basic_checks.yaml

on: [push]
jobs:
  job1:
    runs-on: ubuntu-latest
    container: bioconductor/bioconductor_docker:devel
    steps:
      - uses: actions/checkout@v1

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
        shell: Rscript {0}
        
      - name: Cache R packages
        if: runner.os != 'Windows'
        uses: actions/cache@v1
        with:
          path: /usr/local/lib/R/site-library
          key: ${{ runner.os }}-r-1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-r-1-

      # This lets us augment with additional dependencies
      - name: Install system dependencies
        if: runner.os == 'Linux'
        env:
          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
        run: |
          apt-get update && \
          apt-get install -y libglpk-dev && \
          apt-get clean && \
          rm -rf /var/lib/apt/lists/*
          Rscript -e "remotes::install_github('r-hub/sysreqs')"
          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
          sudo -s eval "$sysreqs"
          
      - name: Install dependencies
        run: |
          options(repos = c(CRAN = "https://cran.r-project.org"))
          BiocManager::repositories()
          remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
          remotes::install_cran("rcmdcheck")
        shell: Rscript {0}

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
#         run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check")
        shell: Rscript {0}
        
      - uses: docker/build-push-action@v1
        with:
          username: ${{ secrets.DOCKERHUB_USER }}
          password: ${{ secrets.DOCKERHUB_PASS }}
          repository: bhklab/gxbioc2020workshop
          tag_with_ref: true
          tag_with_sha: true
          tags: latest

      - name: Build pkgdown
        run: |
           PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'

      # deploy needs rsync? Seems so.
      - name: Install deploy dependencies
        run: |
          apt-get update
          apt-get -y install rsync

      - name: Deploy 🚀
        uses: JamesIves/github-pages-deploy-action@releases/v3
        with:
          ACCESS_TOKEN: ${{ secrets.bhklab_bot_PAT }}
          BRANCH: gh-pages # The branch the action should deploy to.
          FOLDER: docs # The folder the action should deploy.