For https://github.com/r-lib/actions/issues/84

check-bioc.yaml

## Read more about GitHub actions at
## https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/
## which will lead you to
## https://github.com/r-lib/actions/tree/master/examples.
## Also check the reference manual at
## https://help.github.com/en/actions
## I also found this work in progress book
## https://ropenscilabs.github.io/actions_sandbox/
## as well as these two other GitHub actions config files
## https://github.com/seandavi/BiocActions/blob/master/.github/workflows/main.yml
## https://github.com/csoneson/dreval/blob/master/.github/workflows/R-CMD-check.yaml
## See also this blog post
## https://seandavi.github.io/post/learning-github-actions/

on:
  push:
    branches:
      - master
      - 'RELEASE_*'
  pull_request:
    branches:
      - master
      - 'RELEASE_*'

name: R-CMD-check-bioc

jobs:
  define-docker-info:
    runs-on: ubuntu-latest
    outputs:
      imagename: ${{ steps.findinfo.outputs.imagename }}
      biocversion: ${{ steps.findinfo.outputs.biocversion }}
    steps:
      - id: findinfo
        run: |
          ## Find what branch we are working on
          if echo "$GITHUB_REF" | grep -q "master"; then
              biocversion="devel"
          elif echo "$GITHUB_REF" | grep -q "RELEASE_"; then
              biocversion="$(basename -- $GITHUB_REF | tr '[:upper:]' '[:lower:]')"
          fi
          ## Define the image name and print the info
          imagename="bioconductor/bioconductor_docker:${biocversion}"
          echo $imagename
          echo $biocversion

          ## Save the info for the next job
          echo "::set-output name=imagename::${imagename}"
          echo "::set-output name=biocversion::${biocversion}"

  R-CMD-check-bioc:
    runs-on: ubuntu-latest
    needs: define-docker-info

    name: ubuntu-latest (r-biocdocker bioc-${{ needs.define-docker-info.outputs.biocversion }})

    outputs:
      rversion: ${{ steps.findrversion.outputs.rversion }}
      biocversionnum: ${{ steps.findrversion.outputs.biocversionnum }}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      TZ: UTZ
      NOT_CRAN: true
      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    container:
      image: ${{ needs.define-docker-info.outputs.imagename }}
      volumes:
        - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library

    steps:
      - uses: actions/checkout@v2

      - 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
        uses: actions/cache@v1
        with:
          path: /home/runner/work/_temp/Library
          key: ${{ runner.os }}-r-biocdocker-bioc-${{ needs.define-docker-info.outputs.biocversion }}-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-r-biocdocker-bioc-${{ needs.define-docker-info.outputs.biocversion }}-

      - name: Install system dependencies
        if: runner.os == 'Linux'
        env:
          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
        run: |
          Rscript -e "remotes::install_github('r-hub/sysreqs')"
          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
          sudo -s eval "$sysreqs"

      - name: Install dependencies
        run: |
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
          remotes::install_cran("BiocManager")
          BiocManager::install("BiocCheck")

          ## Copy all the installed packages to a location where BiocCheck
          ## will find them later. This is needed when running biocdocker
          ## with the shared volume.
          libs <- .libPaths()
          message(paste(Sys.time(), 'current R library paths:'))
          print(libs)
          if(length(libs) > 1) {
              sapply(dir(libs[1], full.names = TRUE), file.copy, to = libs[2], recursive = TRUE)
          }
        shell: Rscript {0}

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
        run: |
          rcmdcheck::rcmdcheck(
              args = c("--no-build-vignettes", "--no-manual", "--timings"),
              build_args = c("--no-manual", "--no-resave-data"),
              error_on = "warning",
              check_dir = "check"
          )
        shell: Rscript {0}

      - name: Reveal testthat details
        run: find . -name testthat.Rout -exec cat '{}' ';'

      - name: BiocCheck
        run: |
          R CMD BiocCheck --no-check-R-ver --no-check-bioc-help check/*.tar.gz
        ## For more options check http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html

      - name: Install covr and pkgdown
        if: github.ref == 'refs/heads/master'
        run: |
          if (!requireNamespace("covr", quietly = TRUE))
              remotes::install_cran("covr")
          if (!requireNamespace("pkgdown", quietly = TRUE))
              remotes::install_dev("pkgdown")
        shell: Rscript {0}

      - name: Install package
        if: github.ref == 'refs/heads/master'
        run: R CMD INSTALL .

