[R] Installation from source without system `libarrow` fails due to linkage error

david-cortes commented 1 month ago

Describe the bug, including details regarding any error messages, version, and platform.

Installing the R package arrow from source without a core libarrow in the system fails on Debian 12, due to a linkage error.

The issue was reported previously: https://github.com/apache/arrow/issues/43337

And the comments in the thread mentioned that it was due to a bug in a specific version of pkgconf, but the issue still occurs in a system that doesn't use said version of the software where the bug was reported.

The problems happens regardless of whether:

I compile with gcc or with clang.
I use link-time optimization or not.

Compiler info:

gcc --version
gcc (Debian 12.2.0-14) 12.2.0
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE

clang --version
Debian clang version 14.0.6
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

OS info:

cat /etc/os-release
PRETTY_NAME="Debian GNU/Linux 12 (bookworm)"
NAME="Debian GNU/Linux"
VERSION_ID="12"
VERSION="12 (bookworm)"
VERSION_CODENAME=bookworm
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"

R info:

version

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          4                           
minor          3.0                         
year           2023                        
month          04                          
day            21                          
svn rev        84292                       
language       R                           
version.string R version 4.3.0 (2023-04-21)
nickname       Already Tomorrow

To reproduce:

install.packages("arrow")

Log: arrow_log.txt

Component(s)

R

assignUser commented 1 month ago

-- Found thrift: /home/david/anaconda3
...
-- Providing CMake module for FindThriftAlt as part of Parquet CMake package
-- pkg-config package for thrift that is used by parquet for static link isn't found

CMake found conda thrift which likely only provides dynamic libraries and also does not provide a pkg-config file. This means it will not be linked correctly in the R package. AFAIK there is nothing we can really do to support this scenario (cc @kou) other than prevent the libarrow build from picking up any system dependency that only comes as shared, which is also not trivial see #43353.

You can work around this by:

using pre-compiled binaries export LIBARROW_BINARY=true NOT_CRAN=true
use r-arrow from conda-forge (as you seem to be working in a conda env)
use libarrow-all from conda-forge and build the R package against it
remove the dynamic only thrift version

david-cortes commented 1 month ago

Just to clarify: this is a system R installation (through the Debian package manager) outside of conda, in a setup where the user has a conda installation (which doesn't manage R) with its paths added to ${PATH}.

I would venture to guess that it is a very typical setup for desktop users to have a system R installation alongside with a conda installation managing Python kernels, with the conda paths always in ${PATH} (e.g. in order to use reticulate in R).

And also to clarify: there aren't arrow binaries for many linux platforms, so e.g. setting LIBARROW_BINARY=true would still make install.packages compile libarrow from source on Debian and some RH-derived distributions. Getting it to install correctly requires quite a bit of tinkering with environment variables (e.g. removing conda paths, or creating a libarrow install elsewhere and adding it to the config).

assignUser commented 1 month ago

By the way, thanks for the detailed report, it makes it much easier to investigate.

a very typical setup

I'd bet against that as conda is not intended to be a system package manager and the docs actually specifically recommends not adding it to the path: 'Anaconda recommends against adding Anaconda to the PATH manually.' But again, even if you do this, you can also just install libarrow-all via conda and the package should pick it up (if your pkg-conf path is set correctly).

compile libarrow from source on Debian and some RH-derived distributions

This is not true, as long as your are on x86 with libstdc++ with openssl and libcurl dev libraries (e.g. libssl-dev and libcurl4-openssl-dev for debian) installed our binaries will work, see docs. To avoid issue with CRAN you have to opt in to this by setting LIBARROW_BINARY=true or NOT_CRAN=true, the latter will be set by a number of packages like {pak} and {remotes} so you don't even have to do it manually in that case. As you can see below I installed with precompiled binary on debian bookworm, testing and almalinux with no problem.

Getting it to install correctly requires quite a bit of tinkering with environment variables

If you have a non-standard environment this can be the case yes, as mentioned in another issue we do spend a lot of time and effort on making it as easy as possible to install the package without forcing a system dependency of arrow but we are also not :mage:. And in addition there is conda, PPP and r-universe where you can get compiled binaries for linux too.

