# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.
#
# See https://github.com/r-lib/actions/tree/master/examples#readme for
# additional example workflows available for the R community.

# ======================================================== #
# Determines when the action is triggered                  #
# ======================================================== #

on: [push, pull_request]
name: R-CMD-check

# ======================================================== #
# Determine actions to take                                #
# ======================================================== #

jobs:
  R-CMD-check:
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os }} (R ${{ matrix.config.r }})
    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: windows-latest, r: 'release'}
          - {os: macOS-latest, r: 'release'}
          - {os: ubuntu-latest, r: 'release'}
          - {os: ubuntu-latest, r: 'devel'}
    steps:

        # Checking out code -------------------------------------- #
        - name: Checking out the repository
          uses: actions/checkout@v2

        # Setting up environment --------------------------------- #
        - name: Setting up R ${{ matrix.config.r }} on ${{ matrix.config.os }}
          uses: r-lib/actions/setup-r@v1
          with:
            r-version: ${{ matrix.config.r }}

        # Installing Pandoc -------------------------------------- #
        - name: Installing Pandoc
          uses: r-lib/actions/setup-pandoc@v1

        # Querying dependencies ---------------------------------- #
        - name: Querying 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}

        # Restoring R package cache ------------------------------ #
        - name: Restoring R package cache
          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-

        # Installing system dependencies ------------------------- #
        - name: Installing 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"))')

        # Installing package dependencies ------------------------ #
        - name: Installing package dependencies
          run: |
            remotes::install_cran(c("rcmdcheck", "BiocManager"))
            BiocManager::install("Rsamtools")
            remotes::install_deps(dependencies = TRUE)
          shell: Rscript {0}

        # Checking package --------------------------------------- #
        - name: Checking package
          env:
            _R_CHECK_CRAN_INCOMING_REMOTE_: false
          run: |
            options(crayon.enabled = TRUE)
            rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
          shell: Rscript {0}

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