r.yml

# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements.  See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership.  The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.  You may obtain a copy of the License at
#
#   http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied.  See the License for the
# specific language governing permissions and limitations
# under the License.

name: R

on:
  push:
    paths:
      - ".github/workflows/r.yml"
      - "ci/scripts/r_*.sh"
      - "ci/scripts/cpp_*.sh"
      - "ci/scripts/PKGBUILD"
      - "ci/etc/rprofile"
      - "ci/docker/**"
      - "cpp/**"
      - "r/**"
  pull_request:
    paths:
      - ".github/workflows/r.yml"
      - "ci/scripts/r_*.sh"
      - "ci/scripts/cpp_*.sh"
      - "ci/scripts/PKGBUILD"
      - "ci/etc/rprofile"
      - "ci/docker/**"
      - "cpp/**"
      - "r/**"

concurrency:
  group: ${{ github.repository }}-${{ github.head_ref || github.sha }}-${{ github.workflow }}
  cancel-in-progress: true

permissions:
  contents: read

env:
  DOCKER_VOLUME_PREFIX: ".docker/"

jobs:
  ubuntu:
    name: AMD64 Ubuntu ${{ matrix.ubuntu }} R ${{ matrix.r }} Force-Tests ${{ matrix.force-tests }}
    runs-on: ubuntu-latest
    if: ${{ !contains(github.event.pull_request.title, 'WIP') }}
    timeout-minutes: 75
    strategy:
      fail-fast: false
      matrix:
        r: ["4.2"]
        ubuntu: [20.04]
        force-tests: ["true"]
    env:
      R: ${{ matrix.r }}
      UBUNTU: ${{ matrix.ubuntu }}
    steps:
      - name: Checkout Arrow
        uses: actions/checkout@v3
        with:
          fetch-depth: 0
          submodules: recursive
      - name: Cache Docker Volumes
        uses: actions/cache@v3
        with:
          path: .docker
          # As this key is identical on both matrix builds only one will be able to successfully cache,
          # this is fine as there are no differences in the build
          key: ubuntu-${{ matrix.ubuntu }}-r-${{ matrix.r }}-${{ hashFiles('cpp/src/**/*.cc','cpp/src/**/*.h)') }}-${{ github.run_id }}
          restore-keys: |
            ubuntu-${{ matrix.ubuntu }}-r-${{ matrix.r }}-${{ hashFiles('cpp/src/**/*.cc','cpp/src/**/*.h)') }}-
            ubuntu-${{ matrix.ubuntu }}-r-${{ matrix.r }}-
      - name: Check pkgdown reference sections
        run: ci/scripts/r_pkgdown_check.sh
      - name: Setup Python
        uses: actions/setup-python@v4
        with:
          python-version: 3.8
      - name: Setup Archery
        run: pip install -e dev/archery[docker]
      - name: Execute Docker Build
        env:
          ARCHERY_DOCKER_USER: ${{ secrets.DOCKERHUB_USER }}
          ARCHERY_DOCKER_PASSWORD: ${{ secrets.DOCKERHUB_TOKEN }}
        run: |
          sudo sysctl -w kernel.core_pattern="core.%e.%p"
          ulimit -c unlimited
          # Setting a non-default and non-probable Marquesas French Polynesia time
          # it has both with a .45 offset and very very few people who live there.
          archery docker run -e TZ=MART -e ARROW_R_FORCE_TESTS=${{ matrix.force-tests }} ubuntu-r
      - name: Dump install logs
        run: cat r/check/arrow.Rcheck/00install.out
        if: always()
      - name: Dump test logs
        run: cat r/check/arrow.Rcheck/tests/testthat.Rout*
        if: always()
      - name: Save the test output
        if: always()
        uses: actions/upload-artifact@v3
        with:
          name: test-output
          path: r/check/arrow.Rcheck/tests/testthat.Rout*
      - name: Docker Push
        if: success() && github.event_name == 'push' && github.repository == 'apache/arrow'
        env:
          ARCHERY_DOCKER_USER: ${{ secrets.DOCKERHUB_USER }}
          ARCHERY_DOCKER_PASSWORD: ${{ secrets.DOCKERHUB_TOKEN }}
        continue-on-error: true
        run: archery docker push ubuntu-r