      - name: Deploy package
        if: github.ref == 'refs/heads/master'
        run: |
          git config --local user.email "[email protected]"
          git config --local user.name "GitHub Action"
          Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
        shell: bash {0}
        ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
        ## at least one locally before this will work. This creates the gh-pages
        ## branch (erasing anything you haven't version controlled!) and
        ## makes the git history recognizable by pkgdown.

      - name: Test coverage
        if: github.ref == 'refs/heads/master'
        run: |
          covr::codecov()
        shell: Rscript {0}

      - id: findrversion
        run: |
          ## Find what branch we are working on
          if echo "$GITHUB_REF" | grep -q "master"; then
              biocversion="devel"
          elif echo "$GITHUB_REF" | grep -q "RELEASE_"; then
              biocversion="release"
          fi

          ## Define the R and Bioconductor version numbers
          biocversionnum=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'Bioc']; cat(as.character(res))")
          rversion=$(Rscript -e "info <- BiocManager:::.version_map_get_online('https://bioconductor.org/config.yaml'); res <- subset(info, BiocStatus == '${biocversion}')[, 'R']; cat(as.character(res))")

          ## I might need this for now until R 4.0 is out (try without it first)
          if echo "$rversion" | grep -q "4.0"; then
              rversion="devel"
          fi

          ## Print the results
          echo $biocversion
          echo $biocversionnum
          echo $rversion

          ## Save the info for the next job
          echo "::set-output name=rversion::${rversion}"
          echo "::set-output name=biocversionnum::${biocversionnum}"
        shell:
          bash {0}

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@master
        with:
          name: ${{ runner.os }}-r-biocdocker-bioc-${{ needs.define-docker-info.outputs.biocversion }}-results
          path: check

  R-CMD-check-r-lib:
    runs-on: ${{ matrix.config.os }}
    needs: [define-docker-info, R-CMD-check-bioc]

    name: ${{ matrix.config.os }} (r-${{ needs.R-CMD-check-bioc.outputs.rversion }} bioc-${{ needs.define-docker-info.outputs.biocversion }})

    strategy:
      fail-fast: false
      matrix:
        config:
          # ## Un-comment in case you also want to run other versions
          # - {os: windows-latest}
          - {os: macOS-latest}
          # - {os: ubuntu-16.04, rspm: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      BIOCVERSIONNUM: ${{ needs.R-CMD-check-bioc.outputs.biocversionnum }}

    steps:
      - uses: actions/checkout@v2

      - name: Setup R from r-lib
        uses: r-lib/actions/setup-r@master
        with:
          r-version: ${{ needs.R-CMD-check-bioc.outputs.rversion }}

      - name: Setup pandoc from r-lib
        uses: r-lib/actions/setup-pandoc@master

      - 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: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-

      - name: Install system dependencies
        if: runner.os == 'Linux'
        env:
          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
        run: |
          Rscript -e "remotes::install_github('r-hub/sysreqs')"
          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
          sudo -s eval "$sysreqs"

      - name: Install macOS system dependencies
        if: matrix.config.os == 'macOS-latest' && needs.R-CMD-check-bioc.outputs.rversion == 'devel'
        # the xml2 thing is a hack / experiment
        run: |
          brew install imagemagick@6
          Rscript -e "remotes::install_github('r-lib/xml2')"

      - name: Install BiocManager
        run: |
          remotes::install_cran("BiocManager")
        shell: Rscript {0}

      - name: Set BiocVersion
        run: |
          BiocManager::install(version = Sys.getenv('BIOCVERSIONNUM'))
        shell: Rscript {0}

      - name: Install dependencies
        run: |
          remotes::install_deps(dependencies = TRUE)
          remotes::install_cran("rcmdcheck")
          BiocManager::install("BiocCheck")
        shell: Rscript {0}

      - name: Check
        env:
          _R_CHECK_CRAN_INCOMING_REMOTE_: false
        run: |
          rcmdcheck::rcmdcheck(
              args = c("--no-build-vignettes", "--no-manual", "--timings"),
              build_args = c("--no-manual", "--no-resave-data"),
              error_on = "warning",
              check_dir = "check"
          )
        shell: Rscript {0}

      - name: Reveal testthat details
        run: find . -name testthat.Rout -exec cat '{}' ';'

      - name: BiocCheck
        run: |
          R CMD BiocCheck --no-check-R-ver --no-check-bioc-help check/*.tar.gz
        ## For more options check http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@master
        with:
          name: ${{ runner.os }}-r-${{ needs.R-CMD-check-bioc.outputs.rversion }}-bioc-${{ needs.define-docker-info.outputs.biocversion }}-results
          path: check