build-check-install.yaml

---
name: R CMD Check 🧬

on:
  push:
    tags:
      - "v*"
    branches:
      - main
  pull_request:
    types:
      - opened
      - synchronize
      - reopened
      - ready_for_review
    branches:
      - main
  workflow_dispatch:
  workflow_call:
    secrets:
      REPO_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
      enforce-note-blocklist:
        description: Whether to check for specific NOTEs via regexes 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
      additional-r-cmd-check-params:
        description: Additional flags or parameters to add to R CMD check
        required: false
        default: ""
        type: string
      disable-unit-test-reports:
        description: Do not produce unit test reports
        required: false
        default: false
        type: boolean
      additional-env-vars:
        description: |
          Extra environment variables, as a 'key=value' pair, with each pair on a new line.
          Example usage:
          additional-env-vars: |
            ABC=123
            XYZ=456
        required: false
        default: ""
        type: string
      junit-xml-storage:
        description: Branch name to store JUnit XML reports
        required: false
        default: "_junit_xml_reports"
        type: string
      junit-xml-diff-branch:
        description: Against which branch should the JUnit XML report from the current branch be compared?
        required: false
        default: main
        type: string
      junit-xml-comparison:
        description: Turn on JUnit XML comparison
        required: false
        default: true
        type: boolean
      junit-xml-negative-threshold:
        description: |
          If time difference during JUnit XML comparison is between negative-threshold and 0: it's treated as 0.
          This means that if test suite/case executes up to negative-threshold seconds faster,
          this time difference is ignored as insignificant, and test suite/case is not shown in the table
        required: false
        default: 1.0
        type: string
      junit-xml-positive-threshold:
        description: |
          If time difference during JUnit XML comparison is between 0 and positive-threshold: it's treated as 0.
          This means that if test suite/case executes up to positive-threshold seconds slower,
          this time difference is ignored as insignificant, and test suite/case is not shown in the table
        required: false
        default: 1.0
        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_4.2.2_bioc_3.16
            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@v6

      - name: Normalize variables 📏
        run: |
          junit_xml_storage_input="${{ inputs.junit-xml-storage }}"
          junit_xml_diff_branch_input="${{ inputs.junit-xml-diff-branch }}"
          junit_xml_comparison_input="${{ inputs.junit-xml-comparison }}"
          junit_xml_positive_threshold="${{ inputs.junit-xml-positive-threshold }}"
          junit_xml_negative_threshold="${{ inputs.junit-xml-negative-threshold }}"
          echo "junit_xml_storage=${junit_xml_storage_input:-_junit_xml_reports}" >> $GITHUB_ENV
          echo "junit_xml_diff_branch=${junit_xml_diff_branch_input:-main}" >> $GITHUB_ENV
          echo "junit_xml_comparison=${junit_xml_comparison_input:-true}" >> $GITHUB_ENV
          echo "junit_xml_positive_threshold=${junit_xml_positive_threshold:-1.0}" >> $GITHUB_ENV
          echo "junit_xml_negative_threshold=${junit_xml_negative_threshold:-1.0}" >> $GITHUB_ENV
        shell: bash

      - name: Checkout repo (PR) 🛎
        uses: actions/checkout@v3
        if: github.event_name == 'pull_request'
        with:
          ref: ${{ steps.branch-name.outputs.head_ref_branch }}
          path: ${{ github.event.repository.name }}
          repository: ${{ github.event.pull_request.head.repo.full_name }}

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

      - name: Restore SD cache 💰
        uses: actions/cache@v3
        with:
          key: sd-${{ runner.os }}-${{ github.event.repository.name }}
          path: ~/.staged.dependencies

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

      - name: Show session info and installed packages ℹ
        run: |
          sessionInfo()
          as.data.frame(installed.packages()[, c("LibPath", "Version")])
          if (grepl("--as-cran", "${{ inputs.additional-r-cmd-check-params }}", fixed = TRUE)) {
            x <- desc::desc_del("Remotes")
          }
          if ("${{ inputs.disable-unit-test-reports }}" != "true") {
            x <- desc::desc_set_dep("xml2", "Suggests")
          }
        shell: Rscript {0}
        working-directory: ${{ github.event.repository.name }}

      - name: Replace testthat.R for test reporting 🎚
        if: inputs.disable-unit-test-reports != 'true'
        run: |
          if [ -f "tests/testthat.R" ]; then {
            # Overwrite testthat.R for JUnit XML reporting
            cat > tests/testthat.R <<EOF
            pkg_name <- "${{ github.event.repository.name }}"
            if (requireNamespace("testthat", quietly = TRUE)) {
              library(testthat)
              reporter <- MultiReporter\$new(list(
                CheckReporter\$new(),
                JunitReporter\$new(file = "junit-result.xml")
              ))
              test_check(pkg_name, reporter = reporter)
            }
          EOF
          }
          cat tests/testthat.R
          fi
        shell: bash
        working-directory: ${{ github.event.repository.name }}

