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  1. Apache Arrow
  2. ARROW-7033

[C++] Error in./configure step for jemalloc when building on OSX 10.14.6

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 0.16.0
    • Component/s: C++

      Description

      Hello. I'm trying to build the C++ part of Apache Arrow (as a first step to possible contributions). I'm following the C++ Development instructions, but running into an error early. I also looked at ARROW-4935, but the cause there seems different, so I'm opening a new bug report.

      I'm on MacOS 10.14.6. I have the XCode cli tools installed (via xcode-select), and installed the other dependencies with Homebrew, giving it the cpp/Brewfile. I want to be able to run the tests, so I'm configuring a debug build with:

        cmake -DCMAKE_BUILD_TYPE=Debug -DARROW_BUILD_TESTS=ON ..

      from an out-of-source build, in a cpp/debug directory. Then, running make, I get very quickly the following error:

      $ make
      [ 0%] Performing configure step for 'jemalloc_ep'
      CMake Error at /Users/chrish/Code/arrow/cpp/debug/jemalloc_ep-prefix/src/jemalloc_ep-stamp/jemalloc_ep-configure-DEBUG.cmake:49 (message):
      {{ Command failed: 1}}'./configure' 'AR=/Library/Developer/CommandLineTools/usr/bin/ar' 'CC=/Library/Developer/CommandLineTools/usr/bin/cc' '-prefix=/Users/chrish/Code/arrow/cpp/debug/jemalloc_ep-prefix/src/jemalloc_ep/dist/' 'with-jemalloc-prefix=je_arrow_' 'with-private-namespace=je_arrow_private_' 'without-export' 'disable-cxx' 'disable-libdl' 'disable-initial-exec-tls'See also/Users/chrish/Code/arrow/cpp/debug/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

      Looking into the log file as suggested, I see:

      configure: error: in `/Users/chrish/Code/arrow/cpp/debug/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 

      ... which seems a bit suspicuous. Running the ./configure invocation manually, I get the same error:

      $ './configure' 'AR=/Library/Developer/CommandLineTools/usr/bin/ar' 'CC=/Library/Developer/CommandLineTools/usr/bin/cc' '-prefix=/Users/chrish/Code/arrow/cpp/debug/jemalloc_ep-prefix/src/jemalloc_ep/dist/' 'with-jemalloc-prefix=je_arrow_' 'with-private-namespace=je_arrow_private_' 'without-export' 'disable-cxx' 'disable-libdl' '-disable-initial-exec-tls'
      checking for xsltproc... /usr/bin/xsltproc
      checking for gcc... /Library/Developer/CommandLineTools/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... configure: error: in `/Users/chrish/Code/arrow/cpp/debug/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{{}}

      Digging into config.log, I see:

      configure:3213: checking whether we are cross compiling
      configure:3221: /Library/Developer/CommandLineTools/usr/bin/cc -o conftest conftest.c >&5
      conftest.c:9:10: fatal error: 'stdio.h' file not found
      #include <stdio.h>
      ^~~~~~~~~
      1 error generated.
      configure:3225: $? = 1
      configure:3232: ./conftest
      ./configure: line 3234: ./conftest: No such file or directory
      configure:3236: $? = 127
      configure:3243: error: in `/Users/chrish/Code/arrow/cpp/debug/jemalloc_ep-prefix/src/jemalloc_ep':
      configure:3245: error: cannot run C compiled programs.
      If you meant to cross compile, use `--host'.

      (Relevant bit in bold.) Well, that would make more sense, at least. I create a close-enough conftest.c by hand:

      #include <stdio.h>

      {{int main(void) { return 0; }}}

      and try to compile it with the same command-line invocation:

      $  /Library/Developer/CommandLineTools/usr/bin/cc -o conftest conftest.c

      I get that same error:

      conftest.c:1:10: fatal error: 'stdio.h' file not found
      #include <stdio.h>
      ^~~~~~~~~
      1 error generated.

      However, I also have a cc in /usr/bin. If I try that one instead, things works:

      $ /usr/bin/cc -o conftest conftest.c
      $ ls -l conftest
      -rwxr-xr-x 1 chrish staff 4,2K oct 30 16:03 conftest*
      $ ./conftest

      (No error compiling or running conftest.c)

      The two executable seem to be the same compiler (or at least the exact same version):

      {{$ /usr/bin/cc --version
      Apple LLVM version 10.0.1 (clang-1001.0.46.4)
      Target: x86_64-apple-darwin18.7.0
      Thread model: posix
      InstalledDir: /Library/Developer/CommandLineTools/usr/bin}}

      {{$ /Library/Developer/CommandLineTools/usr/bin/cc --version
      Apple LLVM version 10.0.1 (clang-1001.0.46.4)
      Target: x86_64-apple-darwin18.7.0
      Thread model: posix
      InstalledDir: /Library/Developer/CommandLineTools/usr/bin}}{{}}

      So... I guess at least for me, Apple's Clang works correctly only if invoked from the /usr/bin path. Any reason why the configure, etc. scripts make a special effort to invoke it from /Library/Developer/CommandLineTools/usr/bin, if it's also available in /usr/bin (which is even in the path by default). How do I fix this, so others don't run into that problem too? Thanks!

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              • Assignee:
                kou Kouhei Sutou
                Reporter:
                chrish42 Christian Hudon
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