[ci] [R-package] add CI jobs covering more CRAN "additional checks", fix...

[ci] [R-package] add CI jobs covering more CRAN "additional checks", fix R_NO_REMAP warnings (fixes #6369) (#6523)

* [ci] [R-package] add CI jobs testing newer compilers

* set up vignette-processing dependencies

* remove tinytex

* set up pandoc

* allow NOTEs, one more R_NO_REMAP guard

* restore other CI

* one more R_NO_REMAP guard

* fail builds producing more than 1 NOTE

* update approach for running R CMD check

* fix filepath

* fix paths

* fix variable name

* echo lines

* fix piping

* fix file extension

* clean up

* make R CMD check stricter

.ci/install-clang-devel.sh

-#!/bin/bash
-
-# [description]
-#
-#   Installs a development version of clang and the other LLVM tools.
-#
-
-set -e -E -u -o pipefail
-
-CLANG_VERSION=${1}
-
-apt-get autoremove -y --purge \
-    clang-* \
-    libclang-* \
-    libunwind-* \
-    llvm-*
-
-apt-get update -y
-apt-get install --no-install-recommends -y \
-    gnupg \
-    lsb-release \
-    software-properties-common \
-    wget
-
-wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add -
-
-# ref: https://apt.llvm.org/
-add-apt-repository -y "deb http://apt.llvm.org/unstable/ llvm-toolchain main"
-add-apt-repository -y "deb-src http://apt.llvm.org/unstable/ llvm-toolchain main"
-add-apt-repository -y "deb http://apt.llvm.org/unstable/ llvm-toolchain-${CLANG_VERSION} main" || true
-add-apt-repository -y "deb-src http://apt.llvm.org/unstable/ llvm-toolchain-${CLANG_VERSION} main" || true
-apt-get update -y
-
-apt-get install -y --no-install-recommends \
-    clang-${CLANG_VERSION} \
-    clangd-${CLANG_VERSION} \
-    clang-format-${CLANG_VERSION} \
-    clang-tidy-${CLANG_VERSION} \
-    clang-tools-${CLANG_VERSION} \
-    lldb-${CLANG_VERSION} \
-    lld-${CLANG_VERSION} \
-    llvm-${CLANG_VERSION}-dev \
-    llvm-${CLANG_VERSION}-tools \
-    libomp-${CLANG_VERSION}-dev \
-    libc++-${CLANG_VERSION}-dev \
-    libc++abi-${CLANG_VERSION}-dev \
-    libclang-common-${CLANG_VERSION}-dev \
-    libclang-${CLANG_VERSION}-dev \
-    libclang-cpp${CLANG_VERSION}-dev \
-    libunwind-${CLANG_VERSION}-dev
-
-# overwriting the stuff in /usr/bin is simpler and more reliable than
-# updating PATH, LD_LIBRARY_PATH, etc.
-cp --remove-destination /usr/lib/llvm-${CLANG_VERSION}/bin/* /usr/bin/
-
-# per https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-clang
-#
-# clang was built to use libc++: for a version built to default to libstdc++
-# (as shipped by Fedora/Debian/Ubuntu), add -stdlib=libc++ to CXX
-# and install the libcxx-devel/libc++-dev package.
-mkdir -p "${HOME}/.R"
-
-cat << EOF > "${HOME}/.R/Makevars"
-CXX += -stdlib=libc++
-CXX11 += -stdlib=libc++
-CXX14 += -stdlib=libc++
-CXX17 += -stdlib=libc++
-CXX20 += -stdlib=libc++
-EOF
-
-echo ""
-echo "done installing clang"
-clang --version
-echo ""

.ci/run-r-cmd-check.sh

+#!/bin/bash
+
+set -e -u -o pipefail
+
+PKG_TARBALL="${1}"
+declare -i ALLOWED_CHECK_NOTES=${2}
+
+# 'R CMD check' redirects installation logs to a file, and returns
+# a non-0 exit code if ERRORs are raised.
+#
+# The '||' here gives us an opportunity to echo out the installation
+# logs prior to exiting the script.
+check_succeeded="yes"
+R CMD check "${PKG_TARBALL}" \
+    --as-cran \
+    --run-donttest \
+|| check_succeeded="no"
+
+CHECK_LOG_FILE=lightgbm.Rcheck/00check.log
+BUILD_LOG_FILE=lightgbm.Rcheck/00install.out
+
+echo "R CMD check build logs:"
+cat "${BUILD_LOG_FILE}"
+
+if [[ $check_succeeded == "no" ]]; then
+    echo "R CMD check failed"
+    exit 1
+fi
+
+# WARNINGs or ERRORs should be treated as a failure
+if grep -q -E "WARNING|ERROR" "${CHECK_LOG_FILE}"; then
+    echo "WARNINGs or ERRORs have been found by R CMD check"
+    exit 1
+fi
+
+# Allow a configurable number of NOTEs.
+# Sometimes NOTEs are raised in CI that wouldn't show up on an actual CRAN submission.
+set +e
+NUM_CHECK_NOTES=$(
+    grep -o -E '[0-9]+ NOTE' "${CHECK_LOG_FILE}" \
+    | sed 's/[^0-9]*//g'
+)
+if [[ ${NUM_CHECK_NOTES} -gt ${ALLOWED_CHECK_NOTES} ]]; then
+    echo "Found ${NUM_CHECK_NOTES} NOTEs from R CMD check. Only ${ALLOWED_CHECK_NOTES} are allowed"
+    exit 1
+fi

