check-bioc.yml

## Read more about GitHub actions the features of this GitHub Actions workflow
## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
##
## For more details, check the biocthis developer notes vignette at
## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
##
## You can add this workflow to other packages using:
## > biocthis::use_bioc_github_action()
## or
## > usethis::use_github_action("check-bioc", "https://bit.ly/biocthis_gha", "check-bioc.yml")
## without having to install biocthis.
##
## Using GitHub Actions exposes you to many details about how R packages are
## compiled and installed in several operating system.s
### If you need help, please follow the steps listed at
## https://github.com/r-lib/actions#where-to-find-help
##
## If you found an issue specific to biocthis's GHA workflow, please report it
## with the information that will make it easier for others to help you.
## Thank you!



## Acronyms:
## * GHA: GitHub Action
## * OS: operating system

## Specify which branches you want this GHA to run on.
## Bioconductor uses branches such as master (bioc-devel) and RELEASE_* like
## RELEASE_3_10. For more details check
## http://bioconductor.org/developers/how-to/git/
on:
  push:
    branches:
      - master
      - 'RELEASE_*'
  pull_request:
    branches:
      - master
      - 'RELEASE_*'

name: R-CMD-check-bioc

## These environment variables control whether to run GHA code later on that is
## specific to testthat, covr, and pkgdown.
##
## If you need to clear the cache of packages, update the number inside
## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
## Note that you can always run a GHA test without the cache by using the word
## "/nocache" in the commit message.
env:
  has_testthat: 'true'
  run_covr: 'true'
  run_pkgdown: 'true'
  has_RUnit: 'false'
  cache-version: 'cache-v1'

jobs:
  ## This first job uses the GitHub repository branch name to infer what
  ## version of Bioconductor we will be working on.
  define-docker-info:
    runs-on: ubuntu-latest
    outputs:
      imagename: ${{ steps.findinfo.outputs.imagename }}
      biocversion: ${{ steps.findinfo.outputs.biocversion }}
    steps:
      - id: findinfo
        run: |
          ## Find what Bioconductor RELEASE branch we are working on
          ## otherwise, assume we are working on bioc-devel.
          if echo "$GITHUB_REF" | grep -q "RELEASE_"; then
              biocversion="$(basename -- $GITHUB_REF | tr '[:upper:]' '[:lower:]')"
          else
              biocversion="devel"
          fi
          ## Define the image name and print the information
          imagename="bioconductor/bioconductor_docker:${biocversion}"
          echo $imagename
          echo $biocversion

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

  R-CMD-check-bioc:
    ## This job then checks the R package using the Bioconductor docker that
    ## was defined by the previous job. This job will determine what version of
    ## R to use for the macOS and Windows builds on the next job.
    runs-on: ubuntu-latest
    needs: define-docker-info

    ## Name shown on the GHA log
    name: ubuntu-latest (r-biocdocker bioc-${{ needs.define-docker-info.outputs.biocversion }})

    ## Information used by the next job that will run on macOS and Windows
    outputs:
      rversion: ${{ steps.findrversion.outputs.rversion }}
      biocversionnum: ${{ steps.findrversion.outputs.biocversionnum }}

    ## Environment variables unique to this job.
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      TZ: UTC
      NOT_CRAN: true
      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    ## The docker container to use. Note that we link a directory on the GHA
    ## runner to a docker directory, such that we can then cache the linked
    ## directory. This directory will contain the R packages used.
    container:
      image: ${{ needs.define-docker-info.outputs.imagename }}
      volumes:
        - /home/runner/work/_temp/Library:/usr/local/lib/R/host-site-library

    steps:
      - name: Install latest git
        run: |
          ## git version provided
          git --version
          ## to be able to install software properties
          sudo apt-get update -y
          ## to be able to use add-apt-repository
          sudo apt-get install software-properties-common -y
          ## to use stable releases of git that are already in a PPA at
          ## https://launchpad.net/~git-core/+archive/ubuntu/candidate
          sudo add-apt-repository ppa:git-core/candidate -y
          ## Update
          sudo apt-get update -y
          ## Upgrade git and other tools
          sudo apt-get upgrade -y
          ## latest git version
          git --version
        shell: bash {0}
      ## Related to https://github.com/rocker-org/rocker-versioned2/issues/52

      ## Most of these steps are the same as the ones in
      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
      ## If they update their steps, we will also need to update ours.
      - uses: actions/checkout@v2

