ARROW-13199: [R] add ubuntu 21.04 to nightly builds

Closes apache#10611 from jonkeane/ARROW-13199-r-ubuntu-21.04 Authored-by: Jonathan Keane <[email protected]> Signed-off-by: Jonathan Keane <[email protected]>
NetEase · Jul 5, 2021 · 41c4143 · 41c4143
1 parent 905809c
commit 41c4143
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Showing 8 changed files with 219 additions and 4 deletions.
diff --git a/.env b/.env
@@ -61,6 +61,7 @@ SPARK=master
 DOTNET=3.1
 R=4.1
 ARROW_R_DEV=TRUE
+GCC_VERSION=""
 # These correspond to images on Docker Hub that contain R, e.g. rhub/ubuntu-gcc-release:latest
 R_ORG=rhub
 R_IMAGE=ubuntu-gcc-release

diff --git a/ci/docker/linux-apt-r.dockerfile b/ci/docker/linux-apt-r.dockerfile
@@ -61,6 +61,16 @@ RUN apt-get update -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
+ARG gcc_version=""
+RUN if [ "${gcc_version}" != "" ]; then \
+      update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${gcc_version} 100 && \
+      update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-${gcc_version} 100 && \
+      update-alternatives --install /usr/bin/cc cc /usr/bin/gcc 30 && \
+      update-alternatives --set cc /usr/bin/gcc && \
+      update-alternatives --install /usr/bin/c++ c++ /usr/bin/g++ 30 && \
+      update-alternatives --set c++ /usr/bin/g++; \
+    fi
+
 # Ensure parallel R package installation, set CRAN repo mirror,
 # and use pre-built binaries where possible
 COPY ci/etc/rprofile /arrow/ci/etc/

diff --git a/ci/docker/ubuntu-21.04-cpp.dockerfile b/ci/docker/ubuntu-21.04-cpp.dockerfile
@@ -0,0 +1,160 @@
+# 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.
+
+ARG base=amd64/ubuntu:20.04
+FROM ${base}
+ARG arch
+
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+RUN echo "debconf debconf/frontend select Noninteractive" | \
+        debconf-set-selections
+
+# Installs LLVM toolchain, for Gandiva and testing other compilers
+#
+# Note that this is installed before the base packages to improve iteration
+# while debugging package list with docker build.
+ARG clang_tools
+ARG llvm
+RUN if [ "${llvm}" -gt "10" ]; then \
+      apt-get update -y -q && \
+      apt-get install -y -q --no-install-recommends \
+          apt-transport-https \
+          ca-certificates \
+          gnupg \
+          wget && \
+      wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | apt-key add - && \
+      echo "deb https://apt.llvm.org/hirsute/ llvm-toolchain-hirsute-${llvm} main" > \
+         /etc/apt/sources.list.d/llvm.list && \
+      if [ "${clang_tools}" != "${llvm}" -a "${clang_tools}" -gt 10 ]; then \
+        echo "deb https://apt.llvm.org/hirsute/ llvm-toolchain-hirsute-${clang_tools} main" > \
+           /etc/apt/sources.list.d/clang-tools.list; \
+      fi \
+    fi && \
+    apt-get update -y -q && \
+    apt-get install -y -q --no-install-recommends \
+        clang-${clang_tools} \
+        clang-${llvm} \
+        clang-format-${clang_tools} \
+        clang-tidy-${clang_tools} \
+        llvm-${llvm}-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists*
+
+# Installs C++ toolchain and dependencies
+RUN apt-get update -y -q && \
+    apt-get install -y -q --no-install-recommends \
+        autoconf \
+        ca-certificates \
+        ccache \
+        cmake \
+        gdb \
+        git \
+        libbenchmark-dev \
+        libboost-filesystem-dev \
+        libboost-system-dev \
+        libbrotli-dev \
+        libbz2-dev \
+        libc-ares-dev \
+        libcurl4-openssl-dev \
+        libgflags-dev \
+        libgoogle-glog-dev \
+        libgrpc++-dev \
+        liblz4-dev \
+        libprotobuf-dev \
+        libprotoc-dev \
+        libre2-dev \
+        libsnappy-dev \
+        libssl-dev \
+        libthrift-dev \
+        libutf8proc-dev \
+        libzstd-dev \
+        make \
+        ninja-build \
+        pkg-config \
+        protobuf-compiler \
+        protobuf-compiler-grpc \
+        rapidjson-dev \
+        tzdata \
+        wget && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists*
+
+COPY ci/scripts/install_minio.sh \
+     /arrow/ci/scripts/
+RUN /arrow/ci/scripts/install_minio.sh ${arch} linux latest /usr/local
+
+# Prioritize system packages and local installation
+# The following dependencies will be downloaded due to missing/invalid packages
+# provided by the distribution:
+# - libc-ares-dev does not install CMake config files
+# - flatbuffer is not packaged
+# - libgtest-dev only provide sources
+# - libprotobuf-dev only provide sources
+ENV ARROW_BUILD_TESTS=ON \
+    ARROW_DEPENDENCY_SOURCE=SYSTEM \
+    ARROW_DATASET=ON \
+    ARROW_FLIGHT=OFF \
+    ARROW_GANDIVA=ON \
+    ARROW_HDFS=ON \
+    ARROW_HOME=/usr/local \
+    ARROW_INSTALL_NAME_RPATH=OFF \
+    ARROW_NO_DEPRECATED_API=ON \
+    ARROW_ORC=ON \
+    ARROW_PARQUET=ON \
+    ARROW_PLASMA=ON \
+    ARROW_S3=ON \
+    ARROW_USE_ASAN=OFF \
+    ARROW_USE_CCACHE=ON \
+    ARROW_USE_UBSAN=OFF \
+    ARROW_WITH_BROTLI=ON \
+    ARROW_WITH_BZ2=ON \
+    ARROW_WITH_LZ4=ON \
+    ARROW_WITH_SNAPPY=ON \
+    ARROW_WITH_ZLIB=ON \
+    ARROW_WITH_ZSTD=ON \
+    AWSSDK_SOURCE=BUNDLED \
+    GTest_SOURCE=BUNDLED \
+    ORC_SOURCE=BUNDLED \
+    PARQUET_BUILD_EXAMPLES=ON \
+    PARQUET_BUILD_EXECUTABLES=ON \
+    PATH=/usr/lib/ccache/:$PATH \
+    PYTHON=python3
+
+ARG gcc_version=""
+RUN if [ "${gcc_version}" = "" ]; then \
+      apt-get update -y -q && \
+      apt-get install -y -q --no-install-recommends \
+          g++ \
+          gcc; \
+    else \
+      if [ "${gcc_version}" -gt "10" ]; then \
+          apt-get update -y -q && \
+          apt-get install -y -q --no-install-recommends software-properties-common && \
+          add-apt-repository ppa:ubuntu-toolchain-r/volatile; \
+      fi; \
+      apt-get update -y -q && \
+      apt-get install -y -q --no-install-recommends \
+          g++-${gcc_version} \
+          gcc-${gcc_version} && \
+      update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-${gcc_version} 100 && \
+      update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-${gcc_version} 100 && \
+      update-alternatives --install /usr/bin/cc cc /usr/bin/gcc 100 && \
+      update-alternatives --set cc /usr/bin/gcc && \
+      update-alternatives --install /usr/bin/c++ c++ /usr/bin/g++ 100 && \
+      update-alternatives --set c++ /usr/bin/g++; \
+    fi
diff --git a/dev/tasks/docker-tests/github.linux.yml b/dev/tasks/docker-tests/github.linux.yml
@@ -39,7 +39,13 @@ jobs:
 
