel'}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      _R_CHECK_FORCE_SUGGESTS_: false
      RGL_USE_NULL: ${{ matrix.config.rglusenull }}
      RSPM: ${{ matrix.config.rspm }}
      NOT_CRAN: true
      OMP_NUM_THREADS: 1


    steps:
      - uses: actions/checkout@v3

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}

      - uses: r-lib/actions/setup-pandoc@v2

      - name: Brew and macOS config
        if: runner.os == 'macOS'
        run: |
          # conflicts with gfortran from r-lib/actions when linking gcc
          rm '/usr/local/bin/gfortran'
          brew install gdal proj geos
          brew install --cask xquartz

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
        shell: Rscript {0}

      - name: Cache R packages
        if: runner.os != 'Windows'
        uses: actions/cache@v1
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-2-

      - name: Install system dependencies
        if: runner.os == 'Linux'
        run: |
          sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
          sudo apt update
          sudo apt install \
            libgdal-dev \
            libgeos++-dev \
            libudunits2-dev \
            libproj-dev \
            libx11-dev \
            libgl1-mesa-dev \
            libglu1-mesa-dev \
            libfreetype6-dev \
            libnode-dev \
            libxt-dev \
            libfftw3-dev

      - name: Install dependencies
        run: |
          install.packages("BiocManager")
          BiocManager::install("EBImage")
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
          remotes::install_cran("covr")
        shell: Rscript {0}

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
        shell: Rscript {0}

      - name: Show testthat output
        if: always()
        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
        shell: bash

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check

      - name: Test coverage
        if: matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'devel'
        run: covr::codecov(type = "all")
        shell: Rscript {0}