Debian bookworm:

* installing *source* package 'arrow' ...
** package 'arrow' successfully unpacked and MD5 sums checked
** using staged installation
*** pkg-config found.
*** Found libcurl and OpenSSL >= 3.0.0
trying URL 'https://apache.jfrog.io/artifactory/arrow/r/16.1.0/libarrow/bin/linux-openssl-3.0/arrow-16.1.0.zip'
Content type 'application/zip' length 41141217 bytes (39.2 MB)
==================================================
downloaded 39.2 MB

*** Checksum validated successfully for libarrow
*** Successfully retrieved libarrow (linux-openssl-3.0)

Debian trixie

root@4520f567d3ae:/# cat /etc/issue
Debian GNU/Linux trixie/sid \n \l

root@4520f567d3ae:/# LIBARROW_BINARY=true Rscript -e 'install.packages("arrow"); arrow::arrow_info()'
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/arrow_16.1.0.tar.gz'
Content type 'application/x-gzip' length 4439675 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

* installing *source* package ‘arrow’ ...
** package ‘arrow’ successfully unpacked and MD5 sums checked
** using staged installation
*** Disabling Arrow build with GCS on gcc-13.
*** Set ARROW_GCS=ON to explicitly enable.
*** pkg-config found.
*** Found libcurl and OpenSSL >= 3.0.0
*** Checksum validated successfully for libarrow
*** Successfully retrieved libarrow (linux-openssl-3.0)
PKG_CFLAGS=-I/tmp/Rtmpcaj8yV/R.INSTALL10325483e570/arrow/libarrow/arrow-16.1.0/include -I/usr/include/x86_64-linux-gnu -I/usr/lib/include -DPARQUET_STATIC -DARROW_STATIC    -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_ACERO -DARROW_R_WITH_JSON -DARROW_R_WITH_S3 -DARROW_R_WITH_GCS
PKG_LIBS=-L/tmp/Rtmpcaj8yV/R.INSTALL10325483e570/arrow/libarrow/arrow-16.1.0/lib -L/usr/lib/lib/x86_64-linux-gnu  -larrow_dataset -lparquet -larrow_acero -larrow -larrow_bundled_dependencies -ldl -lcurl -lssl -lcrypto
** libs
using C++ compiler: ‘g++ (Debian 13.3.0-1) 13.3.0’
...
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (arrow)

The downloaded source packages are in
        ‘/tmp/RtmpDVsm5j/downloaded_packages’
Arrow package version: 16.1.0

Capabilities:

acero      TRUE
dataset    TRUE
substrait FALSE
parquet    TRUE
json       TRUE
s3         TRUE
gcs        TRUE
utf8proc   TRUE
re2        TRUE
snappy     TRUE
gzip       TRUE
brotli     TRUE
zstd       TRUE
lz4        TRUE
lz4_frame  TRUE
lzo       FALSE
bz2        TRUE
jemalloc   TRUE
mimalloc   TRUE

Almalinux 9:

Making 'packages.html' ... done
* installing *source* package ‘arrow’ ...
** package ‘arrow’ successfully unpacked and MD5 sums checked
** using staged installation
*** pkg-config found.
*** Found libcurl and OpenSSL >= 3.0.0
*** Checksum validated successfully for libarrow
*** Successfully retrieved libarrow (linux-openssl-3.0)
PKG_CFLAGS=-I/tmp/RtmpP1Nc6L/R.INSTALL185d1d9731b/arrow/libarrow/arrow-16.1.0/include -DPARQUET_STATIC -DARROW_STATIC    -DARROW_R_WITH_PARQUET -DARROW_R_WITH_DATASET -DARROW_R_WITH_ACERO -DARROW_R_WITH_JSON -DARROW_R_WITH_S3 -DARROW_R_WITH_GCS
PKG_LIBS=-L/tmp/RtmpP1Nc6L/R.INSTALL185d1d9731b/arrow/libarrow/arrow-16.1.0/lib  -larrow_dataset -lparquet -larrow_acero -larrow -larrow_bundled_dependencies -ldl -lcurl -lssl -lcrypto
** libs
using C++ compiler: ‘g++ (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)’
using C++17

david-cortes commented 1 month ago

FWIW, having LIBARROW_BINARY=true and NOT_CRAN=true doesn't result in a binary of libarrow being downloaded in this debian12 system for me (guess it might be the R version being 4.3?).

Sys.setenv("LIBARROW_BINARY" = "true")
Sys.setenv("NOT_CRAN" = "true")
Sys.setenv("ARROW_R_DEV" = "true")
install.packages("arrow")

