Trouble installing rPackages.arrow

nrj · May 29, 2024, 10:59pm

With current stable nixos 23.11, I want to install R’s arrow but it fails. Any tips would be helpful. The 22.05 version works.

% nix-shell -E 'let pkgs = (import <nixpkgs> {}); in pkgs.mkShell {buildInputs = [pkgs.R pkgs.rPackages.arrow];}'
this derivation will be built:
  /nix/store/4xi797cd3qq3zjivryl8w8amzs1dr0qa-r-arrow-13.0.0.1.drv
building '/nix/store/4xi797cd3qq3zjivryl8w8amzs1dr0qa-r-arrow-13.0.0.1.drv'...
Running phase: unpackPhase
unpacking source archive /nix/store/la59c56m300x7x3kdggr4d0zi0zjzm55-arrow_13.0.0.1.tar.gz
source root is arrow
setting SOURCE_DATE_EPOCH to timestamp 1695378005 of file arrow/MD5
Running phase: patchPhase
Running phase: updateAutotoolsGnuConfigScriptsPhase
Running phase: configurePhase
patching script interpreter paths in configure
configure: interpreter directive changed from "#!/usr/bin/env sh" to "/nix/store/57dqrh5d96g2lriyyf81j53vzphfflh9-bash-5.2-p15/bin/sh"
Running phase: buildPhase
Running phase: checkPhase
Running phase: installPhase
* installing *source* package 'arrow' ...
file 'configure' has the wrong MD5 checksum
** using staged installation
*** Trying Arrow C++ found by pkg-config: /nix/store/l9xbz58n50mdwic049f7519z6hrkr4m7-arrow-cpp-14.0.1
**** Not using: C++ library version (14.0.1) does not match R package (13.0.0.1)
*** 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
**** cmake
*** cmake was not found locally and download failed.
    Make sure cmake >= 3.16 is installed and available on your PATH,
    or download https://github.com/Kitware/CMake/releases/download/v3.26.4/cmake-3.26.4-linux-x86_64.tar.gz
    and define the CMAKE environment variable.
/nix/store/3x3kvc7iiisi3zap4q2gwh3vplg897n1-gnutar-1.35/bin/tar: /build/RtmpddVCvy/filefc21b50db: Cannot open: No such file or directory
/nix/store/3x3kvc7iiisi3zap4q2gwh3vplg897n1-gnutar-1.35/bin/tar: Error is not recoverable: exiting now
**** arrow  
**** Error building Arrow C++. 
**** Printing contents of build log because the build failed while ARROW_R_DEV was set to FALSE
++ pwd
+ : /build/arrow
+ : tools/cpp
+ : /build/RtmpddVCvy/filefc76b78ee4
+ : libarrow/arrow-13.0.0.1
+ : /build/RtmpddVCvy/filefc3d1e9cb9/cmake-3.26.4-linux-x86_64/bin/cmake
++ cd tools/cpp
++ pwd
+ SOURCE_DIR=/build/arrow/tools/cpp
++ mkdir -p libarrow/arrow-13.0.0.1
++ cd libarrow/arrow-13.0.0.1
++ pwd
+ DEST_DIR=/build/arrow/libarrow/arrow-13.0.0.1
+ '[' 2 = '' ']'
+ '[' '' '!=' '' ']'
+ '[' '' = false ']'
+ ARROW_DEFAULT_PARAM=OFF
+ case "$CXX" in
+ mkdir -p /build/RtmpddVCvy/filefc76b78ee4
+ pushd /build/RtmpddVCvy/filefc76b78ee4
/build/RtmpddVCvy/filefc76b78ee4 /build/arrow
+ /build/RtmpddVCvy/filefc3d1e9cb9/cmake-3.26.4-linux-x86_64/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= -DARROW_FILESYSTEM=ON -DARROW_GCS=OFF -DARROW_JEMALLOC=OFF -DARROW_MIMALLOC=ON -DARROW_JSON=ON -DARROW_PARQUET=ON -DARROW_S3=OFF -DARROW_WITH_BROTLI=OFF -DARROW_WITH_BZ2=OFF -DARROW_WITH_LZ4=ON -DARROW_WITH_RE2=ON -DARROW_WITH_SNAPPY=ON -DARROW_WITH_UTF8PROC=ON -DARROW_WITH_ZLIB=OFF -DARROW_WITH_ZSTD=OFF -DARROW_VERBOSE_THIRDPARTY_BUILD=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_DEBUG_MODE=OFF -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_INSTALL_PREFIX=/build/arrow/libarrow/arrow-13.0.0.1 -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_UNITY_BUILD=OFF -Dxsimd_SOURCE= -Dzstd_SOURCE= -G 'Unix Makefiles' /build/arrow/tools/cpp