      - name: Build R package 🏗
        run: |
          if [ "${{ inputs.additional-env-vars }}" != "" ]
          then {
            echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
            export $(tr '\n' ' ' < /tmp/dotenv.env)
          }
          fi
          R CMD build ${{ github.event.repository.name }}
          echo "PKGBUILD=$(echo ${{ github.event.repository.name }}_*.tar.gz)" >> $GITHUB_ENV
        shell: bash

      - name: Set TESTING_DEPTH ⚙
        env:
          COMMIT_NEWEST_MESSAGE: ${{ github.event.head_commit.message }}
          COMMIT_OLDEST_MESSAGE: ${{ github.event.commits[0].message }}
        run: |
          # set TESTING_DEPTH for PR
          if [[ ! -z "${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
        working-directory: ${{ github.event.repository.name }}

      - 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
          ADDITIONAL_PARAMS=${{ inputs.additional-r-cmd-check-params }}
          if [[ ! -z "${{ env.NO_TESTS }}" ]]
          then {
            ADDITIONAL_PARAMS="${ADDITIONAL_PARAMS} --no-tests"
          }
          fi
          if [ "${{ inputs.additional-env-vars }}" != "" ]
          then {
            echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
            export $(tr '\n' ' ' < /tmp/dotenv.env)
          }
          fi
          Rscript - <<EOF
          if ("${{ inputs.disable-unit-test-reports }}" != "true") {
            if (!require("xml2")) {
              install.packages("xml2", repos = "https://cloud.r-project.org", quiet = TRUE)
            }
          }
          EOF
          R CMD check ${ADDITIONAL_PARAMS} ${{ env.PKGBUILD }}
        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: Fetch report from ${{ env.junit_xml_storage }} ⤵️
        if: env.junit_xml_comparison == 'true'
        uses: actions/checkout@v3
        with:
          path: ${{ env.junit_xml_storage }}
          fetch-depth: 0

      - name: Initialize storage branch ${{ env.junit_xml_storage }} 🗄️
        if: env.junit_xml_comparison == 'true'
        working-directory: ${{ env.junit_xml_storage }}
        run: |
          git config --global --add safe.directory ${PWD}
          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
          git config --global user.name "github-actions[bot]"
          # Switch to the branch if it already exists
          git switch ${{ env.junit_xml_storage }} || true
          git pull origin ${{ env.junit_xml_storage }} || true
          # Create the branch if it doesn't exist yet
          git checkout --orphan ${{ env.junit_xml_storage }} || true
          # Ensure that the bare minimum components exist in the branch
          mkdir -p data
          touch README.md data/.gitkeep
          # Copy necessary files and folders to a temporary location
          mkdir -p /tmp/${{ github.sha }}
          echo "Copying data to /tmp/${{ github.sha }}"
          cp -r .git README.md data /tmp/${{ github.sha }}
          # Remove everything else
          # Attribution: https://unix.stackexchange.com/a/77313
          rm -rf ..?* .[!.]* *
          # Restore files from the temporary location
          echo "Copying data from /tmp/${{ github.sha }}"
          cp -r /tmp/${{ github.sha }}/.git /tmp/${{ github.sha }}/README.md /tmp/${{ github.sha }}/data .
          rm -rf /tmp/${{ github.sha }}
          git add --all -f
          git commit -m "Update storage branch: $(date)" || true
        shell: bash

      - name: Push storage branch ${{ env.junit_xml_storage }} 🗄️
        if: env.junit_xml_comparison == 'true'
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.REPO_GITHUB_TOKEN }}
          branch: ${{ env.junit_xml_storage }}
          directory: ${{ env.junit_xml_storage }}
          force: true

      - name: Check whether JUnit XML report exists 🚦
        id: check-junit-xml
        uses: andstor/file-existence-action@v2
        with:
          files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml"

      - name: Publish Unit Test Summary 📑
        uses: EnricoMi/publish-unit-test-result-action@v2
        id: test-results
        if: steps.check-junit-xml.outputs.files_exists == 'true' && github.event_name == 'pull_request'
        with:
          check_name: Unit Tests Summary
          junit_files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml"

      - name: Fetch JUnit XML reports from ${{ env.junit_xml_storage }} ⤵️
        if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
        uses: actions/checkout@v3
        with:
          path: ${{ env.junit_xml_storage }}
          fetch-depth: 0

      - name: Set up ${{ env.junit_xml_storage }} branch for reports 🗃️
        if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
        run: |
          BRANCH=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}
          echo "diff_storage_branch=$BRANCH" >> $GITHUB_ENV
          mkdir -p ${{ env.junit_xml_storage }}/data/${BRANCH}
        shell: bash

