[ITK] [ITK-users] Problem compiling ITK4.8 - MINCIOTransform does not seem to exist

Francois Budin fbudin at email.unc.edu
Thu Jul 9 13:58:36 EDT 2015 

Indeed, compiling commit 88f45f624275986a2ec3b07482d55bee5222d789 
worked. Thanks!

Francois

On 07/09/2015 12:26 PM, Johnson, Hans J wrote:
> Francois,
>
> I think I merged the patch that fixes this earlier this morning.
>
> Hans
>
> ========================================================================
> Hans J. Johnson, Ph.D.,  Associate Professor
> Electrical and Computer Engineering (Primary), Biomedical 
> Engineering, Psychiatry
> hans-johnson at uiowa.edu <mailto:hans-johnson at uiowa.edu>
> (319) 621 7185 (cell)
> (319) 384 3538  ECE Phone (Primary)
> (319) 353 8587 Psychiatry Phone (Secondary)
>
> 4316 Seamans Center
> Iowa City, IA 52242
>
>> On Jul 9, 2015, at 11:22 AM, Francois Budin <fbudin at email.unc.edu 
>> <mailto:fbudin at email.unc.edu>> wrote:
>>
>> Hello everyone,
>>
>> I am trying to compile ITK4.8 with the following options:
>>      -DBUILD_TESTING:BOOL=ON \
>>      -DCMAKE_BUILD_TYPE:STRING=Release \
>>      -DBUILD_SHARED_LIBS:BOOL=ON \
>>      -DModule_ITKIODCMTK:BOOL=ON \
>>      -DModule_ITKIOPhilipsREC=ON \
>>      -DModule_ITKIOMINC=ON \
>>      -DModule_MGHIO:BOOL=ON \
>>      -DITKV3_COMPATIBILITY:BOOL=OFF \
>>      -DModule_ITKReview:BOOL=ON \
>>      -DVTK_DIR:PATH=${VTKConfigDIR} \
>>      -DModule_ITKVtkGlue:BOOL=ON
>>
>>
>> I get the following error message when it tries to compile the examples:
>>
>> Linking CXX executable ../../bin/TransformReadWrite
>> cd 
>> /tools/devel/linux/ITKv4/InsightToolkit-Auto-4.8.0-build/Examples/IO 
>> && /NIRAL/tools/CMake/cmake-3.1.0/bin/cmake -E cmake_link_script 
>> CMakeFiles/TransformReadWrite.dir/link.txt --verbose=1
>> /usr/bin/c++     -Wall -Wno-long-double -Wcast-align 
>> -Wdisabled-optimization -Wextra -Wformat=2 -Winvalid-pch 
>> -Wno-format-nonliteral -Wpointer-arith -Wshadow -Wunused 
>> -Wwrite-strings -funit-at-a-time -Wno-strict-overflow -Wno-deprecated 
>> -Wno-invalid-offsetof -Woverloaded-virtual -Wstrict-null-sentinel 
>>  -msse2  -msse2 -O3 -DNDEBUG 
>> CMakeFiles/TransformReadWrite.dir/TransformReadWrite.cxx.o  -o 
>> ../../bin/TransformReadWrite -rdynamic ../../lib/libITKIOLSM-4.8.so.1 
>> ../../lib/libITKDICOMParser-4.8.so.1 ../../lib/libITKIOMesh-4.8.so.1 
>> ../../lib/libITKIOCSV-4.8.so.1 ../../lib/libITKIODCMTK-4.8.so.1 
>> ../../lib/libITKIOHDF5-4.8.so.1 
>> ../../Modules/ThirdParty/MINC/ITKMINC2_ExternalProject-build/libitk_minc2.a 
>> ../../lib/libITKIOMINC-4.8.so.1 ../../lib/libITKIOMRC-4.8.so.1 
>> ../../lib/libITKIOPhilipsREC-4.8.so.1 
>> ../../lib/libITKOptimizersv4-4.8.so.1 ../../lib/libITKReview-4.8.so.1 
>> ../../lib/libITKVideoIO-4.8.so.1 ../../lib/libITKVtkGlue-4.8.so.1 
>> ../../lib/libitkMGHIO-4.8.so.1 ../../lib/libITKgiftiio-4.8.so.1 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmdata.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmimage.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmimgle.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmjpeg.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmjpls.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmnet.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmpstat.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmqrdb.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmsr.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libdcmtls.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libijg12.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libijg16.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libijg8.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/liboflog.so 
>> ../../Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib/libofstd.so 
>> ../../Modules/ThirdParty/MINC/ITKMINC2_ExternalProject-build/libitk_minc2.a 
>> ../../lib/libITKIOBMP-4.8.so.1 ../../lib/libITKIOBioRad-4.8.so.1 
>> ../../lib/libITKIOGDCM-4.8.so.1 ../../lib/libitkgdcmMSFF-4.8.so.1 
>> ../../lib/libitkgdcmDICT-4.8.so.1 ../../lib/libitkgdcmIOD-4.8.so.1 
>> ../../lib/libitkgdcmDSED-4.8.so.1 ../../lib/libitkgdcmCommon-4.8.so.1 
>> ../../lib/libITKIOGIPL-4.8.so.1 ../../lib/libITKIOJPEG-4.8.so.1 
>> ../../lib/libITKIOTIFF-4.8.so.1 ../../lib/libitktiff-4.8.so.1 
>> ../../lib/libitkjpeg-4.8.so.1 ../../lib/libITKIOMeta-4.8.so.1 
>> ../../lib/libITKIONIFTI-4.8.so.1 ../../lib/libITKniftiio-4.8.so.1 
>> ../../lib/libITKznz-4.8.so.1 ../../lib/libITKIONRRD-4.8.so.1 
>> ../../lib/libITKNrrdIO-4.8.so.1 ../../lib/libITKIOPNG-4.8.so.1 
>> ../../lib/libitkpng-4.8.so.1 ../../lib/libITKIOStimulate-4.8.so.1 
>> ../../lib/libITKIOVTK-4.8.so.1 ../../lib/libITKLabelMap-4.8.so.1 
>> ../../lib/libITKQuadEdgeMesh-4.8.so.1 
>> ../../lib/libITKBiasCorrection-4.8.so.1 
>> ../../lib/libITKPolynomials-4.8.so.1 ../../lib/libITKBioCell-4.8.so.1 
>> ../../lib/libITKIOSpatialObjects-4.8.so.1 
>> ../../lib/libITKIOXML-4.8.so.1 ../../lib/libITKEXPAT-4.8.so.1 
>> ../../lib/libITKFEM-4.8.so.1 ../../lib/libITKMetaIO-4.8.so.1 
>> ../../lib/libITKOptimizers-4.8.so.1 
