[Insight-users] Duplicate symbols from OpenJPEG with system GDCM and ITK 4.4

Thu Jul 25 12:10:09 EDT 2013

An additional piece of information. This worked for VV but when I tried to
compile another software that does not have the command
  FIND_PACKAGE(GDCM REQUIRED)
  include(${GDCM_USE_FILE})
I got the error
ld: library not found for -lgdcmDICT

This is because Modules/ThirdParty/GDCM/itk-module-init.cmake does not
include ${GDCM_USE_FILE}, as shown in
${GDCM_SOURCE_DIR}/Examples/CMakeLists.txt.
Simon

On Wed, Jul 24, 2013 at 10:08 PM, Simon Rit
<simon.rit at creatis.insa-lyon.fr>wrote:

> Thanks, after merging your two branches, everything compiles fine.
> Simon
>
>
> On Wed, Jul 24, 2013 at 8:55 PM, Xiaoxiao Liu <xiaoxiao.liu at kitware.com>wrote:
>
>> and this one to exclude ITKReview from building when ITK_USE_REVIEW is
>> turned OFF:
>> http://review.source.kitware.com/#/c/12084/
>>
>>
>> On Wed, Jul 24, 2013 at 1:58 PM, Xiaoxiao Liu <xiaoxiao.liu at kitware.com>wrote:
>>
>>> Will this help?
>>> http://review.source.kitware.com/#/c/12083/
>>>
>>>
>>>
>>> On Wed, Jul 24, 2013 at 12:47 PM, Simon Rit <
>>> simon.rit at creatis.insa-lyon.fr> wrote:
>>>
>>>> Thanks! But itt's not sufficient. The cmake command gives
>>>> -- Enabled ITKOpenJPEG, needed by [ITKGDCM].
>>>>
>>>> I have been a bit further. If I manually remove the dependency to
>>>> OpenJPEG:
>>>> diff --git a/Modules/ThirdParty/GDCM/itk-module.cmake
>>>> b/Modules/ThirdParty/GDCM/itk-module.cmake
>>>> index 37ba9e4..c67a8f5 100644
>>>> --- a/Modules/ThirdParty/GDCM/itk-module.cmake
>>>> +++ b/Modules/ThirdParty/GDCM/itk-module.cmake
>>>> @@ -6,7 +6,6 @@ itk_module(ITKGDCM
>>>>    DEPENDS
>>>>      ITKZLIB
>>>>      ITKExpat
>>>> -    ITKOpenJPEG
>>>>    DESCRIPTION
>>>>      "${DOCUMENTATION}"
>>>>  )
>>>>
>>>> I get :
>>>> /Users/srit/src/itk4/itk/Modules/Nonunit/Review/src/itkJPEG2000ImageIO.cxx:29:12:
>>>> fatal error:
>>>>       'openjpeg.h' file not found
>>>>   #include "openjpeg.h"
>>>>
>>>> I'm quite surprised because ITK_USE_REVIEW and BUILD_TESTING are OFF...
>>>> Anyway, I ignored this (make -k) and I can then compile my software. So the
>>>> dependency to ITKOpenJPEG would have to be removed in ITKGDCM if
>>>> ITK_USE_SYSTEM_GDCM is ON.
>>>>
>>>> As a side note, I tried to remove the compilation of the module ITKGDCM
>>>> but that failed. I also tried to use gdcm as described in its documentation
>>>> but that failed too:
>>>>
>>>> diff --git a/Modules/ThirdParty/GDCM/itk-module-init.cmake
>>>> b/Modules/ThirdParty/GDCM/itk-module-init.cmak
>>>> index c04c639..90cea5f 100644
>>>> --- a/Modules/ThirdParty/GDCM/itk-module-init.cmake
>>>> +++ b/Modules/ThirdParty/GDCM/itk-module-init.cmake
>>>> @@ -3,4 +3,5 @@ mark_as_advanced(ITK_USE_SYSTEM_GDCM)
>>>>
>>>>  if(ITK_USE_SYSTEM_GDCM)
>>>>    find_package(GDCM REQUIRED)
>>>> +  include(${GDCM_USE_FILE})
>>>>  endif()
>>>>
>>>> I hope this (mess) helps...
>>>> Simon
>>>>
>>>>
>>>> On Wed, Jul 24, 2013 at 5:43 PM, Matt McCormick <
>>>> matt.mccormick at kitware.com> wrote:
>>>>
>>>>> Hi Simon,
>>>>>
>>>>> Please try this patch:
>>>>>
>>>>>   http://review.source.kitware.com/#/c/12078/
>>>>>
>>>>> Thanks,
>>>>> Matt
>>>>>
>>>>> On Wed, Jul 24, 2013 at 9:40 AM, Simon Rit
>>>>> <simon.rit at creatis.insa-lyon.fr> wrote:
>>>>> > Hi,
>>>>> > I am trying to build an application (http://vv.creatis.insa-lyon.fr/)
>>>>> under
>>>>> > MacOS with system GDCM (latest version from git) and ITK 4.4. At
>>>>> link time,
>>>>> > I get duplicate symbol errors because itk and gdcm both compile
>>>>> openjpeg,
>>>>> > for example :
>>>>> >
>>>>> > duplicate symbol _j2k_convert_progression_order in:
>>>>> >     /Users/srit/src/itk4/mac64/lib/libitkopenjpeg-4.4.a(j2k.c.o)
>>>>> >     /Users/srit/src/gdcm/mac64-install/lib/libgdcmopenjpeg.a(j2k.c.o)
>>>>> >
>>>>> > I did not find an easy way to fix this. Is there a way to disable
>>>>> the build
>>>>> > of OpenJPEG when gdcm system is used? No matter what I do, the module
>>>>> > ITKOpenJPEG is built when ITK IOs are built...
>>>>> > Thanks in advance,
>>>>> > Simon
>>>>> >
>>>>> > _____________________________________
>>>>> > Powered by www.kitware.com
>>>>> >
>>>>> > Visit other Kitware open-source projects at
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>>>>>
>>>>
>>>>
>>>> _____________________________________
>>>> 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:
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>>>>
>>>
>>>
>>> --
>>>
>>>
>>> ---------------------------------------------
>>> *Xiaoxiao Liu*, Ph.D.
>>> R & D Engineer
>>> Kitware Inc <http://www.kitware.com/>.
>>> Clifton Park, NY
>>> Phone: (518) 881-4924  or  (518) 371-3971 x124
>>>
>>>
>>
>>
>> --
>>
>>
>> ---------------------------------------------
>> *Xiaoxiao Liu*, Ph.D.
>> R & D Engineer
>> Kitware Inc <http://www.kitware.com/>.
>> Clifton Park, NY
>> Phone: (518) 881-4924  or  (518) 371-3971 x124
>>
>>
>> _____________________________________
>> 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
>>
>>
>
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