R-CMD-check.yaml

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main

name: R-CMD-check

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

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

    strategy:
      fail-fast: false
      matrix:
        config:
        - { os: windows-latest, r: '4.2'}
        - { os: macOS-latest, r: '4.2'}
        - { os: ubuntu-20.04, r: '4.2', cran: "https://packagemanager.rstudio.com/all/__linux__/focal/latest"}
        # - { os: ubuntu-20.04, r: 'devel', cran: "https://packagemanager.rstudio.com/all/__linux__/focal/latest"}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      CRAN: ${{ matrix.config.cran }}
      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Install system libraries
        if: ${{ runner.os == 'Linux'  }}
        run: |
          sudo apt-get update
          sudo apt-get install libcurl4-openssl-dev libglpk-dev
      - uses: actions/checkout@v2

      - uses: r-lib/actions/setup-r@v1
        with:
          r-version: ${{ matrix.config.r }}

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

      - name: Install remotes
        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: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-1-

      - name: Install dependencies
        run: |
          install.packages(c('BiocManager', 'rcmdcheck', 'covr'))
          BiocManager::install(ask = FALSE, update = TRUE)
          toInstall <- remotes::dev_package_deps(dependencies = TRUE)[,'package']
          toInstall <- setdiff(toInstall, installed.packages()[,'Package'])
          if(length(toInstall)) { BiocManager::install(toInstall, ask = FALSE) }
        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
        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error", check_dir = "check")
        shell: Rscript {0}

      - name: BiocCheck
        run: |
          BiocManager::install("BiocCheck")
          BiocCheck::BiocCheck(".")
        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

      - 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 }}-bioc-${{ matrix.config.bioc }}-results
          path: check

      - name: Test coverage
        if: matrix.config.os == 'macOS-latest' && matrix.config.r == 'release'
        run: |
          install.packages("covr")
          covr::codecov(type = "all", token = "${{secrets.CODECOV_TOKEN}}")
        shell: Rscript {0}