[Insight-developers] [ITK Community] Problem building ITK

Thu Feb 6 23:15:19 EST 2014

Hi Brad,

You are officially a genius!

When I turned "Module_SCIFIO" on in Insight-4.5.0, I was still getting the SCIFIO problem (I realized this later because it took many hours to build).  But it worked when I followed your fix to change the line
target_link_libraries(SCIFIO  ${ImageBase_LIBRARIES})

to
target_link_libraries(SCIFIO  ${ITKIOImageBase_LIBRARIES})

in the file Modules/Remote/SCIFIO/src/CMakeLists.txt.

What do we need to do to get this change merged?

Thanks!
Dirk

On Feb 6, 2014, at 7:06 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
 wrote:

> Dirk here is a fix for SCIFIO upstream:
> https://github.com/scifio/scifio-imageio/pull/8
> 
> 
> On Feb 6, 2014, at 4:32 PM, Padfield, Dirk R (GE Global Research) <padfield at research.ge.com> wrote:
> 
>> Hi All,
>> 
>> I just got everything to work.  I needed to set the OSX variables in CMake.  When I did this for the git version, it all compiled correctly.  Below are the three needed settings.  Where is the best place where we can document this for others?
>> 
>> Thanks,
>> Dirk
>> 
>> CMAKE_OSX_SYSROOT:PATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk 
>> 
>> CMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9 
>> 
>> CMAKE_OSX_ARCHITECTURES:STRING=x86_64
>> 
>> 
>> On Feb 6, 2014, at 1:47 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>
>> wrote:
>> 
>>> Dirk,
>>> 
>>> 1) You are not using GNU's GCC. Apple has LLVM  alias as gcc.
>>> 
>>> 2)  I think you are on the right track with changing the c++ standard library. However this should be a flag for the compiler too. Before doing a fresh configure to a CLEAN build directory, set the CXX_FLAGS environmental variable to "-stdlib=libc++", with "export CXX_FLAGS=-stdlib=libc++". CMake should pick that up and place it in the CMAKE_CXX_FLAGS variable, also I think SCIFIO does some type of external project, so hopefully this environmental variable will help it get propagated there too.
>>> 
>>> Good luck,
>>> Brad
>>> 
>>> On Feb 6, 2014, at 1:01 PM, Padfield, Dirk R (GE Global Research) <padfield at research.ge.com> wrote:
>>> 
>>>> Hi Matt,
>>>> 
>>>> I started from a fresh build tree several times yesterday just to make sure (although I will try a fresh source tree today too).  I wiped the entire build tree and started from scratch twice.  I also built 4.5.0 from scratch yesterday, and it worked fine until I enabled "Module_SCIFIO" at which point it gave the same error as the git version.  At least it's consistent!
>>>> 
>>>> I tried adding the following flag to the linker 
>>>> 
>>>> -stdlib=libstdc++
>>>> 
>>>> as suggested in http://mathematica.stackexchange.com/questions/34692/mathlink-linking-error-after-os-x-10-9-mavericks-upgrade, but that didn't help.  I'm not on OSX 10.9, but I am using Xcode 5.0.2.
>>>> 
>>>> Thanks,
>>>> Dirk
>>>> 
>>>> 
>>>> ________________________________________
>>>> From: Matt McCormick [matt.mccormick at kitware.com]
>>>> Sent: Thursday, February 06, 2014 12:50 PM
>>>> To: Padfield, Dirk R (GE Global Research)
>>>> Cc: insight-developers at itk.org
>>>> Subject: Re: [ITK Community] [Insight-developers] Problem building ITK
>>>> 
>>>> Hi Dirk,
>>>> 
>>>> Starting from a a fresh source tree and a fresh build tree, does the
>>>> problem persist?
>>>> 
>>>> Thanks,
>>>> Matt
>>>> 
>>>> On Thu, Feb 6, 2014 at 12:01 PM, Padfield, Dirk R (GE Global Research)
>>>> <padfield at research.ge.com> wrote:
>>>>> Hi All,
>>>>> 
>>>>> I have a problem building ITK on my Mac that I wanted to ask about.  ITK builds all the way to the end but then fails when linking
>>>>> 
>>>>> Linking CXX shared library ../../../../lib/libitkSCIFIO-4.6.dylib
>>>>> Undefined symbols for architecture x86_64:
>>>>> 
>>>>> This is followed by a string of errors inside of SCIFIOImageIO.
>>>>> 
>>>>> Here are my specs:
>>>>> Mac OSX 10.8.5 (Mountain Lion)
>>>>> Xcode 5.0.2
>>>>> CMake 2.8.11
>>>>> ITK latest git pull with:
>>>>> BUILD_SHARED_LIBS = ON
>>>>> CMAKE_BUILD_TYPE = RelWithDebInfo
>>>>> 
>>>>> Also, I am building with "Eclipse CDT4 - Unix Makefiles" and "specify native compilers" of "C = gcc" and "C++ = g++".
>>>>> 
>>>>> When running CMake on this version, there is no flag for "Module_SCIFIO".
>>>>> 
>>>>> By the way, I also tried downloading Insight-4.5.0 and building it exactly the same way, and it worked fine.  I noticed that in CMake for 4.5.0, it has a flag "Module_SCIFIO", which is off by default.  But if I turn this flag on and rebuild, I get the same issue described above.
>>>>> 
>>>>> Does anyone have any ideas?
>>>>> 
>>>>> Thanks,
>>>>> Dirk
>>>>> _______________________________________________
>>>>> 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://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-developers
>>>>> _______________________________________________
>>>>> Community mailing list
>>>>> Community at itk.org
>>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/community
>>>> _______________________________________________
>>>> 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://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-developers
>>> 
>> 
> 