[Insight-users] itk compilation problem

[Kishore Mosaliganti]

I meant to address everyone on the list and not just Luis :).

Kishore

On Thu, Jan 13, 2011 at 4:27 PM, Kishore Mosaliganti
<kishoreraom at gmail.com> wrote:
> Hi Luis,
>
> I am facing a lot of trouble trying to compile ITK from the GIT
> repository on our computing cluster. I have been facing this problem
> for almost 6 months. I am pasting the compilation error that I get and
> also some other details of the computing environment:
>
> bassoon000-218:~/bin/GITROOT/itk$ make
> [ -3%] Built target itksys
> [ -3%] Built target itkzlib
> [ -3%] Built target itkpng
> [ -3%] Built target itkjpeg
> [ -3%] Built target itkmkg3states
> [ -3%] Built target itktiff
> [ -3%] Built target itkopenjpeg
> [ -3%] Built target ITKEXPAT
> [ -3%] Built target gdcmcharls
> [ -3%] Built target gdcmuuid
> [ -3%] Built target gdcmjpeg8
> [ -3%] Built target gdcmjpeg12
> [ -3%] Built target gdcmjpeg16
> [ -3%] Built target gdcmCommon
> [ -3%] Built target gdcmDSED
> [ -3%] Built target gdcmIOD
> [ -3%] Built target gdcmDICT
> [ -3%] Built target gdcmMSFF
> [ -3%] Built target ITKMetaIO
> [ -3%] Built target ITKNrrdIO
> [ -3%] Built target ITKznz
> [ -3%] Built target ITKniftiio
> [ -3%] Built target ITKDICOMParser
> [ -3%] Built target itkvcl
> [ -3%] Built target itkv3p_netlib
> [ -3%] Built target itkv3p_lsqr
> [ -3%] Built target itktestlib
> [ -3%] Built target itkvnl
> [ -3%] Built target itkvnl_algo
> [ -3%] Built target itkNetlibSlatec
> [ -3%] Built target itkvnl_inst
> [ -3%] Built target ITKCommon
> [ -3%] Built target ITKNumerics
> [ -3%] Built target ITKStatistics
> [ -3%] Built target ITKSpatialObject
> [ -3%] Built target ITKIO
> [ -3%] Built target ITKBasicFilters
> [ -3%] Built target ITKFEM
> [ -3%] Built target ITKAlgorithms
> Linking CXX executable ../../bin/itkTestDriver
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `vnl_matrix_ref<double>::vnl_matrix_ref(unsigned int, unsigned int,
> double*)':
> itkTestDriver.cxx:(.text._ZN14vnl_matrix_refIdEC1EjjPd[vnl_matrix_ref<double>::vnl_matrix_ref(unsigned
> int, unsigned int, double*)]+0x26): undefined reference to
> `vnl_c_vector<double>::allocate_Tptr(int)'
> itkTestDriver.cxx:(.text._ZN14vnl_matrix_refIdEC1EjjPd[vnl_matrix_ref<double>::vnl_matrix_ref(unsigned
> int, unsigned int, double*)]+0x9c): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `vnl_matrix_ref<double>::~vnl_matrix_ref()':
> itkTestDriver.cxx:(.text._ZN14vnl_matrix_refIdED1Ev[vnl_matrix_ref<double>::~vnl_matrix_ref()]+0x20):
> undefined reference to `vnl_matrix<double>::~vnl_matrix()'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function `double
> vnl_determinant<double, 6u, 6u>(vnl_matrix_fixed<double, 6u, 6u>
> const&, bool)':
> itkTestDriver.cxx:(.text._Z15vnl_determinantIdLj6ELj6EET_RK16vnl_matrix_fixedIS0_XT0_EXT1_EEb[double
> vnl_determinant<double, 6u, 6u>(vnl_matrix_fixed<double, 6u, 6u>
> const&, bool)]+0x2b): undefined reference to `double
> vnl_determinant<double>(vnl_matrix<double> const&, bool)'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function `double
