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

Fri Nov 16 12:42:43 EST 2012

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<mailto: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<http://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<mailto: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<mailto: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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