build-check-install.yaml

---
name: R CMD Check 🧬

on:
  push:
    tags:
      - "v*"
    branches:
      - main
      - pre-release
  pull_request:
    types:
      - opened
      - synchronize
      - reopened
      - ready_for_review
    branches:
      - main
      - pre-release
  workflow_dispatch:
  workflow_call:
    secrets:
      GITHUB_TOKEN:
        description: |
          Github token with read access to repositories, required for staged.dependencies installation
        required: false
    inputs:
      install-system-dependencies:
        description: Check for and install system dependencies
        required: false
        default: false
        type: boolean
      enable-staged-dependencies-check:
        description: Enable staged dependencies YAML check
        required: false
        default: true
        type: boolean
      R_CHECK_FORCE_SUGGESTS:
        description: If true, give an error if suggested packages are not available
        required: false
        default: true
        type: boolean
      skip-r-cmd-check:
        description: Skip the R CMD check step in this workflow
        required: false
        default: false
        type: boolean
      skip-r-cmd-install:
        description: Skip the R CMD INSTALL step in this workflow
        required: false
        default: false
        type: boolean
      check-note-blocklist:
        description: Whether to check for NOTEs that should cause the pipeline to fail
        required: false
        default: false
        type: boolean
      note-blocklist:
        description: List of regular expressions appearing in NOTEs that should cause the pipeline to fail
        # Example usage:
        # note-blocklist: |
        #   checking package dependencies ... NOTE( )+Depends: includes the non-default packages
        #   checking R code for possible problems ... NOTE( )+.*: no visible global function definition for
        #   checking for unstated dependencies in vignettes ... NOTE( )+\'.*\' import not declared from
        #   checking dependencies in R code ... NOTE( )+Namespace in Imports field not imported from
        #   checking installed package size ... NOTE( )+installed size is
        required: false
        default: ""
        type: string


concurrency:
  group: r-cmd-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  build-install-check:
    strategy:
      fail-fast: false
      matrix:
        config:
          - image: ghcr.io/insightsengineering/rstudio_4.2.1_bioc_3.15
            tag: latest
    name: ${{ matrix.config.image }}, version ${{ matrix.config.tag }}
    runs-on: ubuntu-latest
    if: >
      !contains(github.event.commits[0].message, '[skip r-cmd]')
        && github.event.pull_request.draft == false
    container:
      image: ${{ matrix.config.image }}:${{ matrix.config.tag }}

    steps:
      - name: Get branch names 🌿
        id: branch-name
        uses: tj-actions/branch-names@v5

      - name: Checkout repo 🛎
        uses: actions/checkout@v3
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
          path: ${{ github.event.repository.name }}

      - name: Run Staged dependencies 🎦
        uses: insightsengineering/staged-dependencies-action@v1
        with:
          run-system-dependencies: ${{ inputs.install-system-dependencies }}
        env:
          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
          SD_REPO_PATH: ${{ github.event.repository.name }}
          SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }}

      - name: Show session info and installed packages ℹ
        run: |
          sessionInfo()
          as.data.frame(installed.packages()[, c("LibPath", "Version")])
        shell: Rscript {0}

      - name: Build R package 🏗
        run: |
          R CMD build ${{ github.event.repository.name }}
          echo "PKGBUILD=$(echo *.tar.gz)" >> $GITHUB_ENV
        shell: bash

      - name: Set TESTING_DEPTH ⚙
        env:
          COMMIT_NEWEST_MESSAGE: ${{ github.event.head_commit.message }}
          COMMIT_OLDEST_MESSAGE: ${{ github.event.commits[0].message }}
        run: |
          cd ${{ github.event.repository.name }}
          # set TESTING_DEPTH for PR
          if [[ ! -z "${GITHUB_HEAD_REF}" ]]; then
            TESTING_DEPTH=3
            echo "TESTING_DEPTH=3" >> $GITHUB_ENV
            COMMIT_NEWEST_MESSAGE=$(git log --format=%B -n 1 ${{ github.event.after }})
          fi
          if [[ $COMMIT_NEWEST_MESSAGE == *"[skip tests]"* ]]; then
            echo "NO_TESTS=1" >> $GITHUB_ENV
          fi
          # default TESTING_DEPTH
          if [[ -z "${TESTING_DEPTH}" ]]; then
            echo "TESTING_DEPTH=1" >> $GITHUB_ENV
          fi
        shell: bash

