AMR/.github/workflows/check.yaml

# ==================================================================== #
# TITLE                                                                #
# Antimicrobial Resistance (AMR) Data Analysis for R                   #
#                                                                      #
# SOURCE                                                               #
# https://github.com/msberends/AMR                                     #
#                                                                      #
# LICENCE                                                              #
# (c) 2018-2021 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:
  push:
    branches:
      - premaster
      - master
  pull_request:
    branches:
      - master
  schedule:
    # run a schedule everyday at 3 AM.
    # this is to check that all dependencies are still available (see R/zzz.R)
    - cron:  '0 3 * * *'

name: R-code-check

jobs:
  R-code-check:
    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: macOS-latest,   r: 'oldrel',  allowfail: false}
          
          - {os: windows-latest, r: 'devel',   allowfail: false}
          - {os: windows-latest, r: 'release', allowfail: false}
          - {os: windows-latest, r: 'oldrel',  allowfail: false}
          
          - {os: ubuntu-20.04,   r: 'devel',   allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: 'oldrel',  allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '3.2',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '3.1',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          - {os: ubuntu-20.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
          
          - {os: ubuntu-16.04,   r: 'devel',   allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: 'oldrel',  allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: '3.2',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: '3.1',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
          - {os: ubuntu-16.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}

    steps:
      - uses: actions/checkout@v2

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

      # - uses: r-lib/actions/setup-pandoc@master
      
      # - name: Query dependencies
      #   if: matrix.config.r != '3.0'
      #   run: |
      #     saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
      #   shell: Rscript {0}

      - name: Install Linux dependencies
        if: runner.os == 'Linux'
        # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
        # we don't want to depend on the sysreqs pkg here, as it requires a quite new R version
        run: |
          sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev

      - 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 }}-3
          restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3

      - name: Update AMR package dependencies
        run: |
          install.packages("data-raw/AMR_latest.tar.gz")
          source("data-raw/_install_deps.R")
        shell: Rscript {0}
        
      - name: Session info
        run: |
          options(width = 100)
          utils::sessionInfo()
          as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
        shell: Rscript {0}

      - name: Run R CMD check on Windows
        if: runner.os == 'Windows'
        env:
          _R_CHECK_CRAN_INCOMING_: false
          _R_CHECK_FORCE_SUGGESTS_: false
          _R_CHECK_DEPENDS_ONLY_: true
          _R_CHECK_LENGTH_1_CONDITION_: verbose
          _R_CHECK_LENGTH_1_LOGIC2_: verbose
          R_LIBS_USER: ${{ env.R_LIBS_USER }}
          R_TINYTEST: true
        run: |
          tar -xf data-raw/AMR_latest.tar.gz
          rm -rf AMR/vignettes
          R CMD check AMR
        shell: bash

      - name: Run R CMD check on Linux and macOS
        if: runner.os != 'Windows'
        env:
          _R_CHECK_CRAN_INCOMING_: false
          _R_CHECK_FORCE_SUGGESTS_: false
          _R_CHECK_DEPENDS_ONLY_: true
          _R_CHECK_LENGTH_1_CONDITION_: verbose
          _R_CHECK_LENGTH_1_LOGIC2_: verbose
          R_LIBS_USER: ${{ env.R_LIBS_USER }}
          R_TINYTEST: true
        run: |
          tar -xf data-raw/AMR_latest.tar.gz
          rm -rf AMR/vignettes
          R CMD check AMR --no-manual --no-vignettes
        shell: bash

      - name: Show unit tests output
        if: always()
        run: |
          find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
        shell: bash

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