[ci] run r-package Linux jobs in containers (#5638)

.ci/test_r_package.sh

@@ -23,8 +23,8 @@ if [[ "${R_MAJOR_VERSION}" == "3" ]]; then
 elif [[ "${R_MAJOR_VERSION}" == "4" ]]; then
     export R_MAC_VERSION=4.2.2
     export R_MAC_PKG_URL=${CRAN_MIRROR}/bin/macosx/base/R-${R_MAC_VERSION}.pkg
-    export R_LINUX_VERSION="4.2.2-1.2004.0"
-    export R_APT_REPO="focal-cran40/"
+    export R_LINUX_VERSION="4.2.2-1.2204.0"
+    export R_APT_REPO="jammy-cran40/"
 else
     echo "Unrecognized R version: ${R_VERSION}"
     exit -1
@@ -38,14 +38,15 @@ fi
 if [[ $OS_NAME == "linux" ]]; then
     sudo apt-key adv \
         --keyserver keyserver.ubuntu.com \
-        --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+        --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || exit -1
     sudo add-apt-repository \
-        "deb ${CRAN_MIRROR}/bin/linux/ubuntu ${R_APT_REPO}"
+        "deb ${CRAN_MIRROR}/bin/linux/ubuntu ${R_APT_REPO}" || exit -1
     sudo apt-get update
     sudo apt-get install \
         --no-install-recommends \
-        -y --allow-downgrades \
+        -y \
             devscripts \
+            r-base-core=${R_LINUX_VERSION} \
             r-base-dev=${R_LINUX_VERSION} \
             texinfo \
             texlive-latex-extra \
@@ -60,8 +61,18 @@ if [[ $OS_NAME == "linux" ]]; then
             --no-install-recommends \
             -y \
                 autoconf=$(cat R-package/AUTOCONF_UBUNTU_VERSION) \
+                automake \
                 || exit -1
     fi
+    if [[ $INSTALL_CMAKE_FROM_RELEASES == "true" ]]; then
+        curl -O -L \
+            https://github.com/Kitware/CMake/releases/download/v3.25.1/cmake-3.25.1-linux-x86_64.sh \
+        || exit -1
+
+        sudo mkdir /opt/cmake || exit -1
+        sudo sh cmake-3.25.1-linux-x86_64.sh --skip-license --prefix=/opt/cmake || exit -1
+        sudo ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake || exit -1
+    fi
 fi
 
 # Installing R precompiled for Mac OS 10.11 or higher
@@ -211,6 +222,27 @@ if [[ $check_succeeded == "no" ]]; then
     exit -1
 fi
 
+used_correct_r_version=$(
+    cat $LOG_FILE_NAME \
+    | grep --count "using R version ${R_VERSION}"
+)
+if [[ $used_correct_r_version -ne 1 ]]; then
+    echo "Unexpected R version was used. Expected '${R_VERSION}'."
+    exit -1
+fi
+
+if [[ $R_BUILD_TYPE == "cmake" ]]; then
+    passed_correct_r_version_to_cmake=$(
+        cat $BUILD_LOG_FILE \
+        | grep --count "R version passed into FindLibR.cmake: ${R_VERSION}"
+    )
+    if [[ $used_correct_r_version -ne 1 ]]; then
+        echo "Unexpected R version was passed into cmake. Expected '${R_VERSION}'."
+        exit -1
+    fi
+fi
+
+
 if grep -q -E "NOTE|WARNING|ERROR" "$LOG_FILE_NAME"; then
     echo "NOTEs, WARNINGs, or ERRORs have been found by R CMD check"
     exit -1