      - name: Commit JUnit XML report 📄
        if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
        working-directory: ${{ env.junit_xml_storage }}/data
        run: |
          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
          git config --global user.name "github-actions[bot]"
          git switch ${{ env.junit_xml_storage }} || true
          git config pull.rebase false
          git pull origin ${{ env.junit_xml_storage }}
          cp ../../${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml \
            ./${{ env.diff_storage_branch }}/junit-result.xml
          git add -f "${{ env.diff_storage_branch }}/junit-result.xml"
          git commit -m "Add/Update JUnit report: ${{ github.sha }}" || true
        shell: bash

      - name: Push JUnit XML report to ${{ env.junit_xml_storage }} 📄
        if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
        uses: ad-m/github-push-action@master
        with:
          github_token: ${{ secrets.REPO_GITHUB_TOKEN }}
          branch: ${{ env.junit_xml_storage }}
          directory: ${{ env.junit_xml_storage }}/data

      - name: Run XML comparison 🔍
        if: steps.check-junit-xml.outputs.files_exists == 'true' && env.junit_xml_comparison == 'true'
        run: |
          cp ${{ env.junit_xml_storage }}/data/${{ env.diff_storage_branch }}/junit-result.xml new.xml
          if [ ! -f ${{ env.junit_xml_storage }}/data/${{ env.junit_xml_diff_branch }}/junit-result.xml ]; then
            # If XML for the branch against which we're comparing doesn't exist, we're skipping the comparison.
            echo "JUnit report for branch \`${{ env.junit_xml_diff_branch }}\` " \
              "doesn't exist on \`${{ env.junit_xml_storage }}\` branch yet." > output.md
            echo "Once this workflow runs on \`${{ env.junit_xml_diff_branch }}\` branch, " \
              "you'll see comparison of tests performance between \`${{ env.junit_xml_diff_branch }}\` " \
              "and \`${{ env.diff_storage_branch }}\` as a PR comment." >> output.md
          else
            cp ${{ env.junit_xml_storage }}/data/${{ env.junit_xml_diff_branch }}/junit-result.xml old.xml
            wget https://github.com/insightsengineering/junit-xml-diff/releases/download/v0.3.0/junit-xml-diff_0.3.0_linux_amd64.tar.gz \
              -O junit-xml-diff.tar.gz
            tar xzf junit-xml-diff.tar.gz
            ./junit-xml-diff old.xml new.xml output.md '${{ env.junit_xml_diff_branch }}' \
              '${{ env.junit_xml_positive_threshold }}' '${{ env.junit_xml_negative_threshold }}'
            echo "Results for commit ${{ github.sha }}" >> output.md
            echo "" >> output.md
            echo "♻️ This comment has been updated with latest results." >> output.md
            cp output.md output-artifact.md
            echo "Size of markdown: $(du -b output.md | awk '{print $1}') bytes"
            if [ "$(du -b output.md | awk '{print $1}')" -ge "60000" ]; then
              echo "The result of JUnit XML file comparison exceeded maximum size. " \
                "The report has therefore been uploaded as an R CMD check workflow artifact." > output.md
              echo "junit_xml_comparison_result_method=artifact" >> $GITHUB_ENV
            fi
          fi
          echo "Markdown output:"
          cat output.md

      - name: Post JUnit XML comparison as comment 💬
        if: >
          steps.check-junit-xml.outputs.files_exists == 'true' &&
          env.junit_xml_comparison == 'true'
        uses: marocchino/sticky-pull-request-comment@v2
        with:
          header: markdown-table
          path: output.md

      - name: Upload JUnit XML comparison ⤴
        if: >
          steps.check-junit-xml.outputs.files_exists == 'true' &&
          env.junit_xml_comparison == 'true' &&
          env.junit_xml_comparison_result_method == 'artifact'
        uses: actions/upload-artifact@v3
        with:
          path: output-artifact.md
          name: junit-xml-report-comparison

      - 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.enforce-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 [ "${{ inputs.skip-r-cmd-install }}" == "true" ]
          then {
            echo "Skipping R CMD INSTALL as 'skip-r-cmd-install' was set to 'true'"
            exit 0
          }
          fi
          if [ "${{ inputs.additional-env-vars }}" != "" ]
          then {
            echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
            export $(tr '\n' ' ' < /tmp/dotenv.env)
          }
          fi
          R CMD INSTALL ${{ env.PKGBUILD }}
        shell: bash

      - name: Rebuild R package 🏗
        if: inputs.disable-unit-test-reports != 'true'
        run: |
          # Undo changes to DESCRIPTION and tests/testthat.R
          git checkout DESCRIPTION
          if [ -f "tests/testthat.R" ]; then
            git checkout tests/testthat.R
          fi
          if [ "${{ inputs.additional-env-vars }}" != "" ]
          then {
            echo -e "${{ inputs.additional-env-vars }}" > /tmp/dotenv.env
            export $(tr '\n' ' ' < /tmp/dotenv.env)
          }
          fi
          R CMD build .
          echo "PKGBUILD=$(echo ${{ github.event.repository.name }}_*.tar.gz)" >> $GITHUB_ENV
        shell: bash
        working-directory: ${{ github.event.repository.name }}

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