       - name: Execute Docker Build
         shell: bash
-        run: archery docker run -e SETUPTOOLS_SCM_PRETEND_VERSION="{{ arrow.no_rc_version }}" {{ flags|default("") }} {{ image }}
+        run: archery docker run -e SETUPTOOLS_SCM_PRETEND_VERSION="{{ arrow.no_rc_version }}" {{ flags|default("") }} {{ image }} {{ command|default("") }}
+
+    {% if '-r-' in image %}
+      - name: Dump R install logs
+        run: cat arrow/r/check/arrow.Rcheck/00install.out
+        continue-on-error: true
+    {% endif %}
 
     {% if arrow.branch == 'master' %}
       {{ macros.github_login_dockerhub()|indent }}

diff --git a/dev/tasks/tasks.yml b/dev/tasks/tasks.yml
@@ -934,6 +934,28 @@ tasks:
       r_tag: {{ r_tag }}
 {% endfor %}
 
+  test-r-ubuntu-21.04:
+    ci: github
+    template: docker-tests/github.linux.yml
+    params:
+      env:
+        UBUNTU: 21.04
+        CLANG_TOOLS: 9 # can remove this when >=9 is the default
+      flags: '-e ARROW_SOURCE_HOME="/arrow" -e FORCE_BUNDLED_BUILD=TRUE -e LIBARROW_BUILD=TRUE'
+      image: ubuntu-r
+
+  test-r-gcc-11:
+    ci: github
+    template: docker-tests/github.linux.yml
+    params:
+      env:
+        UBUNTU: 21.04
+        CLANG_TOOLS: 9 # can remove this when >=9 is the default
+        GCC_VERSION: 11
+      # S3 support is not buildable with gcc11 right now
+      flags: '-e ARROW_SOURCE_HOME="/arrow" -e FORCE_BUNDLED_BUILD=TRUE -e LIBARROW_BUILD=TRUE -e ARROW_S3=OFF'
+      image: ubuntu-r-only-r
+
   test-r-rstudio-r-base-3.6-centos7-devtoolset-8:
     ci: azure
     template: r/azure.linux.yml