      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
          message(paste('****', Sys.time(), 'installing BiocManager ****'))
          remotes::install_cran("BiocManager")
        shell: Rscript {0}

      ## Find the corresponding R version based on the Bioconductor version
      ## to use for the macOS and Windows checks by the next GHA job
      - id: findrversion
        name: Find Bioc and R versions
        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))")

          ## 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: Cache R packages
        if: "!contains(github.event.head_commit.message, '/nocache')"
        uses: actions/cache@v1
        with:
          path: /home/runner/work/_temp/Library
          key: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-

      # - name: Manually install affy and svn (currently unavailable for devel)
      #   run: |
      #     BiocManager::install("Bioconductor/affy")
      #     remotes::install_git("https://git.bioconductor.org/packages/vsn")
      #   shell: Rscript {0}

      - name: Manually install genefilter
        run: |
          remotes::install_git("https://git.bioconductor.org/packages/genefilter")
        shell: Rscript {0}

      # - name: Manually install sva
      #   run: |
      #     BiocManager::install("sva")
      #   shell: Rscript {0}

      - name: Install dependencies
        run: |
          ## Try installing the package dependencies in steps. First the local
          ## dependencies, then any remaining dependencies to avoid the
          ## issues described at
          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
          ## https://github.com/r-lib/remotes/issues/296
          ## Ideally, all dependencies should get installed in the first pass.

          ## Pass #1 at installing dependencies
          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
          local_deps <- remotes::local_package_deps(dependencies = TRUE)
          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
          BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])

          ## Pass #2 at installing dependencies
          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
          BiocManager::install(deps$package[deps$diff != 0])

          ## For running the checks
          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
          remotes::install_cran("rcmdcheck")
          BiocManager::install("BiocCheck")
        shell: Rscript {0}

      # ## See https://github.com/Bioconductor/bioconductor_docker/issues/22
      # - name: Manually install preprocessCore
      #   run: |
      #     git clone https://github.com/bmbolstad/preprocessCore.git
      #     cd preprocessCore
      #     R CMD INSTALL --configure-args="--disable-threading"  .

      # - name: Manually install latest QFeatures
      #   run: |
      #     BiocManager::install("RforMassSpectrometry/QFeatures")
      #   shell: Rscript {0}

      - name: Session info
        run: |
          options(width = 100)
          pkgs <- installed.packages()[, "Package"]
          sessioninfo::session_info(pkgs, include_base = TRUE)
        shell: Rscript {0}

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

      - name: Reveal testthat details
        if:  env.has_testthat == 'true'
        run: find . -name testthat.Rout -exec cat '{}' ';'

      - name: Run RUnit tests
        if:  env.has_RUnit == 'true'
        run: |
          ## Install BiocGenerics
          BiocManager::install("BiocGenerics")
          BiocGenerics:::testPackage()
        shell: Rscript {0}

      - name: BiocCheck
        run: |
          ## This syntax works on Windows as well as other OS
          ## plus it doesn't break the GHA workflow in case BiocCheck finds
          ## an error (for example, the package is bigger than the maximum
          ## allowed size). We want the rest of the GHA to proceed even if
          ## there is a BiocCheck error in order to see the full output and
          ## run the tests on all operating systems.
          BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `no-check-R-ver` = TRUE, `no-check-bioc-help` = TRUE)
          ## For more options check http://bioconductor.org/packages/release/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html
        shell: Rscript {0}

      - name: Install covr
        if: github.ref == 'refs/heads/master' && env.run_covr == 'true'
        run: |
          remotes::install_cran("covr")
        shell: Rscript {0}

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

      - name: Install pkgdown
        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true'
        run: |
          remotes::install_github("r-lib/pkgdown")
        shell: Rscript {0}

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

      - name: Deploy package
        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
        run: |
          git config --global user.email "actions@github.com"
          git config --global user.name "GitHub Actions"
          git config --global --add safe.directory /__w/scp/scp
          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: Upload check results
        if: failure()
        uses: actions/upload-artifact@master
        with:
          name: ${{ runner.os }}-biocdocker-biocbranch-${{ needs.define-docker-info.outputs.biocversion }}-r-${{ steps.findrversion.outputs.rversion }}-bioc-${{ steps.findrversion.outputs.biocversionnum }}-results
          path: check