R-CMD-build_check.yml

## This is a test
## Template from here: https://github.com/r-lib/actions/tree/master/examples#standard-ci-workflow
## ubuntu-latest
on:
  push:
    branches:
      - devel
  pull_request:
    branches:
      - devel

name: R-CMD-check

jobs:
  R-CMD-check:
    if: "contains(toJSON(github.event.commits.*.message), 'build_check')"
    runs-on: ${{ matrix.config.os }}

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

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: ubuntu-20.04, r: '4.3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: macOS-latest, r: '4.3.3'}
          - {os: windows-latest, r: '4.3.3'}  

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - uses: actions/checkout@v2

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

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

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
        shell: Rscript {0}

      - name: Cache R packages
        if: runner.os != 'Windows'
        uses: actions/cache@v1
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
     
      - name: Install system dependencies
        if: runner.os == 'Linux'
        env:
          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
        run: |
          sudo apt-get install libv8-dev
          sudo apt install libcurl4-openssl-dev
         
      - name: Install dependencies
        run: |
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
          install.packages(c("BiocManager", "knitcitations", "docopt"))
          remotes::install_github("HenrikBengtsson/matrixStats", ref="develop") ## temp fix - 03/15/22 
          BiocManager::install("tgirke/systemPipeR", dependencies=TRUE)
          BiocManager::install("tgirke/systemPipeRdata")
        shell: Rscript {0}

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
        run: rcmdcheck::rcmdcheck(build_args = c('--compact-vignettes=gs+qpdf'), args = c("--no-manual", "--no-build-vignettes", "--timings"), error_on = "warning", check_dir = "check")
        shell: Rscript {0}

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