.ci/test_r_package.sh

@@ -149,8 +149,8 @@ fi
 Rscript --vanilla -e "options(install.packages.compile.from.source = '${compile_from_source}'); install.packages(${packages}, repos = '${CRAN_MIRROR}', lib = '${R_LIB_PATH}', dependencies = c('Depends', 'Imports', 'LinkingTo'), Ncpus = parallel::detectCores())" || exit 1
 
 cd "${BUILD_DIRECTORY}"
-
-PKG_TARBALL="lightgbm_*.tar.gz"
+PKG_TARBALL="lightgbm_$(head -1 VERSION.txt).tar.gz"
+BUILD_LOG_FILE="lightgbm.Rcheck/00install.out"
 LOG_FILE_NAME="lightgbm.Rcheck/00check.log"
 if [[ $R_BUILD_TYPE == "cmake" ]]; then
     Rscript build_r.R -j4 --skip-install || exit 1
@@ -209,21 +209,10 @@ elif [[ $R_BUILD_TYPE == "cran" ]]; then
     cd ${R_CMD_CHECK_DIR}
 fi
 
-# fails tests if either ERRORs or WARNINGs are thrown by
-# R CMD CHECK
-check_succeeded="yes"
-R CMD check ${PKG_TARBALL} \
-    --as-cran \
-    --run-donttest \
-|| check_succeeded="no"
-
-echo "R CMD check build logs:"
-BUILD_LOG_FILE=lightgbm.Rcheck/00install.out
-cat ${BUILD_LOG_FILE}
-
-if [[ $check_succeeded == "no" ]]; then
-    exit 1
-fi
+declare -i allowed_notes=0
+bash "${BUILD_DIRECTORY}/.ci/run-r-cmd-check.sh" \
+    "${PKG_TARBALL}" \
+    "${allowed_notes}"
 
 # ensure 'grep --count' doesn't cause failures
 set +e
@@ -242,18 +231,12 @@ if [[ $R_BUILD_TYPE == "cmake" ]]; then
         cat $BUILD_LOG_FILE \
         | grep --count "R version passed into FindLibR.cmake: ${R_VERSION}"
     )
-    if [[ $used_correct_r_version -ne 1 ]]; then
+    if [[ $passed_correct_r_version_to_cmake -ne 1 ]]; then
         echo "Unexpected R version was passed into cmake. Expected '${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
-fi
-
 # this check makes sure that CI builds of the package actually use OpenMP
 if [[ $OS_NAME == "macos" ]] && [[ $R_BUILD_TYPE == "cran" ]]; then
     omp_working=$(

