build.yaml

# 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.

name: build

on:
  push:
    branches:
      - "main"
      - "master"
  pull_request:
    branches:
      - "*"

env:
  cache-version: 'cache-v1'
  
jobs:
  build:
    strategy:
      max-parallel: 5
      matrix:
        config:
        #  - { r-version: 4.0, os: ubuntu-latest }
          - { r-version: 4.1, os: ubuntu-latest }
         # - { r-version: 4.0, os: macos-latest }
          - { r-version: 4.1, os: macos-latest }
    runs-on: ${{ matrix.config.os }}
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      NOT_CRAN: true
      TZ: UTC
      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      
    steps:
      - uses: actions/checkout@v2
      - uses: actions/setup-node@v2
      
      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r-version}}
      
      - uses: r-lib/actions/setup-pandoc@v1

      - name: Setup r-lib/remotes      
        run: |
          install.packages('remotes')
        shell: Rscript {0}
      
      - id: bioc
        name: Check bioc version
        run: |
          echo "##[set-output name=mainbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')"
          echo "##[set-output name=subbiocversion;]$(Rscript -e 'cat(unlist(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $2}')"
          echo "##[set-output name=biocversion;]$(Rscript -e 'cat(as.character(tools:::.BioC_version_associated_with_R_version()))' | awk '{print $1}')"
        shell: bash -l {0}
        
      - name: Install ubuntu system dependencies
        if: matrix.config.os == 'ubuntu-latest'
        run: |
          sudo apt-get install libcurl4-openssl-dev
          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04", package = c("reshape2", "ggplot2", "igraph", "ggraph", "vcfR", "knitr", "rmarkdown", "markdown", "pbapply"))), collapse = " "))')
          echo $sysreqs
          sudo -s eval "$sysreqs"
      - name: Install macOS system dependencies
        if: matrix.config.os == 'macos-latest'
        run: |
          brew install cairo pkg-config autoconf automake libtool
      
      - name: Cache ubuntu R packages
        if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os == 'ubuntu-latest'"
        uses: actions/cache@v2
        with:
          path: /home/runner/work/_temp/Library
          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-

      - name: Cache macOS R packages
        if: "!contains(github.event.head_commit.message, '/nocache') && matrix.config.os != 'ubuntu-latest'"
        uses: actions/cache@v2
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ matrix.config.os }}-biocversion-RELEASE_${{ steps.bioc.outputs.mainbiocversion}}_${{ steps.bioc.outputs.subbiocversion}}-r-${{ matrix.config.r-version}}-
      
      - name: Install dependencies
        run: |
          install.packages(c("rcmdcheck", "covr"))
          remotes::install_deps(dependencies = TRUE)
        shell: Rscript {0}
        
      - name: Check
        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
        shell: Rscript {0}

      # - name: Test coverage
      #   run: covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
      #   shell: Rscript {0}