> vnl_determinant<double, 2u, 2u>(vnl_matrix_fixed<double, 2u, 2u>
> const&, bool)':
> itkTestDriver.cxx:(.text._Z15vnl_determinantIdLj2ELj2EET_RK16vnl_matrix_fixedIS0_XT0_EXT1_EEb[double
> vnl_determinant<double, 2u, 2u>(vnl_matrix_fixed<double, 2u, 2u>
> const&, bool)]+0x2b): undefined reference to `double
> vnl_determinant<double>(vnl_matrix<double> const&, bool)'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `vnl_matrix_inverse<double>::vnl_matrix_inverse(vnl_matrix<double>
> const&)':
> itkTestDriver.cxx:(.text._ZN18vnl_matrix_inverseIdEC1ERK10vnl_matrixIdE[vnl_matrix_inverse<double>::vnl_matrix_inverse(vnl_matrix<double>
> const&)]+0x1d): undefined reference to
> `vnl_svd<double>::vnl_svd(vnl_matrix<double> const&, double)'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `vnl_svd<double>::inverse() const':
> itkTestDriver.cxx:(.text._ZNK7vnl_svdIdE7inverseEv[vnl_svd<double>::inverse()
> const]+0x1d): undefined reference to
> `vnl_svd<double>::pinverse(unsigned int) const'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `vnl_diag_matrix<double>::~vnl_diag_matrix()':
> itkTestDriver.cxx:(.text._ZN15vnl_diag_matrixIdED1Ev[vnl_diag_matrix<double>::~vnl_diag_matrix()]+0x11):
> undefined reference to `vnl_vector<double>::~vnl_vector()'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `vnl_svd<double>::~vnl_svd()':
> itkTestDriver.cxx:(.text._ZN7vnl_svdIdED2Ev[vnl_svd<double>::~vnl_svd()]+0x18):
> undefined reference to `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZN7vnl_svdIdED2Ev[vnl_svd<double>::~vnl_svd()]+0xbf):
> undefined reference to `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZN7vnl_svdIdED2Ev[vnl_svd<double>::~vnl_svd()]+0xed):
> undefined reference to `vnl_matrix<double>::~vnl_matrix()'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `itk::Matrix<double, 6u, 6u>::GetInverse() const':
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj6ELj6EE10GetInverseEv[itk::Matrix<double,
> 6u, 6u>::GetInverse() const]+0x1eb): undefined reference to
> `vnl_matrix<double>::vnl_matrix(vnl_matrix<double> const&)'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj6ELj6EE10GetInverseEv[itk::Matrix<double,
> 6u, 6u>::GetInverse() const]+0x26e): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj6ELj6EE10GetInverseEv[itk::Matrix<double,
> 6u, 6u>::GetInverse() const]+0x29b): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj6ELj6EE10GetInverseEv[itk::Matrix<double,
> 6u, 6u>::GetInverse() const]+0x2e1): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj6ELj6EE10GetInverseEv[itk::Matrix<double,
> 6u, 6u>::GetInverse() const]+0x338): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj6ELj6EE10GetInverseEv[itk::Matrix<double,
> 6u, 6u>::GetInverse() const]+0x3b3): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o:itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj6ELj6EE10GetInverseEv[itk::Matrix<double,
> 6u, 6u>::GetInverse() const]+0x3f5): more undefined references to
> `vnl_matrix<double>::~vnl_matrix()' follow
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `itk::Matrix<double, 2u, 2u>::GetInverse() const':
