# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Data Analysis for R                   #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2018-2022 Berends MS, Luz CF et al.                              #
# Developed at the University of Groningen, the Netherlands, in        #
# collaboration with non-profit organisations Certe Medical            #
# Diagnostics & Advice, and University Medical Center Groningen.       # 
#                                                                      #
# This R package is free software; you can freely use and distribute   #
# it for both personal and commercial purposes under the terms of the  #
# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
# the Free Software Foundation.                                        #
# We created this package for both routine data analysis and academic  #
# research and it was publicly released in the hope that it will be    #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
#                                                                      #
# Visit our website for the full manual and a complete tutorial about  #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
# ==================================================================== #

on:
  pull_request:
    # run in each PR in this repo
    branches: '**'

name: R-code-check-PR

jobs:
  R-code-check-PR:
    # do not run if we are the authors - the other checks will already run
    if: ${{ github.event.comment.author_association != 'MEMBER' && github.event.comment.author_association != 'OWNER' }}
    
    runs-on: ${{ matrix.config.os }}

    continue-on-error: ${{ matrix.config.allowfail }}

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

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest,   r: 'devel',   allowfail: true}
          - {os: macOS-latest,   r: 'release', allowfail: false}
          - {os: ubuntu-latest,  r: 'devel',   allowfail: true}
          - {os: ubuntu-latest,  r: 'release', allowfail: false}
          - {os: windows-latest, r: 'devel',   allowfail: true}
          - {os: windows-latest, r: 'release', allowfail: false}

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      R_KEEP_PKG_SOURCE: yes
    
    steps:
      - uses: actions/checkout@v3

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

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}
          # use RStudio Package Manager to quickly install packages
          use-public-rspm: true      

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck
          needs: check

      - uses: r-lib/actions/check-r-package@v2
        env:
          _R_CHECK_LENGTH_1_CONDITION_: verbose
          _R_CHECK_LENGTH_1_LOGIC2_: verbose
          # during 'R CMD check', R_LIBS_USER will be overwritten, so:
          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
          R_RUN_TINYTEST: true