Beginning of the logs:

``` R version 4.3.0 (2023-04-21) -- "Already Tomorrow" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv('LIBARROW_BINARY' = 'true'); Sys.setenv('NOT_CRAN' = 'true'); Sys.setenv('ARROW_R_DEV' = 'true'); install.packages('arrow') Installing package into ‘/home/david/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/arrow_16.1.0.tar.gz' Content type 'application/x-gzip' length 4439675 bytes (4.2 MB) ================================================== downloaded 4.2 MB * installing *source* package ‘arrow’ ... ** package ‘arrow’ successfully unpacked and MD5 sums checked ** using staged installation *** pkg-config found. *** libcurl not found *** Found local C++ source: 'tools/cpp' *** Building libarrow from source For build options and troubleshooting, see the install guide: https://arrow.apache.org/docs/r/articles/install.html *** Building with MAKEFLAGS=-j20 **** cmake 3.25.1: /usr/bin/cmake **** S3/GCS support requires libcurl-devel (rpm) or libcurl4-openssl-dev (deb) ; building with ARROW_S3=OFF and ARROW_GCS=OFF **** arrow with SOURCE_DIR='tools/cpp' BUILD_DIR='/tmp/RtmptZUHBL/file10e0a7242c9e0' DEST_DIR='libarrow/arrow-16.1.0' CMAKE='/usr/bin/cmake' EXTRA_CMAKE_FLAGS='' CC='gcc' CXX='g++ -std=gnu++17' LDFLAGS='-Wl,-z,relro' N_JOBS='20' ARROW_S3='OFF' ARROW_GCS='OFF' ++ pwd + : /tmp/RtmpnIiLoe/R.INSTALL10d0d66a490b9/arrow + : tools/cpp + : /tmp/RtmptZUHBL/file10e0a7242c9e0 + : libarrow/arrow-16.1.0 + : /usr/bin/cmake ++ cd tools/cpp ++ pwd + SOURCE_DIR=/tmp/RtmpnIiLoe/R.INSTALL10d0d66a490b9/arrow/tools/cpp ++ mkdir -p libarrow/arrow-16.1.0 ++ cd libarrow/arrow-16.1.0 ++ pwd + DEST_DIR=/tmp/RtmpnIiLoe/R.INSTALL10d0d66a490b9/arrow/libarrow/arrow-16.1.0 + '[' 20 = '' ']' + '[' false '!=' '' ']' ++ echo false ++ tr '[:upper:]' '[:lower:]' + LIBARROW_MINIMAL=false + '[' false = false ']' + ARROW_DEFAULT_PARAM=ON + case "$CXX" in + mkdir -p /tmp/RtmptZUHBL/file10e0a7242c9e0 + pushd /tmp/RtmptZUHBL/file10e0a7242c9e0 /tmp/RtmptZUHBL/file10e0a7242c9e0 /tmp/RtmpnIiLoe/R.INSTALL10d0d66a490b9/arrow + /usr/bin/cmake -DARROW_BOOST_USE_SHARED=OFF -DARROW_BUILD_TESTS=OFF -DARROW_BUILD_SHARED=OFF -DARROW_BUILD_STATIC=ON -DARROW_ACERO=ON -DARROW_COMPUTE=ON -DARROW_CSV=ON -DARROW_DATASET=ON -DARROW_DEPENDENCY_SOURCE=AUTO -DAWSSDK_SOURCE= -DBoost_SOURCE= -Dlz4_SOURCE= -DARROW_FILESYSTEM=ON -DARROW_GCS=OFF -DARROW_JEMALLOC=ON -DARROW_MIMALLOC=ON -DARROW_JSON=ON -DARROW_PARQUET=ON -DARROW_S3=OFF -DARROW_WITH_BROTLI=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_LZ4=ON -DARROW_WITH_RE2=ON -DARROW_WITH_SNAPPY=ON -DARROW_WITH_UTF8PROC=ON -DARROW_WITH_ZLIB=ON -DARROW_WITH_ZSTD=ON -DARROW_VERBOSE_THIRDPARTY_BUILD=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_DEBUG_MODE=OFF -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_INSTALL_PREFIX=/tmp/RtmpnIiLoe/R.INSTALL10d0d66a490b9/arrow/libarrow/arrow-16.1.0 -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_UNITY_BUILD=OFF -Dre2_SOURCE=BUNDLED -Dxsimd_SOURCE= -Dzstd_SOURCE= -G 'Unix Makefiles' /tmp/RtmpnIiLoe/R.INSTALL10d0d66a490b9/arrow/tools/cpp -- Building using CMake version: 3.25.1 -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Arrow version: 16.1.0 (full: '16.1.0') -- Arrow SO version: 1601 (full: 1601.0.0) -- clang-tidy found at /usr/bin/clang-tidy-14 -- clang-format found at /usr/bin/clang-format-14 -- Found ClangTools: /usr/bin/clang-format-14 -- infer not found -- Found Python3: /home/david/anaconda3/bin/python3 (found version "3.11.0") found components: Interpreter fatal: not a git repository (or any parent up to mount point /) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). -- Using ccache: /usr/bin/ccache -- Found cpplint executable at /home/david/anaconda3/bin/cpplint -- System processor: x86_64 -- Performing Test CXX_SUPPORTS_SSE4_2 -- Performing Test CXX_SUPPORTS_SSE4_2 - Success -- Performing Test CXX_SUPPORTS_AVX2 -- Performing Test CXX_SUPPORTS_AVX2 - Success -- Performing Test CXX_SUPPORTS_AVX512 -- Performing Test CXX_SUPPORTS_AVX512 - Success -- Arrow build warning level: PRODUCTION -- Using ld linker -- Build Type: RELEASE -- Performing Test CXX_LINKER_SUPPORTS_VERSION_SCRIPT -- Performing Test CXX_LINKER_SUPPORTS_VERSION_SCRIPT - Success -- Using AUTO approach to find dependencies -- ARROW_ABSL_BUILD_VERSION: 20211102.0 -- ARROW_ABSL_BUILD_SHA256_CHECKSUM: dcf71b9cba8dc0ca9940c4b316a0c796be8fab42b070bb6b7cab62b48f0e66c4 -- ARROW_AWS_C_AUTH_BUILD_VERSION: v0.6.22 -- ARROW_AWS_C_AUTH_BUILD_SHA256_CHECKSUM: 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-- ARROW_UCX_BUILD_SHA256_CHECKSUM: 9bef31aed0e28bf1973d28d74d9ac4f8926c43ca3b7010bd22a084e164e31b71 -- ARROW_UTF8PROC_BUILD_VERSION: v2.7.0 -- ARROW_UTF8PROC_BUILD_SHA256_CHECKSUM: 4bb121e297293c0fd55f08f83afab6d35d48f0af4ecc07523ad8ec99aa2b12a1 -- ARROW_XSIMD_BUILD_VERSION: 9.0.1 -- ARROW_XSIMD_BUILD_SHA256_CHECKSUM: b1bb5f92167fd3a4f25749db0be7e61ed37e0a5d943490f3accdcd2cd2918cc0 -- ARROW_ZLIB_BUILD_VERSION: 1.3.1 -- ARROW_ZLIB_BUILD_SHA256_CHECKSUM: 9a93b2b7dfdac77ceba5a558a580e74667dd6fede4585b91eefb60f03b72df23 -- ARROW_ZSTD_BUILD_VERSION: 1.5.6 -- ARROW_ZSTD_BUILD_SHA256_CHECKSUM: 8c29e06cf42aacc1eafc4077ae2ec6c6fcb96a626157e0593d5e82a34fd403c1 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for _M_ARM64 -- Looking for _M_ARM64 - not found -- Looking for __SIZEOF_INT128__ -- Looking for __SIZEOF_INT128__ - found -- Found Boost: /home/david/anaconda3/lib/cmake/Boost-1.73.0/BoostConfig.cmake (found suitable version "1.73.0", minimum required is "1.58") -- Boost include dir: /home/david/anaconda3/include -- Providing CMake module for FindSnappyAlt as part of Arrow CMake package -- pkg-config package for snappy that is used by arrow for static link isn't found -- Checking for modules 'libbrotlicommon;libbrotlienc;libbrotlidec' -- Found libbrotlicommon, version 1.0.9 -- Found libbrotlienc, version 1.0.9 -- Found libbrotlidec, version 1.0.9 -- Found BrotliAlt: /usr/lib/x86_64-linux-gnu/libbrotlicommon.so -- Providing CMake module for FindBrotliAlt as part of Arrow CMake package -- Using pkg-config package for libbrotlidec that is used by arrow for static link -- Using pkg-config package for libbrotlienc that is used by arrow for static link -- Building without OpenSSL support. Minimum OpenSSL version 1.0.2 required. -- Found thrift: /home/david/anaconda3 -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.13") -- Found OpenSSL: /usr/lib/x86_64-linux-gnu/libcrypto.so (found version "3.0.13") -- Found libevent include directory: /home/david/anaconda3/include -- Found libevent component: /home/david/anaconda3/lib/libevent_core.so -- Found libevent component: /home/david/anaconda3/lib/libevent_extra.so -- Found libevent component: /home/david/anaconda3/lib/libevent_openssl.so -- Found libevent component: /home/david/anaconda3/lib/libevent_pthreads.so -- Found libevent 2.1.12 in /home/david/anaconda3 -- Providing CMake module for FindThriftAlt as part of Parquet CMake package -- pkg-config package for thrift that is used by parquet for static link isn't found -- Building jemalloc from source -- Building (vendored) mimalloc from source CMake Warning at cmake_modules/FindRapidJSONAlt.cmake:29 (find_package): By not providing "FindRapidJSON.