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj2ELj2EE10GetInverseEv[itk::Matrix<double,
> 2u, 2u>::GetInverse() const]+0x1eb): undefined reference to
> `vnl_matrix<double>::vnl_matrix(vnl_matrix<double> const&)'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj2ELj2EE10GetInverseEv[itk::Matrix<double,
> 2u, 2u>::GetInverse() const]+0x26e): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj2ELj2EE10GetInverseEv[itk::Matrix<double,
> 2u, 2u>::GetInverse() const]+0x29b): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj2ELj2EE10GetInverseEv[itk::Matrix<double,
> 2u, 2u>::GetInverse() const]+0x2e1): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj2ELj2EE10GetInverseEv[itk::Matrix<double,
> 2u, 2u>::GetInverse() const]+0x338): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj2ELj2EE10GetInverseEv[itk::Matrix<double,
> 2u, 2u>::GetInverse() const]+0x3b3): undefined reference to
> `vnl_matrix<double>::~vnl_matrix()'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o:itkTestDriver.cxx:(.text._ZNK3itk6MatrixIdLj2ELj2EE10GetInverseEv[itk::Matrix<double,
> 2u, 2u>::GetInverse() const]+0x3f5): more undefined references to
> `vnl_matrix<double>::~vnl_matrix()' follow
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `itk::Array<double>::SetSize(unsigned int)':
> itkTestDriver.cxx:(.text._ZN3itk5ArrayIdE7SetSizeEj[itk::Array<double>::SetSize(unsigned
> int)]+0x45): undefined reference to
> `vnl_vector<double>::set_size(unsigned int)'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `itk::Array<unsigned long>::SetSize(unsigned int)':
> itkTestDriver.cxx:(.text._ZN3itk5ArrayImE7SetSizeEj[itk::Array<unsigned
> long>::SetSize(unsigned int)]+0x45): undefined reference to
> `vnl_vector<unsigned long>::set_size(unsigned int)'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `itk::Array<double>::Fill(double const&)':
> itkTestDriver.cxx:(.text._ZN3itk5ArrayIdE4FillERKd[itk::Array<double>::Fill(double
> const&)]+0x19): undefined reference to
> `vnl_vector<double>::fill(double const&)'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `itk::Array<unsigned long>::Fill(unsigned long const&)':
> itkTestDriver.cxx:(.text._ZN3itk5ArrayImE4FillERKm[itk::Array<unsigned
> long>::Fill(unsigned long const&)]+0x19): undefined reference to
> `vnl_vector<unsigned long>::fill(unsigned long const&)'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `itk::Array<unsigned long>::~Array()':
> itkTestDriver.cxx:(.text._ZN3itk5ArrayImED1Ev[itk::Array<unsigned
> long>::~Array()]+0x2c): undefined reference to `vnl_vector<unsigned
> long>::~vnl_vector()'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `itk::Array<double>::~Array()':
> itkTestDriver.cxx:(.text._ZN3itk5ArrayIdED1Ev[itk::Array<double>::~Array()]+0x2c):
> undefined reference to `vnl_vector<double>::~vnl_vector()'
> CMakeFiles/itkTestDriver.dir/itkTestDriver.cxx.o: In function
> `itk::ImageFileWriter<itk::Image<unsigned char, 2u> >::Write()':
> itkTestDriver.cxx:(.text._ZN3itk15ImageFileWriterINS_5ImageIhLj2EEEE5WriteEv[itk::ImageFileWriter<itk::Image<unsigned
> char, 2u> >::Write()]+0x1222): undefined reference to
> `vnl_vector<double>::vnl_vector(unsigned int)'
