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wcs build error on Mac OS X Lion #31

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wcs build error on Mac OS X Lion#31
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mdboom

Description

@cdeil
cdeil
opened on Oct 22, 2011

python setup.py install --user

results in an error while trying to install the astropy.wcs._wcs extension (see below).
Is this a known problem with llvm-gcc-4.2 or one specific to the wcs version included in astropy?

In file included from /Users/deil/git/astropy/astropy/wcs/src/wcslib/C/wcs.c:44:
/Users/deil/git/astropy/astropy/wcs/src/wcslib/C/wcsutil.h:227: warning: function declaration isn't a prototype
/Developer/usr/bin/llvm-gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -pipe -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DECHO -DWCSTRIG_MACRO -DASTROPY_WCS_BUILD -D_GNU_SOURCE -DWCSVERSION=4.8.2 -DNDEBUG -UDEBUG -I/Users/deil/Library/Python/2.7/lib/python/site-packages/numpy/core/include -I/Users/deil/git/astropy/astropy/wcs/src/wcslib/C -I/Users/deil/git/astropy/astropy/wcs/src -I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/deil/git/astropy/astropy/wcs/src/wcslib/C/wcserr.c -o build/temp.macosx-10.7-x86_64-2.7/Users/deil/git/astropy/astropy/wcs/src/wcslib/C/wcserr.o
/Users/deil/git/astropy/astropy/wcs/src/wcslib/C/wcserr.c:140: internal compiler error: Segmentation fault: 11
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://developer.apple.com/bugreporter> for instructions.
{standard input}:0:End-of-File not at end of a line
{standard input}:116:End-of-File not at end of a line
{standard input}:unknown:Partial line at end of file ignored
{standard input}:unknown:Undefined local symbol L_.str
{standard input}:unknown:Undefined local symbol L_.str1
{standard input}:unknown:Undefined local symbol L_.str2
error: command '/Developer/usr/bin/llvm-gcc-4.2' failed with exit status 1

Activity

  1. jiffyclub commented on Oct 22, 2011

    @jiffyclub
    jiffyclub
    on Oct 22, 2011
    Contributor

    I'm not getting this same error, but also have not been able to compile the wcs extensions on Lion.

    running build_ext
building 'astropy.wcs._wcs' extension
C compiler: gcc -DNDEBUG -g -O3 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.5.sdk -O -ansi

compile options: '-DECHO -DWCSTRIG_MACRO -DASTROPY_WCS_BUILD -D_GNU_SOURCE -DWCSVERSION=4.8.2 -DNDEBUG -UDEBUG -I/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/numpy/core/include -I/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C -I/Users/jiffyclub/astropy/astropy/wcs/src -I/Library/Frameworks/EPD64.framework/Versions/7.1/include/python2.7 -c'
gcc: /Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:36:19: error: stdio.h: No such file or directory
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:37:20: error: stdlib.h: No such file or directory
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:38:20: error: string.h: No such file or directory
In file included from /Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:41:
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcsprintf.h:123: error: expected ')' before '*' token
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c: In function 'wcserr_set':
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:75: warning: incompatible implicit declaration of built-in function 'calloc'
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c: In function 'wcserr_copy':
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:104: warning: incompatible implicit declaration of built-in function 'memset'
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:110: warning: incompatible implicit declaration of built-in function 'memcpy'
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:36:19: error: stdio.h: No such file or directory
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:37:20: error: stdlib.h: No such file or directory
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:38:20: error: string.h: No such file or directory
In file included from /Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:41:
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcsprintf.h:123: error: expected ')' before '*' token
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c: In function 'wcserr_set':
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:75: warning: incompatible implicit declaration of built-in function 'calloc'
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c: In function 'wcserr_copy':
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:104: warning: incompatible implicit declaration of built-in function 'memset'
/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c:110: warning: incompatible implicit declaration of built-in function 'memcpy'
error: Command "gcc -DNDEBUG -g -O3 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.5.sdk -O -ansi -DECHO -DWCSTRIG_MACRO -DASTROPY_WCS_BUILD -D_GNU_SOURCE -DWCSVERSION=4.8.2 -DNDEBUG -UDEBUG -I/Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/numpy/core/include -I/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C -I/Users/jiffyclub/astropy/astropy/wcs/src -I/Library/Frameworks/EPD64.framework/Versions/7.1/include/python2.7 -c /Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.c -o build/temp.macosx-10.5-x86_64-2.7/Users/jiffyclub/astropy/astropy/wcs/src/wcslib/C/wcserr.o" failed with exit status 1

    This error is caused by the fact that on Lion there is no /Developer/SDKs/MacOSX10.5.sdk. I'm not sure why 10.5 being grabbed, but it could be because of my Python version. If I try to compile with the 10.6 or 10.7 SDKs I get the same error as cdeil.