inst/build_arrow_static.sh: line 67: /build/RtmpddVCvy/filefc3d1e9cb9/cmake-3.26.4-linux-x86_64/bin/cmake: No such file or directory
**** Complete build log may still be present at /build/RtmpddVCvy/filefc6d061a7c.log 
Warning message:
In untar(cmake_tar, exdir = cmake_dir) :
  '/nix/store/3x3kvc7iiisi3zap4q2gwh3vplg897n1-gnutar-1.35/bin/tar -xf '/build/RtmpddVCvy/filefc21b50db' -C '/build/RtmpddVCvy/filefc3d1e9cb9'' returned error code 2
PKG_CFLAGS=
PKG_LIBS= 
** libs
using C++ compiler: 'g++ (GCC) 12.3.0'
using C++17
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c RTasks.cpp -o RTasks.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c altrep.cpp -o altrep.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c array.cpp -o array.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c array_to_vector.cpp -o array_to_vector.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c arraydata.cpp -o arraydata.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c arrowExports.cpp -o arrowExports.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c bridge.cpp -o bridge.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c buffer.cpp -o buffer.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c chunkedarray.cpp -o chunkedarray.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c compression.cpp -o compression.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c compute-exec.cpp -o compute-exec.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c compute.cpp -o compute.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c config.cpp -o config.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c csv.cpp -o csv.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c dataset.cpp -o dataset.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c datatype.cpp -o datatype.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c expression.cpp -o expression.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c extension-impl.cpp -o extension-impl.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c feather.cpp -o feather.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c field.cpp -o field.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c filesystem.cpp -o filesystem.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c io.cpp -o io.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c json.cpp -o json.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c memorypool.cpp -o memorypool.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c message.cpp -o message.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c parquet.cpp -o parquet.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c r_to_arrow.cpp -o r_to_arrow.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c recordbatch.cpp -o recordbatch.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c recordbatchreader.cpp -o recordbatchreader.