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "RapidJSON", but CMake did not find one. Could not find a package configuration file provided by "RapidJSON" (requested version 1.1.0) with any of the following names: RapidJSONConfig.cmake rapidjson-config.cmake Add the installation prefix of "RapidJSON" to CMAKE_PREFIX_PATH or set "RapidJSON_DIR" to a directory containing one of the above files. If "RapidJSON" provides a separate development package or SDK, be sure it has been installed. Call Stack (most recent call first): cmake_modules/ThirdpartyToolchain.cmake:291 (find_package) cmake_modules/ThirdpartyToolchain.cmake:2451 (resolve_dependency) CMakeLists.txt:543 (include) -- Could NOT find RapidJSONAlt (missing: RAPIDJSON_INCLUDE_DIR) (Required is at least version "1.1.0") -- Building RapidJSON from source CMake Warning at cmake_modules/ThirdpartyToolchain.cmake:291 (find_package): By not providing "Findxsimd.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "xsimd", but CMake did not find one. Could not find a package configuration file provided by "xsimd" with any of the following names: xsimdConfig.cmake xsimd-config.cmake Add the installation prefix of "xsimd" to CMAKE_PREFIX_PATH or set "xsimd_DIR" to a directory containing one of the above files. If "xsimd" provides a separate development package or SDK, be sure it has been installed. Call Stack (most recent call first): cmake_modules/ThirdpartyToolchain.cmake:2491 (resolve_dependency) CMakeLists.txt:543 (include) -- Building xsimd from source -- Using pkg-config package for zlib that is used by arrow for static link CMake Warning at cmake_modules/Findlz4Alt.cmake:29 (find_package): By not providing "Findlz4.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "lz4", but CMake did not find one. Could not find a package configuration file provided by "lz4" with any of the following names: lz4Config.cmake lz4-config.cmake Add the installation prefix of "lz4" to CMAKE_PREFIX_PATH or set "lz4_DIR" to a directory containing one of the above files. If "lz4" provides a separate development package or SDK, be sure it has been installed. Call Stack (most recent call first): cmake_modules/ThirdpartyToolchain.cmake:291 (find_package) cmake_modules/ThirdpartyToolchain.cmake:2599 (resolve_dependency) CMakeLists.txt:543 (include) -- Checking for module 'liblz4' -- Package 'liblz4', required by 'virtual:world', not found -- Could NOT find lz4Alt (missing: LZ4_LIB LZ4_INCLUDE_DIR) -- Building LZ4 from source -- Providing CMake module for FindzstdAlt as part of Arrow CMake package -- Using pkg-config package for libzstd that is used by arrow for static link -- Found Zstandard: zstd::libzstd_shared -- Building RE2 from source -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- pkg-config package for bzip2 that is used by arrow for static link isn't found -- Could NOT find utf8proc: (Required is at least version "2.2.0") (found utf8proc_LIB-NOTFOUND) -- Building utf8proc from source -- Found hdfs.h at: /tmp/RtmpnIiLoe/R.INSTALL10d0d66a490b9/arrow/tools/cpp/thirdparty/hadoop/include/hdfs.h -- All bundled static libraries: jemalloc::jemalloc;mimalloc::mimalloc;LZ4::lz4;re2::re2;utf8proc::utf8proc -- CMAKE_C_FLAGS: -g -O2 -ffile-prefix-map=/build/r-base-tjkk0w/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -march=native -fno-math-errno -fno-trapping-math -flto -Wall -fno-semantic-interposition -msse4.2 -- CMAKE_CXX_FLAGS: -Wno-noexcept-type -g -O2 -ffile-prefix-map=/build/r-base-tjkk0w/r-base-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -march=native -fno-math-errno -fno-trapping-math -flto -fdiagnostics-color=always -Wall -fno-semantic-interposition -msse4.2 -- CMAKE_C_FLAGS_RELEASE: -O3 -DNDEBUG -O2 -ftree-vectorize -- CMAKE_CXX_FLAGS_RELEASE: -O3 -DNDEBUG -O2 -ftree-vectorize -- Creating bundled static library target arrow_bundled_dependencies at /tmp/RtmptZUHBL/file10e0a7242c9e0/release/libarrow_bundled_dependencies.a -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- --------------------------------------------------------------------- -- Arrow version: 16.1.0 -- -- Build configuration summary: -- Generator: Unix Makefiles -- Build type: RELEASE -- Source directory: /tmp/RtmpnIiLoe/R.INSTALL10d0d66a490b9/arrow/tools/cpp -- Install prefix: /tmp/RtmpnIiLoe/R.INSTALL10d0d66a490b9/arrow/libarrow/arrow-16.1.0 -- Compile commands: /tmp/RtmptZUHBL/file10e0a7242c9e0/compile_commands.json -- -- Compile and link options: -- -- ARROW_CXXFLAGS="" [default=""] -- Compiler flags to append when compiling Arrow -- ARROW_BUILD_STATIC=ON [default=ON] -- Build static libraries -- ARROW_BUILD_SHARED=OFF [default=ON] -- Build shared libraries -- ARROW_PACKAGE_KIND="" [default=""] -- Arbitrary string that identifies the kind of package -- (for informational purposes) -- ARROW_GIT_ID="" [default=""] -- The Arrow git commit id (if any) -- ARROW_GIT_DESCRIPTION="" [default=""] -- The Arrow git commit description (if any) -- ARROW_NO_DEPRECATED_API=OFF [default=OFF] -- Exclude deprecated APIs from build -- ARROW_POSITION_INDEPENDENT_CODE=ON [default=ON] -- Whether to create position-independent target -- ARROW_USE_CCACHE=ON [default=ON] -- Use ccache when compiling (if available) -- ARROW_USE_SCCACHE=ON [default=ON] -- Use sccache when compiling (if available), -- takes precedence over ccache if a storage backend is configured -- ARROW_USE_LD_GOLD=OFF [default=OFF] -- Use ld.gold for linking on Linux (if available) -- ARROW_USE_LLD=OFF [default=OFF] -- Use the LLVM lld for linking (if available) -- ARROW_USE_MOLD=OFF [default=OFF] -- Use mold for linking on Linux (if available) -- ARROW_USE_PRECOMPILED_HEADERS=OFF [default=OFF] -- Use precompiled headers when compiling -- ARROW_SIMD_LEVEL=SSE4_2 [default=DEFAULT|NONE|SSE4_2|AVX2|AVX512|NEON|SVE|SVE128|SVE256|SVE512] -- Compile-time SIMD optimization level -- ARROW_RUNTIME_SIMD_LEVEL=MAX [default=MAX|NONE|SSE4_2|AVX2|AVX512] -- Max runtime SIMD optimization level -- ARROW_ALTIVEC=ON [default=ON] -- Build with Altivec if compiler has support -- ARROW_RPATH_ORIGIN=OFF [default=OFF] -- Build Arrow libraries with RATH set to $ORIGIN -- ARROW_INSTALL_NAME_RPATH=ON [default=ON] -- Build Arrow libraries with install_name set to @rpath -- ARROW_GGDB_DEBUG=ON [default=ON] -- Pass -ggdb flag to debug builds -- ARROW_WITH_MUSL=OFF [default=OFF] -- Whether the system libc is musl or not -- ARROW_ENABLE_THREADING=ON [default=ON] -- Enable threading in Arrow core -- -- Test and benchmark options: -- -- ARROW_BUILD_EXAMPLES=OFF [default=OFF] -- Build the Arrow examples -- ARROW_BUILD_TESTS=OFF [default=OFF] -- Build the Arrow googletest unit tests -- ARROW_ENABLE_TIMING_TESTS=ON [default=ON] -- Enable timing-sensitive tests -- ARROW_BUILD_INTEGRATION=OFF [default=OFF] -- Build the Arrow integration test executables -- ARROW_BUILD_BENCHMARKS=OFF [default=OFF] -- Build the Arrow micro benchmarks -- ARROW_BUILD_BENCHMARKS_REFERENCE=OFF [default=OFF] -- Build the Arrow micro reference benchmarks -- ARROW_BUILD_OPENMP_BENCHMARKS=OFF [default=OFF] -- Build the Arrow benchmarks that rely on OpenMP -- ARROW_BUILD_DETAILED_BENCHMARKS=OFF [default=OFF] -- Build benchmarks that do a longer exploration of performance -- ARROW_TEST_LINKAGE=static [default=static|shared] -- Linkage of Arrow libraries with unit tests executables. -- ARROW_FUZZING=OFF [default=OFF] -- Build Arrow Fuzzing executables -- ARROW_LARGE_MEMORY_TESTS=OFF [default=OFF] -- Enable unit tests which use large memory -- -- Lint options: -- -- ARROW_ONLY_LINT=OFF [default=OFF] -- Only define the lint and check-format targets -- ARROW_VERBOSE_LINT=OFF [default=OFF] -- If off, 'quiet' flags will be passed to linting tools -- ARROW_GENERATE_COVERAGE=OFF [default=OFF] -- Build with C++ code coverage enabled -- -- Checks options: -- -- ARROW_TEST_MEMCHECK=OFF [default=OFF] -- Run the test suite using valgrind --tool=memcheck -- ARROW_USE_ASAN=OFF [default=OFF] -- Enable Address Sanitizer checks -- ARROW_USE_TSAN=OFF [default=OFF] -- Enable Thread Sanitizer checks -- ARROW_USE_UBSAN=OFF [default=OFF] -- Enable Undefined Behavior sanitizer checks -- -- Project component options: -- -- ARROW_ACERO=ON [default=OFF] -- Build the Arrow Acero Engine Module -- ARROW_AZURE=OFF [default=OFF] -- Build Arrow with Azure support (requires the Azure SDK for C++) -- ARROW_BUILD_UTILITIES=OFF [default=OFF] -- Build Arrow commandline utilities -- ARROW_COMPUTE=ON [default=OFF] -- Build all Arrow Compute kernels -- ARROW_CSV=ON [default=OFF] -- Build the Arrow CSV Parser Module -- ARROW_CUDA=OFF [default=OFF] -- Build the Arrow CUDA extensions (requires CUDA toolkit) -- ARROW_DATASET=ON [default=OFF] -- Build the Arrow Dataset Modules -- ARROW_FILESYSTEM=ON [default=OFF] -- Build the Arrow Filesystem Layer -- ARROW_FLIGHT=OFF [default=OFF] -- Build the Arrow Flight RPC System (requires GRPC, Protocol Buffers) -- ARROW_FLIGHT_SQL=OFF [default=OFF] -- Build the Arrow Flight SQL extension -- ARROW_GANDIVA=OFF [default=OFF] -- Build the Gandiva libraries -- ARROW_GCS=OFF [default=OFF] -- Build Arrow with GCS support (requires the GCloud SDK for C++) -- ARROW_HDFS=OFF [default=OFF] -- Build the Arrow HDFS bridge -- ARROW_IPC=ON [default=ON] -- Build the Arrow IPC extensions -- ARROW_JEMALLOC=ON [default=ON] -- Build the Arrow jemalloc-based allocator -- ARROW_JSON=ON [default=OFF] -- Build Arrow with JSON support (requires RapidJSON) -- ARROW_MIMALLOC=ON [default=OFF] -- Build the Arrow mimalloc-based allocator -- ARROW_PARQUET=ON [default=OFF] -- Build the Parquet libraries -- ARROW_ORC=OFF [default=OFF] -- Build the Arrow ORC adapter -- ARROW_PYTHON=OFF [default=OFF] -- Build some components needed by PyArrow. -- (This is a deprecated option. Use CMake presets instead.) -- ARROW_S3=OFF [default=OFF] -- Build Arrow with S3 support (requires the AWS SDK for C++) -- ARROW_SKYHOOK=OFF [default=OFF] -- Build the Skyhook libraries -- ARROW_SUBSTRAIT=OFF [default=OFF] -- Build the Arrow Substrait Consumer Module -- ARROW_TENSORFLOW=OFF [default=OFF] -- Build Arrow with TensorFlow support enabled -- ARROW_TESTING=OFF [default=OFF] -- Build the Arrow testing libraries -- -- Thirdparty toolchain options: -- -- ARROW_DEPENDENCY_SOURCE=AUTO [default=AUTO|BUNDLED|SYSTEM|CONDA|VCPKG|BREW] -- Method to use for acquiring arrow's build dependencies -- ARROW_VERBOSE_THIRDPARTY_BUILD=OFF [default=OFF] -- Show output from ExternalProjects rather than just logging to files -- ARROW_DEPENDENCY_USE_SHARED=ON [default=ON] -- Link to shared libraries -- ARROW_BOOST_USE_SHARED=OFF [default=ON] -- Rely on Boost shared libraries where relevant -- ARROW_BROTLI_USE_SHARED=ON [default=ON] -- Rely on Brotli shared libraries where relevant -- ARROW_BZ2_USE_SHARED=ON [default=ON] -- Rely on Bz2 shared libraries where relevant -- ARROW_GFLAGS_USE_SHARED=ON [default=ON] -- Rely on GFlags shared libraries where relevant -- ARROW_GRPC_USE_SHARED=ON [default=ON] -- Rely on gRPC shared libraries where relevant -- ARROW_JEMALLOC_USE_SHARED=OFF [default=ON] -- Rely on jemalloc shared libraries where relevant -- ARROW_LLVM_USE_SHARED=ON [default=ON] -- Rely on LLVM shared libraries where relevant -- ARROW_LZ4_USE_SHARED=ON [default=ON] -- Rely on lz4 shared libraries where relevant -- ARROW_OPENSSL_USE_SHARED=ON [default=ON] -- Rely on OpenSSL shared libraries where