      - name: Run R CMD check 🏁
        run: |
          if [ "${{ inputs.skip-r-cmd-check }}" == "true" ]
          then {
            echo "Skipping R CMD check as 'skip-r-cmd-check' was set to 'true'"
            exit 0
          }
          fi
          if [ "${{ inputs.R_CHECK_FORCE_SUGGESTS }}" == "" ]
          then {
            _R_CHECK_FORCE_SUGGESTS_="FALSE"
          }
          fi
          if [[ -z "${{ env.NO_TESTS }}" ]]; then
            R CMD check ${{ env.PKGBUILD }}
          else
            R CMD check --no-tests ${{ env.PKGBUILD }}
          fi
        shell: bash
        continue-on-error: true
        env:
          _R_CHECK_TESTS_NLINES_: 0
          _R_CHECK_VIGNETTES_NLINES_: 0
          _R_CHECK_FORCE_SUGGESTS_: ${{ inputs.R_CHECK_FORCE_SUGGESTS }}

      - name: Check whether JUnit XML report exists 🚦
        id: check-junit-xml
        uses: andstor/file-existence-action@v1
        with:
          files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml"

      - name: Publish Unit Test Summary 📑
        uses: EnricoMi/publish-unit-test-result-action@v1
        if: steps.check-junit-xml.outputs.files_exists == 'true' && github.event_name == 'pull_request'
        with:
          check_name: Unit Tests Summary
          files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml"

      - name: Catch warnings in R CMD check output 🗳
        id: catch-errors
        run: |
          check_log <- "${{ github.event.repository.name }}.Rcheck/00check.log"
          if (file.exists(check_log)) {
            x <- tail(readLines(check_log), 1)
            if (grepl("ERROR", x)) {
              writeLines(readLines(check_log))
              stop("❌ R CMD check has errors")
            }
            if (grepl("WARNING", x)) {
              writeLines(readLines(check_log))
              stop("⚠ R CMD check has warnings")
            }
            if ("${{ inputs.check-note-blocklist }}" == "true") {
              print("Checking notes...")
              regexes <- "${{ inputs.note-blocklist }}"
              regexes <- unlist(strsplit(regexes, split = "\n"))
              lines <- paste(readLines(check_log), collapse = " ")
              notes_result <- vapply(
                regexes, 
                function(r){
                  if (grepl(r, lines)) {
                    print(r)
                    return(TRUE)
                  }
                  return(FALSE)
                },
                logical(1)
              )
              if (any(notes_result)) {
                stop("NOTEs on the blocklist were found (see above).")
              }
            }
          }
        shell: Rscript {0}

      - name: Install R package 🚧
        run: |
          if [ "${{ inputs.skip-r-cmd-install }}" == "true" ]
          then {
            echo "Skipping R CMD INSTALL as 'skip-r-cmd-install' was set to 'true'"
            exit 0
          }
          fi
          R CMD INSTALL ${{ env.PKGBUILD }}
        shell: bash

      - name: Upload package build ⤴
        if: startsWith(github.ref, 'refs/tags/v')
        uses: actions/upload-artifact@v3
        with:
          path: ${{ env.PKGBUILD }}
          name: ${{ env.PKGBUILD }}

  upload-release-assets:
    name: Upload build tar.gz
    needs: build-install-check
    runs-on: ubuntu-latest
    if: >
      startsWith(github.ref, 'refs/tags/v')
        && (!contains(github.event.commits[0].message, '[skip r-cmd]'))
        && github.event.pull_request.draft == false
    steps:
      - name: Checkout repo 🛎
        uses: actions/checkout@v3

      - name: Set release version and package build filename 📐
        run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/v}" >> $GITHUB_ENV

      - name: Get package build filename 📦
        run: echo "PKGBUILD=${{ github.event.repository.name }}_${{ env.RELEASE_VERSION }}.tar.gz" >> $GITHUB_ENV

      - name: Download artifact ⏬
        uses: actions/download-artifact@v3
        with:
          name: ${{ env.PKGBUILD }}

      - name: Upload binaries to release 🔼
        uses: svenstaro/upload-release-action@v2
        with:
          repo_token: ${{ secrets.GITHUB_TOKEN }}
          file: ${{ env.PKGBUILD }}
          asset_name: ${{ env.PKGBUILD }}
          tag: ${{ github.ref }}
          overwrite: true