>> ../../lib/libITKIOSiemens-4.8.so.1 ../../lib/libITKIOGE-4.8.so.1 
>> ../../lib/libITKIOIPL-4.8.so.1 
>> ../../lib/libITKIOTransformHDF5-4.8.so.1 
>> ../../lib/libitkhdf5_cpp-4.8.so.1 ../../lib/libitkhdf5-4.8.so.1 
>> ../../lib/libITKIOTransformInsightLegacy-4.8.so.1 
>> ../../lib/libITKIOTransformMatlab-4.8.so.1 
>> ../../lib/libITKIOTransformBase-4.8.so.1 
>> ../../lib/libITKKLMRegionGrowing-4.8.so.1 
>> ../../lib/libITKWatersheds-4.8.so.1 
>> ../../lib/libITKSpatialObjects-4.8.so.1 ../../lib/libITKMesh-4.8.so.1 
>> ../../lib/libITKPath-4.8.so.1 ../../lib/libITKStatistics-4.8.so.1 
>> ../../lib/libitkNetlibSlatec-4.8.so.1 
>> ../../lib/libitkopenjpeg-4.8.so.1 ../../lib/libITKVideoCore-4.8.so.1 
>> ../../lib/libITKVTK-4.8.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkRenderingFreeTypeOpenGL-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkRenderingOpenGL-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkImagingHybrid-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkIOImage-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkDICOMParser-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkIOCore-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkmetaio-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkpng-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtktiff-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkjpeg-6.2.so.1 
>> -lGLU -lSM -lICE -lX11 -lXext -lSM -lICE -lX11 -lXext -lXt 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkRenderingFreeType-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkftgl-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkfreetype-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkzlib-6.2.so.1 
>> -lGL 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkInteractionStyle-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkRenderingCore-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkCommonColor-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkFiltersGeometry-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkFiltersExtraction-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkFiltersStatistics-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkImagingFourier-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkalglib-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkFiltersSources-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkFiltersGeneral-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkFiltersCore-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkCommonComputationalGeometry-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkImagingSources-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkImagingCore-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkCommonExecutionModel-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkCommonDataModel-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkCommonMisc-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkCommonSystem-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtksys-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkCommonTransforms-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkCommonMath-6.2.so.1 
>> /tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib/libvtkCommonCore-6.2.so.1 
>> ../../lib/libITKIOImageBase-4.8.so.1 ../../lib/libITKCommon-4.8.so.1 
>> ../../lib/libitkdouble-conversion-4.8.so.1 
>> ../../lib/libitksys-4.8.so.1 
>> ../../lib/libITKVNLInstantiation-4.8.so.1 
>> ../../lib/libitkvnl_algo-4.8.so.1 ../../lib/libitkv3p_lsqr-4.8.so.1 
>> ../../lib/libitkvnl-4.8.so.1 ../../lib/libitkvcl-4.8.so.1 
>> ../../lib/libitkv3p_netlib-4.8.so.1 -lm -lpthread -ldl -lm 
>> ../../lib/libitkzlib-4.8.so.1 
>> -Wl,-rpath,/tools/devel/linux/ITKv4/InsightToolkit-Auto-4.8.0-build/lib:/tools/devel/linux/ITKv4/InsightToolkit-Auto-4.8.0-build/Modules/ThirdParty/DCMTK/ITKDCMTK_ExtProject-build/lib:/tools/VTK/VTK_6.2.0/VTK_6.2.0_linux64_dyn-Qt4.8.6-Python2.7.7_Release/lib 
>> -Wl,-rpath-link,/tools/devel/linux/ITKv4/InsightToolkit-Auto-4.8.0-build/lib 
>>
>> CMakeFiles/TransformReadWrite.dir/TransformReadWrite.cxx.o:(.data+0x10): 
>> undefined reference to `itk::MINCTransformIOFactoryRegister__Private()'
>> collect2: ld returned 1 exit status
>> make[3]: *** [bin/TransformReadWrite] Error 1
>>
>>
>> I am attaching the itkTransformIOFactoryRegisterManager.h file 
>> generated automatically for TransformReadWrite. It tries to register 
>> MINCTransformIOFactoryRegister which makes sense because this 
>> transform IO is specified in the UseITK.cmake (also attached), but I 
>> don't seem to have any library that corresponds to that in my 
>> ITK-build/lib directory.
>>
>> Is there an option I forgot to activate that is required for that? 
>> For now I am just going to deactivate the support of the MINC format, 
>> but I wanted to report my problem in case it is a bug in ITK.
>>
>> Francois
>> <itkTransformIOFactoryRegisterManager.h><UseITK.cmake>_____________________________________
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