.github/workflows/r_package.yml

@@ -30,6 +30,7 @@ jobs:
   test:
     name: ${{ matrix.task }} (${{ matrix.os }}, ${{ matrix.compiler }}, R ${{ matrix.r_version }}, ${{ matrix.build_type }})
     runs-on: ${{ matrix.os }}
+    container: ${{ matrix.container }}
     timeout-minutes: 60
     strategy:
       fail-fast: false
@@ -38,58 +39,68 @@ jobs:
           ################
           # CMake builds #
           ################
-          - os: ubuntu-22.04
+          - os: ubuntu-latest
             task: r-package
             compiler: gcc
             r_version: 3.6
             build_type: cmake
-          - os: ubuntu-22.04
+            container: 'ubuntu:18.04'
+          - os: ubuntu-latest
             task: r-package
             compiler: gcc
             r_version: 4.2
             build_type: cmake
-          - os: ubuntu-22.04
+            container: 'ubuntu:22.04'
+          - os: ubuntu-latest
             task: r-package
             compiler: clang
             r_version: 3.6
             build_type: cmake
-          - os: ubuntu-22.04
+            container: 'ubuntu:18.04'
+          - os: ubuntu-latest
             task: r-package
             compiler: clang
             r_version: 4.2
             build_type: cmake
+            container: 'ubuntu:22.04'
           - os: macOS-latest
             task: r-package
             compiler: gcc
             r_version: 3.6
             build_type: cmake
+            container: null
           - os: macOS-latest
             task: r-package
             compiler: gcc
             r_version: 4.2
             build_type: cmake
+            container: null
           - os: macOS-latest
             task: r-package
             compiler: clang
             r_version: 3.6
             build_type: cmake
+            container: null
           - os: macOS-latest
             task: r-package
             compiler: clang
             r_version: 4.2
             build_type: cmake
+            container: null
           - os: windows-latest
             task: r-package
             compiler: MINGW
             toolchain: MINGW
             r_version: 3.6
             build_type: cmake
+            container: null
           - os: windows-latest
             task: r-package
             compiler: MINGW
             toolchain: MSYS
             r_version: 4.2
             build_type: cmake
+            container: null
           # Visual Studio 2019
           - os: windows-2019
             task: r-package
@@ -97,6 +108,7 @@ jobs:
             toolchain: MSVC
             r_version: 3.6
             build_type: cmake
+            container: null
           # Visual Studio 2022
           - os: windows-2022
             task: r-package
@@ -104,6 +116,7 @@ jobs:
             toolchain: MSVC
             r_version: 4.2
             build_type: cmake
+            container: null
           ###############
           # CRAN builds #
           ###############
@@ -113,35 +126,64 @@ jobs:
             toolchain: MINGW
             r_version: 3.6
             build_type: cran
+            container: null
           - os: windows-latest
             task: r-package
             compiler: MINGW
             toolchain: MSYS
             r_version: 4.2
             build_type: cran
-          - os: ubuntu-22.04
+            container: null
+          - os: ubuntu-latest
             task: r-package
             compiler: gcc
             r_version: 4.2
             build_type: cran
+            container: 'ubuntu:22.04'
           - os: macOS-latest
             task: r-package
             compiler: clang
             r_version: 4.2
             build_type: cran
+            container: null
           ################
           # Other checks #
           ################
-          - os: ubuntu-22.04
+          - os: ubuntu-latest
             task: r-rchk
             compiler: gcc
             r_version: 4.2
             build_type: cran
+            container: 'ubuntu:22.04'
     steps:
       - name: Prevent conversion of line endings on Windows
         if: startsWith(matrix.os, 'windows')
         shell: pwsh
         run: git config --global core.autocrlf false
+      - name: Install packages used by third-party actions
+        if: startsWith(matrix.os, 'ubuntu')
+        shell: bash
+        run: |
+          apt-get update -y
+          apt-get install --no-install-recommends -y \
+            ca-certificates \
+            dirmngr \
+            gpg \
+            gpg-agent \
+            software-properties-common \
+            sudo
+          # install newest version of git
+          # ref:
+          #     - https://unix.stackexchange.com/a/170831/550004
+          #     - https://git-scm.com/download/linux
+          add-apt-repository ppa:git-core/ppa -y
+          apt-get update -y
+          apt-get install --no-install-recommends -y \
+            git
+      - name: Trust git cloning LightGBM
+        if: startsWith(matrix.os, 'ubuntu')
+        run: |
+          git config --global --add safe.directory "${GITHUB_WORKSPACE}"
       - name: Checkout repository
         uses: actions/checkout@v3
         with:
@@ -156,7 +198,7 @@ jobs:
           CTAN_MIRROR: https://ctan.math.illinois.edu/systems/win32/miktex
           TINYTEX_INSTALLER: TinyTeX
       - name: Setup and run tests on Linux and macOS
-        if: matrix.os == 'macOS-latest' || matrix.os == 'ubuntu-22.04'
+        if: matrix.os == 'macOS-latest' || matrix.os == 'ubuntu-latest'
         shell: bash
         run: |
           export TASK="${{ matrix.task }}"
@@ -164,8 +206,14 @@ jobs:
           export GITHUB_ACTIONS="true"
           if [[ "${{ matrix.os }}" == "macOS-latest" ]]; then
               export OS_NAME="macos"
-          elif [[ "${{ matrix.os }}" == "ubuntu-22.04" ]]; then
+          elif [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
               export OS_NAME="linux"
+              export IN_UBUNTU_BASE_CONTAINER="true"
+              # the default version of cmake provided on Ubuntu 18.04 (v3.10.2), is not supported by LightGBM
+              # see https://github.com/microsoft/LightGBM/issues/5642
+              if [[ "${{ matrix.container }}" == "ubuntu:18.04" ]]; then
+                export INSTALL_CMAKE_FROM_RELEASES="true"
+              fi
           fi
           export BUILD_DIRECTORY="$GITHUB_WORKSPACE"
           export R_VERSION="${{ matrix.r_version }}"