  2. jiffyclub commented on Oct 22, 2011

    @jiffyclub
    jiffyclub
    on Oct 22, 2011
    Contributor

    It looks like this has been a common issue for projects on Lion. On Lion the compilers default to llvm-gcc:

     >:gcc --version
i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)
Copyright (C) 2007 Free Software Foundation, Inc.

    Here's a thread discussing this for another project: http://web.archiveorange.com/archive/v/yj6N4VBSrwkOaZ5VhQtw

    Some bit of wcserr.c does not agree with this compiler, maybe the ellipsis on line 64?

    The regular gcc compilers are still available on Lion as /usr/bin/gcc-4.2 and /usr/bin/gcc++-4.2 so by setting CC and CXX to these those of us on Lion may be able to get wcs compiled. It would be nice to have it work with the default compilers, though.

  3. cdeil commented on Oct 22, 2011

    @cdeil
    cdeil
    on Oct 22, 2011
    MemberAuthor

    Yes, it works with the system GCC and also with the system CLANG on Lion.
    So it's not really a problem now, although I think with the next XCode no GCC will be shipped anymore.

    Maybe this is a bug in i686-apple-darwin11-llvm-gcc-4.2 or something in wcserr.c is not quite C standard-conform?

  4. jiffyclub commented on Oct 22, 2011

    @jiffyclub
    jiffyclub
    on Oct 22, 2011
    Contributor

    With the EPD I also found it necessary to set CFLAGS = "-isysroot /Developer/SDKs/MacOSX10.7.sdk" because the EPD is compiled with the 10.5 SDK which is not available on Lion. We should probably fix this as well, since chances are fairly high that people will be trying to install astropy with the EPD and Lion.

  5. ghost assigned
    mdboom
    on Oct 26, 2011

  6. mdboom commented on Oct 26, 2011

    @mdboom
    mdboom
    on Oct 26, 2011
    Contributor

    I'm trying to get access to a Lion machine to reproduce this and get to the bottom of it. (For what it's worth, it builds find with llvm-clang on Linux).

    The ellipsis is standard C -- I'm not sure if there's a way around it, but I'll see if I can come up with anything.

    @cdeil: When you say it works with the system CLANG, how are you setting that up? The default compiler is llvm-gcc which is clang with a gcc argument-handling compatibility layer, so I'm surprised one works and the other doesn't.

  7. mdboom commented on Oct 26, 2011

    @mdboom
    mdboom
    on Oct 26, 2011
    Contributor

    Ugh -- of course I'm confused. clang != llvm-gcc, so I suppose it's not surprising that one works and the other doesn't.

  8. cdeil commented on Oct 26, 2011

    @cdeil
    cdeil
    on Oct 26, 2011
    MemberAuthor

    This is how I invoked clang and the build worked:

    export CC=CLANG; python setup.py build

  9. jiffyclub commented on Oct 27, 2011

    @jiffyclub
    jiffyclub
    on Oct 27, 2011
    Contributor

    I can help provide a Lion machine if you have trouble getting hold of one.

  10. mdboom commented on Oct 31, 2011

    @mdboom
    mdboom
    on Oct 31, 2011
    Contributor

    It seems like a legitimate compiler bug. I have filed a report with Apple as issue #10370713.

    I have a patch to fix this -- setup.py detects the broken compiler version and if found, uses clang instead. See pull request #40.

  11. eteq
    closed this as completedin d2b2350on Oct 31, 2011
  12. keflavich
    added a commit that references this issue on Oct 9, 2013

    Merge pull request astropy#40 from mdboom/osx/llvm-gcc-crash

    6aade47
  13. eteq
    added a commit that references this issue on May 20, 2014

    Merge pull request #31 from astrofrog/coordinates-docs-representations

    f25adbf
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