[Insight-users] How to get ITK4+ and Python wrapping to work on Mac OSX (10.7)?

Mon Nov 19 12:52:24 EST 2012

On Mon, Nov 12, 2012 at 7:53 PM, Ahmed Halaweish, Ph.D.
<ahmed.halaweish at duke.edu> wrote:
>    I'm trying to get ITK 4.1 and ITK 4.2 + Python wrapping to work on my
> macbook and mac pro desktop (both running 10.7) without any luck.

On Fri, Nov 16, 2012 at 9:42 AM, Ahmed Halaweish, Ph.D. <
ahmed.halaweish at duke.edu> wrote:
>
> Here are the errors I have been getting ...
>
> /bin/sh: /Users/Documents/DIAL-Code/gccxml-BUILD: is a directory
>
> make[2]: *** [Wrapping/Modules/ITKCommon/vcl_complex.xml] Error 126
>
> make[1]: ***
[Wrapping/Modules/ITKCommon/CMakeFiles/ITKCommonGccXML.dir/all] Error 2

You might try running

make VERBOSE=1

(preferably without any -j flag) to see what command is failing.

Mark

On Fri, Nov 16, 2012 at 9:42 AM, Ahmed Halaweish, Ph.D. <
ahmed.halaweish at duke.edu> wrote:

>  Here are the errors I have been getting ...
>
>  /bin/sh: /Users/Documents/DIAL-Code/gccxml-BUILD: is a directory
>
> make[2]: *** [Wrapping/Modules/ITKCommon/vcl_complex.xml] Error 126
>
> make[1]: ***
> [Wrapping/Modules/ITKCommon/CMakeFiles/ITKCommonGccXML.dir/all] Error 2
>
>
>  I have implemented the comments from Mark into the build/compile process
> and still get the same results.
>
>
>  Thanks in advance for any tips and suggestions ... Cheers.
>
>  ahmed.halaweish at duke.edu
> telephone:       919-684-7927
>    ------------------------------
> *From:* Mark Tsuchida [marktsuchida at gmail.com]
> *Sent:* Monday, November 12, 2012 8:28 PM
> *To:* Matt McCormick
> *Cc:* Ahmed Halaweish, Ph.D.; insight-users at itk.org
> *Subject:* Re: [Insight-users] How to get ITK4+ and Python wrapping to
> work on Mac OSX (10.7)?
>
>   On Mon, Nov 12, 2012 at 7:53 PM, Ahmed Halaweish, Ph.D.
> <ahmed.halaweish at duke.edu> wrote:
> >    I'm trying to get ITK 4.1 and ITK 4.2 + Python wrapping to work on my
> > macbook and mac pro desktop (both running 10.7) without any luck. I
> always
> > seem to get a make: error 2 in the Wrapping/Modules section of the
> > compilation process.
>
>  I don't know if the following applies to your case (would need to see
> the error messages you got), but here is what I have found necessary trying
> to compile WrapITK for Python on Lion.
>
>  Xcode comes with two sets of compilers (clan/clang++ and
> llvm-gcc/llvm-g++).
> While either appears to work for compiling ITK itself, I have only been
> able to get llvm-gcc to work for WrapITK.
>
>  By default, cmake chooses /usr/bin/gcc (a symlink to llvm-gcc) and
> /usr/bin/c++ (a symlink to clang++), which is not just inconsistent but
> causes some weird problems with GCC_XML, a program required for generating
> the wrappers.
>
>
>  I have been able to get WrapITK to compile by following these steps
> (Lion, Xcode 4.5, cmake 2.8.8):
>
>  1. Download GCC_XML from
> http://itk.org/files/gccxml/gccxml-2012-08-08.tar.bz2 (see the thread in
> this list today titled "build fails to download gccxml (4.2.1)").
>
>  2. Configure GCC_XML with the following, build, and install (to
> /usr/local).
>
>  CMAKE_BUILD_TYPE=Release
> CMAKE_C_COMPILER=/usr/bin/llvm-gcc
> CMAKE_CXX_COMPILER=/usr/bin/llvm-g++
>
>  [If the compilers are not explicitly set here, building WrapITK will
> fail. If they are set to clang/clang++, configuration of GCC_XML will fail.]
>
>  3. Configure ITK 4.2.1. First set the compilers:
>
>   CMAKE_C_COMPILER=/usr/bin/llvm-gcc
> CMAKE_CXX_COMPILER=/usr/bin/llvm-g++
>
>  [If you are using ccmake, all other settings will be reset after
> changing the compiler.]
>
>  Then,
>  BUILD_SHARED_LIBS=ON
> BUILD_EXAMPLES=OFF   # Not the point here, but this is what I did
> BUILD_TESTING=OFF    # Ditto.
>
>  Add
> ITK_WRAP_PYTHON=ON
>
>  This (if using ccmake) will disclose additional options.
> We need to set
>
>  ITK_USE_SYSTEM_GCCXML=ON
>
>  to use the GCC_XML installed above in 2.
>
>  Also, they Python paths are usually detected incorrectly (the paths may
> exist but may be wrong or belong to a different installation of Python). In
> my case, I am using Python 2.7 compiled from the source, which is installed
> under /Library (as is Python 2.7 from the python.org installer package).
> It is best to set all of the following explicitly, or at least check that
> they are correct:
>
>
> PYTHON_INCLUDE_DIR=/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
>
> PYTHON_LIBRARY=/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config/libpython2.7.dylib
>
> PY_SITE_PACKAGES_PATH=/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
>
> PYTHON_EXECUTABLE=/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
>
>  (end of steps)
>
>  I have not tried building ITK from the git head. It is probably
> sufficient to just set the compilers in ITK's config and let those
> propagate to GCC_XML's, rather than doing a separate build and installation
> of GCC_XML. At least, that used to work with ITK 4.2.1 before the GCC_XML
> repository got moved.
>
>  Hope this helps,
>
>  Mark
>
>
>
>
> On Mon, Nov 12, 2012 at 1:25 PM, Matt McCormick <
> matt.mccormick at kitware.com> wrote:
>
>> Hi AFH,
>>
>> Could you please reply with the error message that you get.
>>
>> Thanks,
>> Matt
>>
>> On Mon, Nov 12, 2012 at 7:53 PM, Ahmed Halaweish, Ph.D.
>> <ahmed.halaweish at duke.edu> wrote:
>> > All,
>> >    I'm trying to get ITK 4.1 and ITK 4.2 + Python wrapping to work on my
>> > macbook and mac pro desktop (both running 10.7) without any luck. I
>> always
>> > seem to get a make: error 2 in the Wrapping/Modules section of the
>> > compilation process.
>> >
>> > Here are the variables I set in cmake:
>> > BUILD_SHARED_LIBS = ON
>> > CMAKE_BUILD_TYPE = Release
>> > ITK_USE_REVIEW = ON
>> > ITK_WRAPPING = ON
>> > ITK_WRAP_PYTHON = ON
>> >
>> > If anyone has had any luck with this, please do share any tips or
>> pointers.
>> >
>> > Cheers
>> > AFH
>> >
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