[Insight-users] ITK 4.3.2 compilation with python wrappers: problem with gccxml

Tue Apr 30 02:23:51 EDT 2013

Hello,

I tried to compile with gcc 4.4.7 and gcc 4.6.4 In both cases I get this 
error:

[ 21%] Generating vcl_complex.xml
In file included from /usr/include/endian.h:60,
                  from /usr/include/ctype.h:40,
                  from 
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.4.7/../../../../include/c++/4.4.7/cctype:44,
                  from 
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h:44,
                  from 
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.4.7/../../../../include/c++/4.4.7/ios:42,
                  from 
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.4.7/../../../../include/c++/4.4.7/ostream:40,
                  from 
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.4.7/../../../../include/c++/4.4.7/iostream:40,
                  from 
/localdata/martin/setup_files/InsightToolkit-4.3.2/Modules/Core/Common/include/itkSmartPointer.h:21,
                  from 
/localdata/martin/setup_files/InsightToolkit-4.3.2/Modules/Core/Common/include/itkLightObject.h:21,
                  from 
/localdata/martin/setup_files/InsightToolkit-4.3.2/Modules/Core/Common/include/itkObject.h:31,
                  from 
/localdata/martin/setup_files/InsightToolkit-4.3.2/Modules/Core/Common/include/itkCommand.h:21,
                  from 
/localdata/martin/setup_files/InsightToolkit-4.3.2/build/Wrapping/Modules/ITKCommon/vcl_complex.cxx:1:
/usr/include/bits/byteswap.h: In function 'unsigned int 
__bswap_32(unsigned int)':
/usr/include/bits/byteswap.h:47: error: '__builtin_bswap32' was not 
declared in this scope
/usr/include/bits/byteswap.h: In function '__uint64_t 
__bswap_64(__uint64_t)':
/usr/include/bits/byteswap.h:111: error: '__builtin_bswap64' was not 
declared in this scope
make[2]: *** [Wrapping/Modules/ITKCommon/vcl_complex.xml] Error 1
make[1]: *** 
[Wrapping/Modules/ITKCommon/CMakeFiles/ITKCommonGccXML.dir/all] Error 2
make: *** [all] Error 2

On 29.04.2013 15:55, Bradley Lowekamp wrote:
> Hello,
>
> I am able to build it on my Redhat 6 system with gcc 4.4.7 and gcc 4.7.2.
>
> I don't think gcc_xml support gcc 4.8.
>
> In my build directory I see files like the following:
>
> ITK-build/Wrapping/Generators/GccXML/gccxml/src/GCC_XML/GCC_XML/Support/GCC/4.?/gccxml_builtins.h
>
> Where the gcc version goes from 4.0 to 4.7.
>
> I believe that a freshly upgraded Arch Linux  is close to the opposite side of the stability spectrum as Redhat. So you are quite on the bleeding edge of things. Are you up able to obtain an older compiler that has actually been officially release by gcc?
>
> Brad
>
> On Apr 29, 2013, at 9:40 AM, Martin Schober <m.schober at fz-juelich.de> wrote:
>
>> What is the gcc version you were able to compile itk with?
>>
>> My configuration options to build itk:
>> BUILD_EXAMPLES OFF
>> BUILD_SHARED_LIBS ON
>> BUILD_TESTING OFF
>> CMAKE_BUILD_TYPE Release
>> INSTALL_WRAP_ITK_COMPATIBILITY ON
>> ITKV3_COMPATIBILITY ON
>> ITK_BUILD_ALL_MODULES ON
>> ITK_USE_SYSTEM_SWIG OFF
>> ITK_WRAP_DIMS 2;3
>> ITK_WRAP_DOC OFF
>> ITK_WRAP_EXPLICIT OFF
>> ITK_WRAP_GCCXML ON
>> ITK_WRAP_JAVA OFF
>> ITK_WRAP_PERL OFF
>> ITK_WRAP_PYTHON ON
>> ITK_WRAP_RUBY OFF
>> ITK_WRAP_SWIGINTERFACE ON
>> ITK_WRAP_TCL OFF
>> ITK_WRAP_complex_double OFF
>> ITK_WRAP_complex_float OFF
>> ITK_WRAP_covariant_vector_doub OFF
>> ITK_WRAP_covariant_vector_floa OFF
>> ITK_WRAP_double OFF
>> ITK_WRAP_float ON
>> ITK_WRAP_rgb_unsigned_char ON
>> ITK_WRAP_rgb_unsigned_short OFF
>> ITK_WRAP_rgba_unsigned_char OFF
>> ITK_WRAP_rgba_unsigned_short OFF
>> ITK_WRAP_signed_char ON
>> ITK_WRAP_signed_long OFF
>> ITK_WRAP_signed_short OFF
>> ITK_WRAP_unsigned_char ON
>> ITK_WRAP_unsigned_long OFF
>> ITK_WRAP_unsigned_short OFF
>> ITK_WRAP_vector_double OFF
>> ITK_WRAP_vector_float            ON
>>
>> I tried both versions of gccxml: system and itk built.
>> My gcc version is the system compiler. I installed it with pacman -S gcc on arch-linux operation system.
>> My cmake version is 2.8.10.2
>>
>>
>> On 29.04.2013 15:14, Bradley Lowekamp wrote:
>>> Hello Martin,
>>>
>>> I was just able to build ITK with ITK_WRAP_PYTHON and shared libraries turned on without a problem from the master branch. You indicate that you are using a pre-release version of the compiler, so I am a little skeptical that the problem is with ITK.
>>>
>>> What configuration options did you set?
>>>
>>> Are you using the version of gcc_xml that get built with ITK?
>>>
>>> Is that pre-release version of gcc the system compiler? If you use the system compiler do you get the same error?
>>>
>>> What version of CMake are you using?
>>>
>>> Thanks for the the additional info,
>>> Brad
>>>
>>> On Apr 29, 2013, at 8:13 AM, Martin Schober <m.schober at fz-juelich.de> wrote:
>>>
>>>> I tried compiling ITK 4.3.2 with ITK python wrappers. I use gcc (GCC)
>>>> 4.8.0 20130411 (prerelease) in arch-linux.
>>>>
>>>> The compilation aborts with the following error:
>>>>
>>>> [ 36%] Generating vcl_complex.xml
>>>> gccxml_cc1plus: error: gccxml_builtins.h: No such file or directory
>>>>
>>>> Are there any ideas to fix this problem?
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------------------------
>>>> ------------------------------------------------------------------------------------------------
>>>> Forschungszentrum Juelich GmbH
>>>> 52425 Juelich
>>>> Sitz der Gesellschaft: Juelich
>>>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
>>>> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
>>>> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
>>>> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>>>> Prof. Dr. Sebastian M. Schmidt
>>>> ------------------------------------------------------------------------------------------------
>>>> ------------------------------------------------------------------------------------------------
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://www.itk.org/mailman/listinfo/insight-users