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https://issues.apache.org/jira/browse/ARROW-4935?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16795158#comment-16795158
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Gregory Hayes commented on ARROW-4935:
--------------------------------------
That worked to get me past the jemalloc error. Now I'm seeing an unable to
locate gandiva library error, when I try to run setup.py. This happens even if
I flag GANDIVA =OFF and set
{code:java}
export PYARROW_WITH_GANDIVA=0
{code}
> Errors from jemalloc when building pyarrow from source on OSX and Debian
> ------------------------------------------------------------------------
>
> Key: ARROW-4935
> URL: https://issues.apache.org/jira/browse/ARROW-4935
> Project: Apache Arrow
> Issue Type: Bug
> Components: C++, Python
> Affects Versions: 0.12.1
> Environment: OSX, Debian, Python==3.6.7
> Reporter: Gregory Hayes
> Priority: Critical
> Labels: build, newbie
>
> My attempts to build pyarrow from source are failing. I've set up the conda
> environment using the instructions provided in the Develop instructions, and
> have tried this on both Debian and OSX. When I run CMAKE in debug mode on
> OSX, the output is:
> {code:java}
> -- Building using CMake version: 3.14.0
> -- Arrow version: 0.13.0 (full: '0.13.0-SNAPSHOT')
> -- clang-tidy not found
> -- clang-format not found
> -- infer found at /usr/local/bin/infer
> -- Using ccache: /usr/local/bin/ccache
> -- Found cpplint executable at
> /Users/Greg/documents/repos/arrow/cpp/build-support/cpplint.py
> -- Compiler command: env LANG=C
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
> -v
> -- Compiler version: Apple LLVM version 10.0.0 (clang-1000.11.45.5)
> Target: x86_64-apple-darwin18.2.0
> Thread model: posix
> InstalledDir:
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
> -- Compiler id: AppleClang
> Selected compiler clang 4.1.0svn
> -- Arrow build warning level: CHECKIN
> Configured for DEBUG build (set with cmake
> -DCMAKE_BUILD_TYPE={release,debug,...})
> -- Build Type: DEBUG
> -- BOOST_VERSION: 1.67.0
> -- BROTLI_VERSION: v0.6.0
> -- CARES_VERSION: 1.15.0
> -- DOUBLE_CONVERSION_VERSION: v3.1.1
> -- FLATBUFFERS_VERSION: v1.10.0
> -- GBENCHMARK_VERSION: v1.4.1
> -- GFLAGS_VERSION: v2.2.0
> -- GLOG_VERSION: v0.3.5
> -- GRPC_VERSION: v1.18.0
> -- GTEST_VERSION: 1.8.1
> -- JEMALLOC_VERSION: 17c897976c60b0e6e4f4a365c751027244dada7a
> -- LZ4_VERSION: v1.8.3
> -- ORC_VERSION: 1.5.4
> -- PROTOBUF_VERSION: v3.6.1
> -- RAPIDJSON_VERSION: v1.1.0
> -- RE2_VERSION: 2018-10-01
> -- SNAPPY_VERSION: 1.1.3
> -- THRIFT_VERSION: 0.11.0
> -- ZLIB_VERSION: 1.2.8
> -- ZSTD_VERSION: v1.3.7
> -- Boost version: 1.68.0
> -- Found the following Boost libraries:
> -- regex
> -- system
> -- filesystem
> -- Boost include dir: /Users/Greg/anaconda3/envs/pyarrow-dev/include
> -- Boost libraries:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libboost_regex.dylib/Users/Greg/anaconda3/envs/pyarrow-dev/lib/libboost_system.dylib/Users/Greg/anaconda3/envs/pyarrow-dev/lib/libboost_filesystem.dylib
> Added shared library dependency boost_system_shared:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libboost_system.dylib
> Added shared library dependency boost_filesystem_shared:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libboost_filesystem.dylib
> Added shared library dependency boost_regex_shared:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libboost_regex.dylib
> Added static library dependency double-conversion_static:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libdouble-conversion.a
> -- double-conversion include dir:
> /Users/Greg/anaconda3/envs/pyarrow-dev/include
> -- double-conversion static library:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libdouble-conversion.a
> -- GFLAGS_HOME: /Users/Greg/anaconda3/envs/pyarrow-dev
> -- GFlags include dir: /Users/Greg/anaconda3/envs/pyarrow-dev/include
