lint.yaml

# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]

name: lint

jobs:
  lint:
    runs-on: ${{ matrix.config.os }}
    name: ${{ matrix.config.os }} (${{ matrix.config.r}})
    container: ${{ 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).
      - name: Set R Library home on Linux
        if: runner.os == 'Linux'
        run: |
          mkdir /__w/_temp/Library
          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile

      - name: Checkout Repository
        uses: actions/checkout@v3

      # R is already included in the Bioconductor Docker image

      - name: "[Stage] Dependencies"
        run: |
            sudo apt install libopenmpi-dev

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

      - 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 }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-

      - name: Install Linux system dependencies
        if: runner.os == 'Linux'
        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 dependencies pass 2
        run: |
          ## Pass #2 at installing dependencies
          ## This pass does not use AnVIL and will thus update any packages
          ## that have seen been updated in Bioconductor
          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
        shell: Rscript {0}

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

      - name: Lint
        run: lintr::lint_package()
        shell: Rscript {0}