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c recordbatchwriter.cpp -o recordbatchwriter.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c safe-call-into-r-impl.cpp -o safe-call-into-r-impl.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c scalar.cpp -o scalar.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c schema.cpp -o schema.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c symbols.cpp -o symbols.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c table.cpp -o table.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c threadpool.cpp -o threadpool.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -I"/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/include" -DNDEBUG  -I'/nix/store/84cqwxhm004v3f2bgrjxpqkp94mjyn53-r-cpp11-0.4.6/library/cpp11/include'     -fpic  -g -O2  -c type_infer.cpp -o type_infer.o
/nix/store/a9kr77jici5pfcv8hprqncnmjlsrjhi4-gcc-wrapper-12.3.0/bin/c++ -std=gnu++17 -shared -L/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/lib -o arrow.so RTasks.o altrep.o array.o array_to_vector.o arraydata.o arrowExports.o bridge.o buffer.o chunkedarray.o compression.o compute-exec.o compute.o config.o csv.o dataset.o datatype.o expression.o extension-impl.o feather.o field.o filesystem.o io.o json.o memorypool.o message.o parquet.o r_to_arrow.o recordbatch.o recordbatchreader.o recordbatchwriter.o safe-call-into-r-impl.o scalar.o schema.o symbols.o table.o threadpool.o type_infer.o -L/nix/store/jd594jn7bv20qfwgnrj38nn92s2flqyd-R-4.3.2/lib/R/lib -lR
installing to /nix/store/v3gj33qg0w27jh62ywl47g8wmwnsrgfd-r-arrow-13.0.0.1/library/00LOCK-arrow/00new/arrow/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'arrow' in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/nix/store/v3gj33qg0w27jh62ywl47g8wmwnsrgfd-r-arrow-13.0.0.1/library/00LOCK-arrow/00new/arrow/libs/arrow.so':
  /nix/store/v3gj33qg0w27jh62ywl47g8wmwnsrgfd-r-arrow-13.0.0.1/library/00LOCK-arrow/00new/arrow/libs/arrow.so: undefined symbol: _ZTIN5arrow7compute8FunctionE
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/nix/store/v3gj33qg0w27jh62ywl47g8wmwnsrgfd-r-arrow-13.0.0.1/library/arrow'
error: builder for '/nix/store/4xi797cd3qq3zjivryl8w8amzs1dr0qa-r-arrow-13.0.0.1.drv' failed with exit code 1;
       last 10 log lines:
       > *** installing help indices
       > ** building package indices
       > ** testing if installed package can be loaded from temporary location
       > Error: package or namespace load failed for 'arrow' in dyn.load(file, DLLpath = DLLpath, ...):
       >  unable to load shared object '/nix/store/v3gj33qg0w27jh62ywl47g8wmwnsrgfd-r-arrow-13.0.0.1/library/00LOCK-arrow/00new/arrow/libs/arrow.so':
       >   /nix/store/v3gj33qg0w27jh62ywl47g8wmwnsrgfd-r-arrow-13.0.0.1/library/00LOCK-arrow/00new/arrow/libs/arrow.so: undefined symbol: _ZTIN5arrow7compute8FunctionE
       > Error: loading failed
       > Execution halted
       > ERROR: loading failed
       > * removing '/nix/store/v3gj33qg0w27jh62ywl47g8wmwnsrgfd-r-arrow-13.0.0.1/library/arrow'
       For full logs, run 'nix-store -l /nix/store/4xi797cd3qq3zjivryl8w8amzs1dr0qa-r-arrow-13.0.0.1.drv'.