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -110,6 +110,7 @@ x-hierarchy:
       - ubuntu-docs
     - ubuntu-python-sdist-test
     - ubuntu-r
+    - ubuntu-r-only-r
   - ubuntu-cuda-cpp:
     - ubuntu-cuda-python
   - ubuntu-csharp
@@ -300,6 +301,7 @@ services:
         base: "${ARCH}/ubuntu:${UBUNTU}"
         clang_tools: ${CLANG_TOOLS}
         llvm: ${LLVM}
+        gcc_version: ${GCC_VERSION}
     shm_size: *shm-size
     ulimits: *ulimits
     environment:
@@ -1008,19 +1010,27 @@ services:
         arch: ${ARCH}
         r: ${R}
         base: ${REPO}:${ARCH}-ubuntu-${UBUNTU}-cpp
+        gcc_version: ${GCC_VERSION}
     shm_size: *shm-size
     environment:
       <<: *ccache
       ARROW_R_CXXFLAGS: '-Werror'
       LIBARROW_BUILD: 'false'
       NOT_CRAN: 'true'
+      ARROW_R_DEV: ${ARROW_R_DEV}
     volumes: *ubuntu-volumes
     command: >
       /bin/bash -c "
         /arrow/ci/scripts/cpp_build.sh /arrow /build &&
         /arrow/ci/scripts/python_build.sh /arrow /build &&
         /arrow/ci/scripts/r_test.sh /arrow"
 
+  ubuntu-r-only-r:
+    extends: ubuntu-r
+    command: >
+      /bin/bash -c "
+        /arrow/ci/scripts/r_test.sh /arrow"
+
   r:
     # This lets you test building/installing the arrow R package
     # (including building the C++ library) on any Docker image that contains R

diff --git a/r/configure b/r/configure
@@ -69,7 +69,7 @@ if [ "$FORCE_AUTOBREW" = "true" ] || [ "$FORCE_BUNDLED_BUILD" = "true" ]; then
 fi
 
 # Note that cflags may be empty in case of success
-if [ "$ARROW_HOME" ]; then
+if [ "$ARROW_HOME" ] && [ "$FORCE_BUNDLED_BUILD" != "true" ]; then
   echo "*** Using ARROW_HOME as the source of libarrow"
   PKG_CFLAGS="-I$ARROW_HOME/include $PKG_CFLAGS"
   PKG_DIRS="-L$ARROW_HOME/lib"
@@ -88,7 +88,8 @@ else
   fi
 
   if [ "$PKGCONFIG_CFLAGS" ] && [ "$PKGCONFIG_LIBS" ]; then
-    echo "*** Arrow C++ libraries found via pkg-config"
+    FOUND_LIB_DIR=`echo $PKG_DIRS | sed -e 's/^-L//'`
+    echo "*** Arrow C++ libraries found via pkg-config at $FOUND_LIB_DIR"
     PKG_CFLAGS="$PKGCONFIG_CFLAGS"
     PKG_LIBS=${PKGCONFIG_LIBS}
     PKG_DIRS=${PKGCONFIG_DIRS}
@@ -244,7 +245,7 @@ if [ $? -eq 0 ] || [ "$UNAME" = "Darwin" ]; then
     fi
   fi
   # prepend PKG_DIRS and append BUNDLED_LIBS to PKG_LIBS
-  PKG_LIBS="$PKG_DIRS $PKG_LIBS $BUNDLED_LIBS"
+  PKG_LIBS="$PKG_DIRS $PKG_LIBS $BUNDLED_LIBS -fno-lto"
   echo "PKG_CFLAGS=$PKG_CFLAGS"
   echo "PKG_LIBS=$PKG_LIBS"
 else

diff --git a/r/tools/nixlibs.R b/r/tools/nixlibs.R
@@ -326,6 +326,7 @@ build_libarrow <- function(src_dir, dst_dir) {
     CC = R_CMD_config("CC"),
     CXX = paste(R_CMD_config("CXX11"), R_CMD_config("CXX11STD")),
     # CXXFLAGS = R_CMD_config("CXX11FLAGS"), # We don't want the same debug symbols
+    ARROW_R_CXXFLAGS = paste(Sys.getenv("ARROW_R_CXXFLAGS", ""), "-fno-lto"),
     LDFLAGS = R_CMD_config("LDFLAGS")
   )
   env_vars <- paste0(names(env_var_list), '="', env_var_list, '"', collapse = " ")
@@ -415,6 +416,10 @@ cmake_version <- function(cmd = "cmake") {
 
 with_s3_support <- function(env_vars) {
   arrow_s3 <- toupper(Sys.getenv("ARROW_S3")) == "ON" || tolower(Sys.getenv("LIBARROW_MINIMAL")) == "false"
+  # but if ARROW_S3=OFF explicitly, we are definitely off, so override
+  if (toupper(Sys.getenv("ARROW_S3")) == "OFF" ) {
+    arrow_s3 <- FALSE
+  }
   if (arrow_s3) {
     # User wants S3 support. If they're using gcc, let's make sure the version is >= 4.9
     # and make sure that we have curl and openssl system libs