> -- GFlags static library:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libgflags.a
> Added static library dependency gflags_static:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libgflags.a
> -- RapidJSON include dir: /Users/Greg/anaconda3/envs/pyarrow-dev/include
> -- Found the Flatbuffers library:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libflatbuffers.a
> -- Flatbuffers include dir: /Users/Greg/anaconda3/envs/pyarrow-dev/include
> -- Flatbuffers compiler: /Users/Greg/anaconda3/envs/pyarrow-dev/bin/flatc
> Added static library dependency jemalloc_static:
> /Users/Greg/documents/repos/arrow/cpp/build/jemalloc_ep-prefix/src/jemalloc_ep/dist//lib/libjemalloc_pic.a
> Added shared library dependency jemalloc_shared:
> /Users/Greg/documents/repos/arrow/cpp/build/jemalloc_ep-prefix/src/jemalloc_ep/dist//lib/libjemalloc.dylib
> -- Found hdfs.h at:
> /Users/Greg/documents/repos/arrow/cpp/thirdparty/hadoop/include/hdfs.h
> -- Found the ZLIB shared library:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libz.dylib
> Added shared library dependency zlib_shared:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libz.dylib
> -- SNAPPY_HOME: /Users/Greg/anaconda3/envs/pyarrow-dev
> -- Found the Snappy library:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libsnappy.dylib
> Added static library dependency snappy_static:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libsnappy.a
> -- Found the Brotli library:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libbrotlienc-static.a;/Users/Greg/anaconda3/envs/pyarrow-dev/lib/libbrotlidec-static.a;/Users/Greg/anaconda3/envs/pyarrow-dev/lib/libbrotlicommon-static.a
> Added static library dependency brotli_enc_static:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libbrotlienc-static.a
> Added static library dependency brotli_dec_static:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libbrotlidec-static.a
> Added static library dependency brotli_common_static:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libbrotlicommon-static.a
> Added static library dependency lz4_static:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/liblz4.a
> Added static library dependency zstd_static:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libzstd.a
> -- THRIFT_HOME: /Users/Greg/anaconda3/envs/pyarrow-dev
> -- Thrift version: 0.12.0
> -- Thrift include dir: /Users/Greg/anaconda3/envs/pyarrow-dev/include
> -- Thrift static library:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libthrift.a
> -- Thrift compiler: /Users/Greg/anaconda3/envs/pyarrow-dev/bin/thrift
> -- GLOG_HOME: /Users/Greg/anaconda3/envs/pyarrow-dev
> -- Found the GLog library:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libglog.dylib
> -- Glog include dir: /Users/Greg/anaconda3/envs/pyarrow-dev/include
> -- Glog static library: /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libglog.a
> Added static library dependency glog_static:
> /Users/Greg/anaconda3/envs/pyarrow-dev/lib/libglog.a
> -- CMAKE_C_FLAGS: -Qunused-arguments -ggdb -O0 -Weverything
> -Wno-c++98-compat -Wno-c++98-compat-pedantic -Wno-deprecated
> -Wno-weak-vtables -Wno-padded -Wno-comma -Wno-unused-macros
> -Wno-unused-parameter -Wno-unused-template -Wno-undef -Wno-shadow
> -Wno-switch-enum -Wno-exit-time-destructors -Wno-global-constructors
> -Wno-weak-template-vtables -Wno-undefined-reinterpret-cast
> -Wno-implicit-fallthrough -Wno-unreachable-code-return -Wno-float-equal
> -Wno-missing-prototypes -Wno-documentation-unknown-command
> -Wno-old-style-cast -Wno-covered-switch-default -Wno-cast-align
> -Wno-vla-extension -Wno-shift-sign-overflow -Wno-used-but-marked-unused
> -Wno-missing-variable-declarations -Wno-gnu-zero-variadic-macro-arguments
> -Wconversion -Wno-sign-conversion -Wno-disabled-macro-expansion
> -Wno-format-nonliteral -Wno-missing-noreturn -Wno-gnu-folding-constant
> -Wno-reserved-id-macro -Wno-range-loop-analysis -Wno-double-promotion
