r.yml

name: R

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

env:
  cache-version: 'cache-v1'

jobs:
  build:
    strategy:
      max-parallel: 5
      matrix:
        config:
          - { r-version: release, os: ubuntu-latest}
          - { r-version: release, 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: Install ubuntu system dependencies
        if: matrix.config.os == 'ubuntu-latest'
        run: |
          sudo apt-get install git libcurl4-openssl-dev libssl-dev libicu-dev libxml2-dev make pandoc libgit2-dev libharfbuzz-dev libfribidi-dev
      - name: Install macOS system dependencies
        if: matrix.config.os == 'macos-latest'
        run: |
          brew install cairo pkg-config autoconf automake libtool

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r-version}}

      - name: Setup r-lib/remotes
        run: |
          install.packages(c("remotes", "devtools"))
        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: 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: |
          Rscript -e 'rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")'
        shell: bash -l {0}

      - name: Test coverage
        run: |
          Rscript -e 'covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")'
        shell: bash -l {0}