check-bioc.yml

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master

name: check-bioc

jobs:
  build-check:
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os}} (R ${{ matrix.config.r }}, Bioc ${{ matrix.config.bioc }})
    container:
      image: ${{ matrix.config.cont }}
    strategy:
      fail-fast: false
      matrix:
        config:
          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16" }
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:

      ## Set the R library to the directory matching the
      ## R packages cache step further below when running on Docker (Linux).
      ## (lcolladotor/biocthis)
      - name: Set R Library home on Linux
        if: runner.os == 'Linux'
        run: |
          mkdir /__w/_temp/Library
          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile

      ## (r-lib/check-standard)
      - name: Checkout Repository
        uses: actions/checkout@v3

      ## R and pandoc already installed in Bioconductor docker containers

      ## (lcolladotor/biocthis)
      - name: Query dependencies
        run: |
          install.packages('remotes')
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
        shell: Rscript {0}

      ## (lcolladotor/biocthis)
      - name: Cache R packages on Linux
        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
        uses: actions/cache@v3
        with:
          path: /home/runner/work/_temp/Library
          key: ${{ env.cache-version }}-${{ runner.os }}-Bioc-RELEASE_3_16-R-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-Bioc-RELEASE_3_16-R-${{ matrix.config.r }}-

      ## Prevent an error due to 'libcurl4-openssl-dev is not available'
      ## (lcolladotor/biocthis)
      - name: Install Linux system dependencies
        run: |
          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
          echo $sysreqs
          sudo -s eval "$sysreqs"

      - name: Install BiocManager
        run: |
          message(paste('****', Sys.time(), 'installing BiocManager ****'))
          remotes::install_cran("BiocManager")
        shell: Rscript {0}

      - name: Set BiocVersion
        run: |
          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
        shell: Rscript {0}

      - name: Install dependencies pass 1
        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.
          ## Set the repos source depending on the OS
          ## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
          ## though based on https://bit.ly/bioc2021-package-binaries
          ## the Azure link will be the main one going forward.
          gha_repos <- if(
              .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
          ) c(
              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.16/bioc",
              BiocManager::repositories()
              ) else BiocManager::repositories()


          ## For running the checks
          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
          install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)


          ## Pass #1 at installing dependencies
          ## This pass uses AnVIL-powered fast binaries
          ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
          ## The speed gains only apply to the docker builds.
          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
          remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
        continue-on-error: true
        shell: Rscript {0}

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

      - name: Install pkgdown
        if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
        run: |
          remotes::install_cran("pkgdown")
        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: Run CMD check
        env:
          _R_CHECK_CRAN_INCOMING_: false
          DISPLAY: 99.0
        run: |
          options(crayon.enabled = TRUE)
          rcmdcheck::rcmdcheck(
              args = c("--no-manual", "--no-vignettes", "--timings"),
              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
              error_on = "warning",
              check_dir = "check"
          )
        shell: Rscript {0}

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

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

      - name: Install package for pkgdown
        if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
        run: R CMD INSTALL .

      - name: Build pkgdown site
        if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
        shell: Rscript {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: Install deploy dependencies
        if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
        run: |
          apt-get update && apt-get -y install rsync

      - name: Deploy pkgdown site to GitHub pages 🚀
        if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
        uses: JamesIves/github-pages-deploy-action@releases/v4
        with:
          clean: false
          branch: gh-pages
          folder: docs

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@master
        with:
          name: ${{ runner.os }}-Bioc-RELEASE_3_16-R-${{ matrix.config.bioc }}-results
          path: check