> -Wno-undefined-func-template -Wno-zero-as-null-pointer-constant
> -Wno-unknown-warning-option -Werror -Wno-unknown-warning-option -msse4.2
> -maltivec -stdlib=libc++
> -- CMAKE_CXX_FLAGS: -Qunused-arguments -ggdb -O0 -Weverything
> -Wno-c++98-compat -Wno-c++98-compat-pedantic -Wno-deprecated
> -Wno-weak-vtables -Wno-padded -Wno-comma -Wno-unused-macros
> -Wno-unused-parameter -Wno-unused-template -Wno-undef -Wno-shadow
> -Wno-switch-enum -Wno-exit-time-destructors -Wno-global-constructors
> -Wno-weak-template-vtables -Wno-undefined-reinterpret-cast
> -Wno-implicit-fallthrough -Wno-unreachable-code-return -Wno-float-equal
> -Wno-missing-prototypes -Wno-documentation-unknown-command
> -Wno-old-style-cast -Wno-covered-switch-default -Wno-cast-align
> -Wno-vla-extension -Wno-shift-sign-overflow -Wno-used-but-marked-unused
> -Wno-missing-variable-declarations -Wno-gnu-zero-variadic-macro-arguments
> -Wconversion -Wno-sign-conversion -Wno-disabled-macro-expansion
> -Wno-format-nonliteral -Wno-missing-noreturn -Wno-gnu-folding-constant
> -Wno-reserved-id-macro -Wno-range-loop-analysis -Wno-double-promotion
> -Wno-undefined-func-template -Wno-zero-as-null-pointer-constant
> -Wno-unknown-warning-option -Werror -Wno-unknown-warning-option -msse4.2
> -maltivec -stdlib=libc++
> -- Configuring done
> CMake Warning (dev):
> Policy CMP0068 is not set: RPATH settings on macOS do not affect
> install_name. Run "cmake --help-policy CMP0068" for policy details. Use
> the cmake_policy command to set the policy and suppress this warning.
> For compatibility with older versions of CMake, the install_name fields for
> the following targets are still affected by RPATH settings:
> arrow_python_shared
> arrow_shared
> parquet_shared
> plasma_shared
> This warning is for project developers. Use -Wno-dev to suppress it.
> -- Generating done
> -- Build files have been written to:
> /Users/Greg/documents/repos/arrow/cpp/build{code}
> After I run make -j4, the output is:
> {code:java}
> 0%] Built target metadata_fbs
> [ 1%] Performing configure step for 'jemalloc_ep'
> [ 2%] Built target parquet-thrift-deps
> [ 12%] Built target arrow_python_objlib
> [ 19%] Built target plasma_objlib
> [ 19%] Built target arrow_python_static
> CMake Error at
> /Users/Greg/documents/repos/arrow/cpp/build/jemalloc_ep-prefix/src/jemalloc_ep-stamp/jemalloc_ep-configure-DEBUG.cmake:49
> (message):
> Command failed: 1
> './autogen.sh'
> 'AR=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar'
>
> 'CC=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc'
>
> '--prefix=/Users/Greg/documents/repos/arrow/cpp/build/jemalloc_ep-prefix/src/jemalloc_ep/dist/'
> '--with-jemalloc-prefix=je_arrow_'
> '--with-private-namespace=je_arrow_private_' '--disable-tls'
> See also
>
> /Users/Greg/documents/repos/arrow/cpp/build/jemalloc_ep-prefix/src/jemalloc_ep-stamp/jemalloc_ep-configure-*.log
> make[2]: *** [jemalloc_ep-prefix/src/jemalloc_ep-stamp/jemalloc_ep-configure]
> Error 1
> make[1]: *** [CMakeFiles/jemalloc_ep.dir/all] Error 2
> make: *** [all] Error 2
> {code}
> And the output of the jemalloc log file is:
> {code:java}
> configure: error: in
> `/Users/Greg/documents/repos/arrow/cpp/build/jemalloc_ep-prefix/src/jemalloc_ep':
> configure: error: cannot run C compiled programs.
> If you meant to cross compile, use `--host'.
> See `config.log' for more details
> autoconf
> ./configure --enable-autogen
> AR=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ar
>
> CC=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
>
> --prefix=/Users/Greg/documents/repos/arrow/cpp/build/jemalloc_ep-prefix/src/jemalloc_ep/dist/
> --with-jemalloc-prefix=je_arrow_ --with-private-namespace=je_arrow_private_
> --disable-tls
> checking for xsltproc... /usr/bin/xsltproc
> checking for gcc...
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... Error 0 in ./configure
> {code}
> Any help / guidance I can get is appreciated.
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