.github/workflows/r_package.yml

@@ -18,7 +18,12 @@ env:
   #
   # this could be removed (hopefully) when R 3.6 support is removed
   ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
+  # in CMake-driven builds, parallelize compilation
   CMAKE_BUILD_PARALLEL_LEVEL: 4
+  # on Debian-based images, avoid interactive prompts
+  DEBIAN_FRONTEND: noninteractive
+  # parallelize compilation (extra important for Linux, where CRAN doesn't supply pre-compiled binaries)
+  MAKEFLAGS: "-j4"
   # hack to get around this:
   # https://stat.ethz.ch/pipermail/r-package-devel/2020q3/005930.html
   _R_CHECK_SYSTEM_CLOCK_: 0
@@ -258,58 +263,83 @@ jobs:
           RDscript${{ matrix.r_customization }} testthat.R >> tests.log 2>&1 || exit_code=-1
           cat ./tests.log
           exit ${exit_code}
-  test-r-debian-clang:
-    name: r-package (debian, R-devel, clang-${{ matrix.clang-version }})
+  test-r-extra-checks:
+    name: r-package (${{ matrix.image }}, R-devel)
     timeout-minutes: 60
     strategy:
       fail-fast: false
       matrix:
-        # list of versions tested in CRAN "Additional Checks":
-        # https://cran.r-project.org/web/checks/check_issue_kinds.html
-        clang-version:
-          - 16
-          - 17
+        # references:
+        #   * CRAN "additional checks": https://cran.r-project.org/web/checks/check_issue_kinds.html
+        #   * images: https://r-hub.github.io/containers/containers.html
+        image:
+          - clang16
+          - clang17
+          - clang18
+          - clang19
+          - gcc14
+          - intel
     runs-on: ubuntu-latest
-    container: rhub/debian-clang-devel
-    env:
-      DEBIAN_FRONTEND: noninteractive
+    container: ghcr.io/r-hub/containers/${{ matrix.image }}:latest
     steps:
-      - name: Install Git before checkout
-        shell: bash
-        run: |
-          apt-get update --allow-releaseinfo-change
-          apt-get install --no-install-recommends -y git
-      - name: Trust git cloning LightGBM
-        run: |
-          git config --global --add safe.directory "${GITHUB_WORKSPACE}"
       - name: Checkout repository
         uses: actions/checkout@v4
         with:
           fetch-depth: 5
           submodules: true
-      - name: install clang
+      - name: Install pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+      - name: Install LaTeX
+        shell: bash
         run: |
-          ./.ci/install-clang-devel.sh ${{ matrix.clang-version }}
+          if type -f apt 2>&1 > /dev/null; then
+            apt-get update
+            apt-get install --no-install-recommends -y \
+                devscripts \
+                texinfo \
+                texlive-latex-extra \
+                texlive-latex-recommended \
+                texlive-fonts-recommended \
+                texlive-fonts-extra \
+                tidy \
+                qpdf
+          else
+            yum update -y
+            yum install -y \
+                devscripts \
+                qpdf \
+                texinfo \
+                texinfo-tex \
+                texlive-latex \
+                tidy
+          fi
       - name: Install packages and run tests
         shell: bash
         run: |
-          export PATH=/opt/R-devel/bin/:${PATH}
           Rscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'knitr', 'markdown', 'Matrix', 'RhpcBLASctl', 'testthat'), repos = 'https://cran.rstudio.com', Ncpus = parallel::detectCores())"
           sh build-cran-package.sh
-          R CMD check --as-cran --run-donttest lightgbm_*.tar.gz || exit 1
-          echo ""
-          echo "install logs:"
-          echo ""
-          cat lightgbm.Rcheck/00install.out
-          echo ""
-          if grep -q -E "NOTE|WARNING|ERROR" lightgbm.Rcheck/00check.log; then
-              echo "NOTEs, WARNINGs, or ERRORs have been found by R CMD check"
-              exit 1
+          if [[ "${{ matrix.image }}" =~ "clang" ]]; then
+            # allowing the following NOTEs (produced by default in the clang images):
+            #
+            #   * checking compilation flags used ... NOTE
+            #       Compilation used the following non-portable flag(s):
+            #       ‘-Wp,-D_FORTIFY_SOURCE=3’
+            #
+            # even though CRAN itself sets that:
+            # https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-clang
+            #
+            declare -i allowed_notes=1
+          else
+            declare -i allowed_notes=0
           fi
+
+          bash .ci/run-r-cmd-check.sh \
+            "$(echo lightgbm_$(head -1 VERSION.txt).tar.gz)" \
+            "${allowed_notes}"
   all-r-package-jobs-successful:
     if: always()
     runs-on: ubuntu-latest
-    needs: [test, test-r-sanitizers, test-r-debian-clang]
+    needs: [test, test-r-sanitizers, test-r-extra-checks]
     steps:
     - name: Note that all tests succeeded
       uses: re-actors/alls-green@v1.2.2

R-package/src/lightgbm_R.cpp

@@ -13,8 +13,14 @@
 #include <R_ext/Rdynload.h>
 #include <R_ext/Altrep.h>
 
+#ifndef R_NO_REMAP
 #define R_NO_REMAP
+#endif
+
+#ifndef R_USE_C99_IN_CXX
 #define R_USE_C99_IN_CXX
+#endif
+
 #include <R_ext/Error.h>
 
 #include <string>

R-package/src/lightgbm_R.h

@@ -7,8 +7,14 @@
 
 #include <LightGBM/c_api.h>
 
+#ifndef R_NO_REMAP
 #define R_NO_REMAP
+#endif
+
+#ifndef R_USE_C99_IN_CXX
 #define R_USE_C99_IN_CXX
+#endif
+
 #include <Rinternals.h>
 
 /*!

include/LightGBM/utils/log.h

@@ -16,8 +16,15 @@
 #include <string>
 
 #ifdef LGB_R_BUILD
+
+#ifndef R_NO_REMAP
 #define R_NO_REMAP
+#endif
+
+#ifndef R_USE_C99_IN_CXX
 #define R_USE_C99_IN_CXX
+#endif
+
 #include <R_ext/Print.h>
 extern "C" void R_FlushConsole(void);
 #endif