  bundled:
    name: "${{ matrix.config.org }}/${{ matrix.config.image }}:${{ matrix.config.tag }}"
    runs-on: ubuntu-latest
    if: ${{ !contains(github.event.pull_request.title, 'WIP') }}
    timeout-minutes: 60
    strategy:
      fail-fast: false
      matrix:
        config:
          - { org: "rhub", image: "debian-gcc-devel", tag: "latest", devtoolset: "" }
    env:
      R_ORG: ${{ matrix.config.org }}
      R_IMAGE: ${{ matrix.config.image }}
      R_TAG: ${{ matrix.config.tag }}
      DEVTOOLSET_VERSION: ${{ matrix.config.devtoolset }}
    steps:
      - name: Checkout Arrow
        uses: actions/checkout@v3
        with:
          fetch-depth: 0
          submodules: recursive
      - name: Setup Python
        uses: actions/setup-python@v4
        with:
          python-version: 3.8
      - name: Setup Archery
        run: pip install -e dev/archery[docker]
      - name: Execute Docker Build
        env:
          ARCHERY_DOCKER_USER: ${{ secrets.DOCKERHUB_USER }}
          ARCHERY_DOCKER_PASSWORD: ${{ secrets.DOCKERHUB_TOKEN }}
        run: |
          sudo sysctl -w kernel.core_pattern="core.%e.%p"
          ulimit -c unlimited
          # Don't set a TZ here to test that case. These builds will have the following warning in them:
          #   System has not been booted with systemd as init system (PID 1). Can't operate.
          #   Failed to connect to bus: Host is down
          archery docker run -e TZ="" r
      - name: Dump install logs
        run: cat r/check/arrow.Rcheck/00install.out
        if: always()
      - name: Dump test logs
        run: cat r/check/arrow.Rcheck/tests/testthat.Rout*
        if: always()
      - name: Save the test output
        if: always()
        uses: actions/upload-artifact@v3
        with:
          name: test-output
          path: r/check/arrow.Rcheck/tests/testthat.Rout*
      - name: Docker Push
        if: success() && github.event_name == 'push' && github.repository == 'apache/arrow'
        env:
          ARCHERY_DOCKER_USER: ${{ secrets.DOCKERHUB_USER }}
          ARCHERY_DOCKER_PASSWORD: ${{ secrets.DOCKERHUB_TOKEN }}
        continue-on-error: true
        run: archery docker push r

  windows-cpp:
    name: AMD64 Windows C++ RTools ${{ matrix.config.rtools }} ${{ matrix.config.arch }}
    runs-on: windows-2019
    if: ${{ !contains(github.event.pull_request.title, 'WIP') }}
    timeout-minutes: 90
    strategy:
      fail-fast: false
      matrix:
        config:
        - { rtools: 40, arch: 'ucrt64' }
    steps:
      - run: git config --global core.autocrlf false
      - name: Checkout Arrow
        uses: actions/checkout@v3
        with:
          fetch-depth: 0
      - name: Setup ccache
        shell: bash
        run: |
          ci/scripts/ccache_setup.sh
          echo "CCACHE_DIR=$(cygpath --absolute --windows ccache)" >> $GITHUB_ENV
      - name: Cache ccache
        uses: actions/cache@v3
        with:
          path: ccache
          key: r-${{ matrix.config.rtools }}-ccache-mingw-${{ matrix.config.arch }}-${{ hashFiles('cpp/src/**/*.cc','cpp/src/**/*.h)') }}-${{ github.run_id }}
          restore-keys: |
            r-${{ matrix.config.rtools }}-ccache-mingw-${{ matrix.config.arch }}-${{ hashFiles('cpp/src/**/*.cc','cpp/src/**/*.h)') }}-
            r-${{ matrix.config.rtools }}-ccache-mingw-${{ matrix.config.arch }}-
      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: "4.1"
          rtools-version: 40
          Ncpus: 2
      - name: Build Arrow C++
        shell: bash
        env:
          MINGW_ARCH: ${{ matrix.config.arch }}
        run: ci/scripts/r_windows_build.sh
      - name: Rename libarrow.zip
        # So that they're unique when multiple are downloaded in the next step
        shell: bash
        run: mv libarrow.zip libarrow-rtools${{ matrix.config.rtools }}-${{ matrix.config.arch }}.zip
      - uses: actions/upload-artifact@v3
        with:
          name: libarrow-rtools${{ matrix.config.rtools }}-${{ matrix.config.arch }}.zip
          path: libarrow-rtools${{ matrix.config.rtools }}-${{ matrix.config.arch }}.zip

