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

[Simon Rit]

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
> >
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