relevant -- ARROW_PROTOBUF_USE_SHARED=ON [default=ON] -- Rely on Protocol Buffers shared libraries where relevant -- ARROW_SNAPPY_USE_SHARED=ON [default=ON] -- Rely on snappy shared libraries where relevant -- ARROW_THRIFT_USE_SHARED=ON [default=ON] -- Rely on thrift shared libraries where relevant -- ARROW_UTF8PROC_USE_SHARED=ON [default=ON] -- Rely on utf8proc shared libraries where relevant -- ARROW_ZSTD_USE_SHARED=ON [default=ON] -- Rely on zstd shared libraries where relevant -- ARROW_USE_GLOG=OFF [default=OFF] -- Build libraries with glog support for pluggable logging -- ARROW_WITH_BACKTRACE=ON [default=ON] -- Build with backtrace support -- ARROW_WITH_OPENTELEMETRY=OFF [default=OFF] -- Build libraries with OpenTelemetry support for distributed tracing -- ARROW_WITH_BROTLI=ON [default=OFF] -- Build with Brotli compression -- ARROW_WITH_BZ2=ON [default=OFF] -- Build with BZ2 compression -- ARROW_WITH_LZ4=ON [default=OFF] -- Build with lz4 compression -- ARROW_WITH_SNAPPY=ON [default=OFF] -- Build with Snappy compression -- ARROW_WITH_ZLIB=ON [default=OFF] -- Build with zlib compression -- ARROW_WITH_ZSTD=ON [default=OFF] -- Build with zstd compression -- ARROW_WITH_UCX=OFF [default=OFF] -- Build with UCX transport for Arrow Flight -- (only used if ARROW_FLIGHT is ON) -- ARROW_WITH_UTF8PROC=ON [default=ON] -- Build with support for Unicode properties using the utf8proc library -- (only used if ARROW_COMPUTE is ON or ARROW_GANDIVA is ON) -- ARROW_WITH_RE2=ON [default=ON] -- Build with support for regular expressions using the re2 library -- (only used if ARROW_COMPUTE or ARROW_GANDIVA is ON) -- -- Parquet options: -- -- PARQUET_MINIMAL_DEPENDENCY=OFF [default=OFF] -- Depend only on Thirdparty headers to build libparquet. -- Always OFF if building binaries -- PARQUET_BUILD_EXECUTABLES=OFF [default=OFF] -- Build the Parquet executable CLI tools. Requires static libraries to be built. -- PARQUET_BUILD_EXAMPLES=OFF [default=OFF] -- Build the Parquet examples. Requires static libraries to be built. -- PARQUET_REQUIRE_ENCRYPTION=OFF [default=OFF] -- Build support for encryption. Fail if OpenSSL is not found -- -- Gandiva options: -- -- ARROW_GANDIVA_STATIC_LIBSTDCPP=OFF [default=OFF] -- Include -static-libstdc++ -static-libgcc when linking with -- Gandiva static libraries -- ARROW_GANDIVA_PC_CXX_FLAGS="" [default=""] -- Compiler flags to append when pre-compiling Gandiva operations -- -- Advanced developer options: -- -- ARROW_EXTRA_ERROR_CONTEXT=OFF [default=OFF] -- Compile with extra error context (line numbers, code) -- ARROW_OPTIONAL_INSTALL=OFF [default=OFF] -- If enabled install ONLY targets that have already been built. Please be -- advised that if this is enabled 'install' will fail silently on components -- that have not been built -- ARROW_GDB_INSTALL_DIR="" [default=""] -- Use a custom install directory for GDB plugin. -- In general, you don't need to specify this because the default -- (CMAKE_INSTALL_FULL_BINDIR on Windows, CMAKE_INSTALL_FULL_LIBDIR otherwise) -- is reasonable. -- Outputting build configuration summary to /tmp/RtmptZUHBL/file10e0a7242c9e0/cmake_summary.json -- Configuring done -- Generating done -- Build files have been written to: /tmp/RtmptZUHBL/file10e0a7242c9e0 + /usr/bin/cmake --build . --target install -- -j 20 [ 0%] Creating directories for 'lz4_ep' ```

assignUser commented 1 month ago

*** libcurl not found

As mentioned before you need libcurl and openssl installed, see my previous post for exact package names.

apache / arrow

[R] Installation from source without system `libarrow` fails due to linkage error #43545

Describe the bug, including details regarding any error messages, version, and platform.

Component(s)