build.yml

# 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.
#

name: build

on:
  push:
    branches: [ release, master ]
  pull_request:
    branches: [ release, master ]

jobs:
  build:
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os }} (${{ matrix.r }})
    strategy:
      fail-fast: false
      matrix:
        r: ['release', 'devel']
        config:
          - {os: windows-latest, suffix: 'zip'}
          - {os: macOS-latest, suffix: 'tgz'}
          - {os: ubuntu-16.04, suffix: 'tar.gz', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
        isMaster:
          - ${{ contains(github.ref, 'master') }}
        exclude:
          - isMaster: false
            r: devel
          - isMaster: true
            r: release
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
    
    steps:
      - uses: actions/checkout@v2
      - name: Set up R ${{ matrix.r }}
        uses: r-lib/actions/setup-r@master
        with:
          r-version: ${{ matrix.r }}
          http-user-agent: ${{ matrix.config.http-user-agent }}

      - uses: r-lib/actions/setup-pandoc@v1
      
      - name: set token for cytoinstaller(and remotes) to increase github API rate limit
        env:
          SUPER_SECRET: ${{ secrets.CYTOINSTALLER_TOKEN }}
        run: echo "GITHUB_TOKEN=$SUPER_SECRET" >> $GITHUB_ENV
 
      - name: Query 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}
        
      - name: Get bioc ver
        run: echo "bioc_ver=$(Rscript -e 'writeLines(as.character(remotes::bioc_version()))')" >> $GITHUB_ENV
        shell: bash
        
      - name: Cache R packages
        if: runner.os != 'Windows'
        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-

      - name: check bioc ver
        run: echo $bioc_ver
        shell: bash
        
      - name: Install system dependencies
        if: runner.os == 'Linux'
        run: |
          while read -r cmd
          do
            eval sudo $cmd
          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))')
          sudo apt-get install -y libcurl4-openssl-dev
          
      - name: Install Mac OS depdendencies.
        if: runner.os == 'macOS'
        run: brew install libgit2

      - name: Install dependencies
        run: |
          remotes::install_cran(c("rcmdcheck", "devtools"))
          remotes::install_github("RGLab/cytoinstaller")
          cytoinstaller::cyto_install_deps(dependencies = TRUE)
        shell: Rscript {0}

      - name: check rate limit
        run: |
          gh::gh("GET /rate_limit")$resources$core$remaining
        shell: Rscript {0}
        
      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), check_dir = "check")
        shell: Rscript {0}

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check
          
      - name: build src pkg
        if: runner.os == 'Linux'
        run: devtools::build()
        shell: Rscript {0}
        
      - name: build bin pkg
        if: runner.os != 'Linux'
        run: devtools::build(binary = TRUE)
        shell: Rscript {0}  
        
      - name: Upload Release Asset
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          file: '../*.${{ matrix.config.suffix }}'
          file_glob: true
          tag: bioc_${{ env.bioc_ver}}
          overwrite: true
          body: "This is my release text"