R-CMD-check.yaml

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master

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: macOS-latest,   r: 'devel'}
          - {os: macOS-latest,   r: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-latest,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-latest,   r: '3.6',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-latest,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-latest,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      RETICULATE_AUTOCONFIGURE: 'FALSE'
      CI: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_PAT }}

    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: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "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('depends.Rds') }}
          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-

      - name: Install system dependencies (Linux)
        if: runner.os == 'Linux'
        run: |
          export DEBIAN_FRONTEND=noninteractive
          sudo apt-get -y update
          sudo apt-get install -y make python-is-python3 pandoc pandoc-citeproc git-core libv8-dev libxml2-dev libcurl4-openssl-dev libssl-dev libssh2-1-dev zlib1g-dev libgit2-dev

      - name: Install system dependencies (macOS)
        if: runner.os == 'macOS' && matrix.config.r == 'devel'
        run: |
          brew install libgit2

      - name: Install dependencies
        run: |
          Sys.setenv(DOWNLOAD_STATIC_LIBV8 = 1)
          library(remotes)
          deps <- readRDS('depends.Rds')
          deps[['installed']] <- vapply(deps[['package']], remotes:::local_sha, character(1))
          update(deps)
          remotes::install_cran('rcmdcheck')
        shell: Rscript {0}

      - name: Install Miniconda
        run: |
          Rscript -e "remotes::install_github('rstudio/reticulate')"
          Rscript -e "reticulate::install_miniconda()"

      - name: Add Miniconda to .Rprofile on macOS
        if: runner.os == 'macOS'
        run: echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile

      - name: Install Python deps
        run: |
          Rscript -e "reticulate::py_discover_config()"
          Rscript -e "reticulate::py_install(c('pandas', 'numpy', 'boto3', 'synapseclient'), pip = TRUE)"

      - name: Check
        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
        shell: Rscript {0}

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