R-CMD-check.yaml

# NOTE: This workflow is overkill for most R packages
# check-standard.yaml is likely a better choice
# usethis::use_github_action("check-standard") will install it.
#
# 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:
      - main
      - master
      - devel
      - dev
  pull_request:
    branches:
      - main
      - master
      - devel
      - dev

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: 'release'}
          - {os: windows-latest, r: 'release'}
          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
          - {os: ubuntu-20.04,   r: 'release'}
          - {os: ubuntu-20.04,   r: '4.0'}
    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 }}
          http-user-agent: ${{ matrix.config.http-user-agent }}

      - uses: r-lib/actions/setup-pandoc@v1

      - name: Query dependencies
        run: |
          install.packages(c('remotes', 'covr'))
          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@v2
        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: |
          ls
          pwd
          echo -e 'LC_CTYPE = "en_US.UTF-8"\nLC_NUMERIC="C"\nLC_TIME="en_US.UTF-8"\nLC_COLLATE="C"\nLC_MONETARY="en_US.UTF-8"\nLC_MESSAGES="en_US.UTF-8"\nLC_PAPER="en_US.UTF-8"\nLC_NAME="C"\nLC_ADDRESS="C"\nLC_TELEPHONE="C"\nLC_MEASUREMENT="en_US.UTF-8"\nLC_IDENTIFICATION="C"' > .Renviron

          while read -r cmd
          do
            eval sudo $cmd
          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')

      - name: Install dependencies
        run: |
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
          remotes::install_cran("covr")
          remotes::install_cran("xml2")
          remotes::install_cran("DT")
        shell: Rscript {0}

      - name: Session info
        run: |
          options(width = 100)
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}
        
      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_: false
        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--run-donttest"), 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: always()
        uses: actions/upload-artifact@main
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check

      - name: Codecov
        run: |
          covr::codecov()
        shell: Rscript {0}
        
      - name: Test coverage report
        if: always()
        run: |
          covr_report <- covr::package_coverage(wrap = TRUE)
          covr::report(x = covr_report, file = 'covr_report.html')
          print(getwd())
          print(dir())
        shell: Rscript {0}

      - name: Upload test coverage report
        if: always()
        uses: actions/upload-artifact@v3
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: |
            covr_report.html
            lib