  windows-r:
    needs: [windows-cpp]
    name: AMD64 Windows R ${{ matrix.config.rversion }} RTools ${{ matrix.config.rtools }}
    runs-on: windows-2019
    if: ${{ !contains(github.event.pull_request.title, 'WIP') }}
    timeout-minutes: 75
    strategy:
      fail-fast: false
      matrix:
        config:
        - { rtools: 42, rversion: "4.2" }
        - { rtools: 42, rversion: "devel" }
    env:
      ARROW_R_CXXFLAGS: "-Werror"
      _R_CHECK_TESTS_NLINES_: 0
    steps:
      - run: git config --global core.autocrlf false
      - name: Checkout Arrow
        uses: actions/checkout@v3
        with:
          fetch-depth: 0
      - run: mkdir r/windows
      - name: Download artifacts
        if: ${{ matrix.config.rtools == 42 }}
        uses: actions/download-artifact@v3
        with:
          name: libarrow-rtools40-ucrt64.zip
          path: r/windows
      - name: Unzip and rezip libarrows
        shell: bash
        run: |
          cd r/windows
          ls *.zip | xargs -n 1 unzip -uo
          rm -rf *.zip
      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.rversion }}
          rtools-version: ${{ matrix.config.rtools }}
          Ncpus: 2
      - uses: r-lib/actions/setup-r-dependencies@v2
        env:
          GITHUB_PAT: "${{ github.token }}"
        with:
          # For some arcane reason caching does not work on the windows runners
          # most likely due to https://github.com/actions/cache/issues/815
          cache: false
          working-directory: 'r'
          extra-packages: |
            any::rcmdcheck
      - name: Install MinIO
        shell: bash
        run: |
          mkdir -p "$HOME/.local/bin"
          curl \
            --output "$HOME/.local/bin/minio.exe" \
            https://dl.min.io/server/minio/release/windows-amd64/archive/minio.RELEASE.2022-05-26T05-48-41Z
          chmod +x "$HOME/.local/bin/minio.exe"
          echo "$HOME/.local/bin" >> $GITHUB_PATH
      # TODO(ARROW-17149): figure out why the GCS tests are hanging on Windows
      # - name: Install Google Cloud Storage Testbench
      #   shell: bash
      #   run: ci/scripts/install_gcs_testbench.sh default
      - name: Check
        shell: Rscript {0}
        run: |
          # Because we do R CMD build and r/windows is in .Rbuildignore,
          # assemble the libarrow.zip file and pass it as an env var
          setwd("r/windows")
          zip("libarrow.zip", ".")
          setwd("..")

          Sys.setenv(
            RWINLIB_LOCAL = file.path(Sys.getenv("GITHUB_WORKSPACE"), "r", "windows", "libarrow.zip"),
            MAKEFLAGS = paste0("-j", parallel::detectCores()),
            ARROW_R_DEV = TRUE,
            "_R_CHECK_FORCE_SUGGESTS_" = FALSE
          )
          rcmdcheck::rcmdcheck(".",
            build_args = '--no-build-vignettes',
            args = c('--no-manual', '--as-cran', '--ignore-vignettes', '--run-donttest'),
            error_on = 'warning',
            check_dir = 'check',
            timeout = 3600
          )
      - name: Run lintr
        if: ${{ matrix.config.rversion == '4.2' }}
        env:
          NOT_CRAN: "true"
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
        shell: Rscript {0}
        working-directory: r
        run: |
          Sys.setenv(
            RWINLIB_LOCAL = file.path(Sys.getenv("GITHUB_WORKSPACE"), "r", "windows", "libarrow.zip"),
            MAKEFLAGS = paste0("-j", parallel::detectCores()),
            ARROW_R_DEV = TRUE,
            "_R_CHECK_FORCE_SUGGESTS_" = FALSE
          )
          # we use pak for package installation since it is faster, safer and more convenient
          pak::local_install()
          pak::pak("lintr")
          lintr::expect_lint_free()
      - name: Dump install logs
        shell: cmd
        run: cat r/check/arrow.Rcheck/00install.out
        if: always()
      - name: Dump test logs
        shell: bash
        run: find r/check -name 'testthat.Rout*' -exec cat '{}' \; || true
        if: always()