OMOP/.github/workflows/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:
      - '**'
  pull_request:
    branches:
      - '**'
  schedule:
    - cron: '0 19 * * 0' # every Sunday at 7pm UTC

name: R-CMD-check

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

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

    strategy:
      # Test create and drop tables in a database so they cannot be executed in parallel
      max-parallel: 1
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest, r: 'release'}
          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: windows-latest, r: 'release'}  # Does not appear to have Java 32-bit, hence the --no-multiarch

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      CDMDDLBASE_POSTGRESQL_USER: ${{ secrets.CDMDDLBASE_POSTGRESQL_USER }}
      CDMDDLBASE_POSTGRESQL_PASSWORD: ${{ secrets.CDMDDLBASE_POSTGRESQL_PASSWORD }}
      CDMDDLBASE_POSTGRESQL_SERVER: ${{ secrets.CDMDDLBASE_POSTGRESQL_SERVER }}
      CDMDDLBASE_POSTGRESQL_SCHEMA: ${{ secrets.CDMDDLBASE_POSTGRESQL_SCHEMA }}
      CDMDDLBASE_REDSHIFT_USER: ${{ secrets.CDMDDLBASE_REDSHIFT_USER }}
      CDMDDLBASE_REDSHIFT_PASSWORD: ${{ secrets.CDMDDLBASE_REDSHIFT_PASSWORD }}
      CDMDDLBASE_REDSHIFT_SERVER: ${{ secrets.CDMDDLBASE_REDSHIFT_SERVER }}
      CDMDDLBASE_REDSHIFT_SCHEMA: ${{ secrets.CDMDDLBASE_REDSHIFT_SCHEMA }}
      CDMDDLBASE_SQL_SERVER_USER: ${{ secrets.CDMDDLBASE_SQL_SERVER_USER }}
      CDMDDLBASE_SQL_SERVER_PASSWORD: ${{ secrets.CDMDDLBASE_SQL_SERVER_PASSWORD }}
      CDMDDLBASE_SQL_SERVER_SERVER: ${{ secrets.CDMDDLBASE_SQL_SERVER_SERVER }}
      CDMDDLBASE_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_SQL_SERVER_CDM_SCHEMA }}
      CDMDDLBASE_ORACLE_USER: ${{ secrets.CDMDDLBASE_ORACLE_USER }}
      CDMDDLBASE_ORACLE_PASSWORD: ${{ secrets.CDMDDLBASE_ORACLE_PASSWORD }}
      CDMDDLBASE_ORACLE_SERVER: ${{ secrets.CDMDDLBASE_ORACLE_SERVER }}
      CDMDDLBASE_ORACLE_CDM_SCHEMA: ${{ secrets.CDMDDLBASE_ORACLE_CDM_SCHEMA }}

    steps:
      - uses: actions/checkout@v4
      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}

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

      - 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)
          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@v3.3.1
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

      - name: Install system dependencies
        if: runner.os == 'Linux'
        run: |
          while read -r cmd
          do
            eval sudo $cmd
          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')

      - name: Install libssh
        if: runner.os == 'Linux'
        run: |
          sudo apt-get install libssh-dev

      - name: Install dependencies
        run: |
          remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
          remotes::install_cran("rcmdcheck")
        shell: Rscript {0}

      - name: Install covr
        if: runner.os == 'macOS'
        run: |
          remotes::install_cran("covr")
        shell: Rscript {0}

      - name: Remove check folder if exists
        if: runner.os == 'macOS'
        run: unlink("check", recursive = TRUE)
        shell: Rscript {0}

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

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@v2
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check

      - name: Upload source package
        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/master'
        uses: actions/upload-artifact@v2
        with:
          name: package_tarball
          path: check/*.tar.gz

      - name: Test coverage
        if: runner.os == 'macOS'
        run: covr::codecov()
        shell: Rscript {0}