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

Johnson, Hans J hans-johnson at uiowa.edu
Thu Jul 9 12:26:34 EDT 2015 

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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