efx · May 30, 2024, 2:50pm

rPackages.arrow seems brittle. I found this issue that describes a similar problem. I recreated it today on my NixOS machine with nix-shell -p rPackages.arrow

github.com/NixOS/nixpkgs

Build failure: rPackages.arrow

opened 03:36AM - 02 Jul 23 UTC

closed 07:59AM - 03 Jul 23 UTC

PmUUK

0.kind: build failure

### Steps To Reproduce Steps to reproduce the behavior: I am trying to ins…tall R arrow package, system wide. I add arrow as any other R library I use. ### Build log ``` installing * installing *source* package 'arrow' ... file 'configure' has the wrong MD5 checksum ** using staged installation *** Arrow C++ libraries found via pkg-config at /nix/store/mwavk5kg8rjjcjjz2b4nnhmchbyybrg3-arrow-cpp-12.0.0/lib **** Warning: library version mismatch **** C++ is 12.0.0 but R is 11.0.0.3 **** If installation fails, upgrade the C++ library to match **** or retry with ARROW_USE_PKG_CONFIG=false PKG_CFLAGS=-I/nix/store/mwavk5kg8rjjcjjz2b4nnhmchbyybrg3-arrow-cpp-12.0.0/include PKG_LIBS=-L/nix/store/mwavk5kg8rjjcjjz2b4nnhmchbyybrg3-arrow-cpp-12.0.0/lib -larrow ** libs /nix/store/d9fndiing52fkalp5knfalrvlb3isi6w-gcc-wrapper-12.2.0/bin/c++ -std=gnu++17 -I"/nix/store/d0i117srx5jgqf0c33mw0p6s3jam04vp-R-4.2.3/lib/R/include" -DNDEBUG -I/nix/store/mwavk5kg8rjjcjjz2b4nnhmchbyybrg3-arrow-cpp-12.0.0/include -I'/nix/store/wdhxn7lklildc2n0vd6c9sds4f6fz7bs-r-cpp11-0.4.3/library/cpp11/include' -fpic -g -O2 -c RTasks.cpp -o RTasks.o /nix/store/d9fndiing52fkalp5knfalrvlb3isi6w-gcc-wrapper-12.2.0/bin/c++ -std=gnu++17 -I"/nix/store/d0i117srx5jgqf0c33mw0p6s3jam04vp-R-4.2.3/lib/R/include" -DNDEBUG -I/nix/store/mwavk5kg8rjjcjjz2b4nnhmchbyybrg3-arrow-cpp-12.0.0/include -I'/nix/store/wdhxn7lklildc2n0vd6c9sds4f6fz7bs-r-cpp11-0.4.3/library/cpp11/include' -fpic -g -O2 -c altrep.cpp -o altrep.o In file included from altrep.cpp:18: ./arrow_types.h:41:10: fatal error: arrow/compute/exec/options.h: No such file or directory 41 | #include <arrow/compute/exec/options.h> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make: *** [/nix/store/d0i117srx5jgqf0c33mw0p6s3jam04vp-R-4.2.3/lib/R/etc/Makeconf:178: altrep.o] Error 1 ERROR: compilation failed for package 'arrow' * removing '/nix/store/46qp7h3cl6l9lddl950b3dy5c8gjdw43-r-arrow-11.0.0.3/library/arrow' error: builder for '/nix/store/z446iqac67kjc0869x4fi2ai50vkrnw0-r-arrow-11.0.0.3.drv' failed with exit code 1 error: 1 dependencies of derivation '/nix/store/8asvbibp48gmqg6vr190519qp7q608fc-R-4.2.3-wrapper.drv' failed to build building '/nix/store/blsyjcwnlgjz8wkl4msjbinmbjlj5l51-system-generators.drv'... error: 1 dependencies of derivation '/nix/store/5kjjq4z9fmflxb8sfh7h2frf80d56jjd-system-path.drv' failed to build error: 1 dependencies of derivation '/nix/store/bh9dir11w7p7sslw7g5il9ac50wadz2h-nixos-system-nixVM-23.05.1471.b72aa95f7f0.drv' failed to build ``` ### Additional context I want to switch to nixos, so I am trying to recreate my Debian working environment on a VM and an old laptop. For now, I hardly understand the nix language, but all other R packages I add were build without problems. ### Notify maintainers I think there are no maintainers listed for the R arrow. ### Metadata ```console [user@system:~]$ nix-shell -p nix-info --run "nix-info -m" - system: `"x86_64-linux"` - host os: `Linux 6.1.35, NixOS, 23.05 (Stoat), 23.05.1353.35130d4b4f0` - multi-user?: `yes` - sandbox: `yes` - version: `nix-env (Nix) 2.13.3` - channels(root): `"nixos-23.05"` - nixpkgs: `/nix/var/nix/profiles/per-user/root/channels/nixos` ```

efx · May 30, 2024, 3:07pm

rPackages.arrow from latest nixpkgs builds correctly.

For a practical solution you’ll want to use unstable nixpkgs as the basis for your shell.
I’d recommend adapting the following guide’s shell.nix for your use case: Setting up a Python development environment — nix.dev documentation

Here is an example shell.nix that worked for me:

{ pkgs ? import (fetchTarball "https://github.com/NixOS/nixpkgs/tarball/ac82a513e55582291805d6f09d35b6d8b60637a1") {} }:

pkgs.mkShellNoCC {
  packages = with pkgs; [
    rPackages.arrow
    R
  ];
}