> itkTestDriver.cxx:(.text._ZN3itk15ImageFileWriterINS_5ImageIhLj2EEEE5WriteEv[itk::ImageFileWriter<itk::Image<unsigned
> char, 2u> >::Write()]+0x12a1): undefined reference to
> `vnl_vector<double>::~vnl_vector()'
> itkTestDriver.cxx:(.text._ZN3itk15ImageFileWriterINS_5ImageIhLj2EEEE5WriteEv[itk::ImageFileWriter<itk::Image<unsigned
> char, 2u> >::Write()]+0x12cb): undefined reference to
> `vnl_vector<double>::~vnl_vector()'
> ../../bin/libITKIO.a(itkMetaImageIO.cxx.o): In function
> `itk::MetaImageIO::ReadImageInformation()':
> itkMetaImageIO.cxx:(.text+0x4f86): undefined reference to
> `vnl_vector<double>::vnl_vector(unsigned int)'
> itkMetaImageIO.cxx:(.text+0x54fe): undefined reference to
> `vnl_vector<double>::~vnl_vector()'
> itkMetaImageIO.cxx:(.text+0x5532): undefined reference to
> `vnl_vector<double>::~vnl_vector()'
> ../../bin/libITKIO.a(itkDICOMImageIO2.cxx.o): In function
> `itk::Array<float>::Array(unsigned int)':
> itkDICOMImageIO2.cxx:(.text._ZN3itk5ArrayIfEC1Ej[itk::Array<float>::Array(unsigned
> int)]+0x17): undefined reference to
> `vnl_vector<float>::vnl_vector(unsigned int)'
> ../../bin/libITKIO.a(itkDICOMImageIO2.cxx.o): In function
> `itk::Array<float>::SetSize(unsigned int)':
> itkDICOMImageIO2.cxx:(.text._ZN3itk5ArrayIfE7SetSizeEj[itk::Array<float>::SetSize(unsigned
> int)]+0x45): undefined reference to
> `vnl_vector<float>::set_size(unsigned int)'
> ../../bin/libITKIO.a(itkDICOMImageIO2.cxx.o): In function
> `itk::Array<float>::operator=(itk::Array<float> const&)':
> itkDICOMImageIO2.cxx:(.text._ZN3itk5ArrayIfEaSERKS1_[itk::Array<float>::operator=(itk::Array<float>
> const&)]+0x41): undefined reference to
> `vnl_vector<float>::operator=(vnl_vector<float> const&)'
> ../../bin/libITKIO.a(itkDICOMImageIO2.cxx.o): In function
> `itk::Array<float>::~Array()':
> itkDICOMImageIO2.cxx:(.text._ZN3itk5ArrayIfED1Ev[itk::Array<float>::~Array()]+0x2c):
> undefined reference to `vnl_vector<float>::~vnl_vector()'
> ../../bin/libITKIO.a(itkGDCMImageIO.cxx.o): In function
> `itk::GDCMImageIO::InternalReadImageInformation(std::basic_ifstream<char,
> std::char_traits<char> >&)':
> itkGDCMImageIO.cxx:(.text+0x248d): undefined reference to
> `vnl_vector<double>::vnl_vector(unsigned int)'
> itkGDCMImageIO.cxx:(.text+0x249e): undefined reference to
> `vnl_vector<double>::vnl_vector(unsigned int)'
> itkGDCMImageIO.cxx:(.text+0x2ba0): undefined reference to
> `vnl_vector<double>::~vnl_vector()'
> itkGDCMImageIO.cxx:(.text+0x2bca): undefined reference to
> `vnl_vector<double>::~vnl_vector()'
> itkGDCMImageIO.cxx:(.text+0x2be9): undefined reference to
> `vnl_vector<double>::~vnl_vector()'
> itkGDCMImageIO.cxx:(.text+0x2c13): undefined reference to
> `vnl_vector<double>::~vnl_vector()'
> itkGDCMImageIO.cxx:(.text+0x2c32): undefined reference to
> `vnl_vector<double>::~vnl_vector()'
> ../../bin/libITKIO.a(itkGDCMImageIO.cxx.o):itkGDCMImageIO.cxx:(.text+0x2c5c):
> more undefined references to `vnl_vector<double>::~vnl_vector()'
> follow
> ../../bin/libITKIO.a(itkGDCMImageIO.cxx.o): In function
> `itk::Array<double>::operator=(itk::Array<double> const&)':
> itkGDCMImageIO.cxx:(.text._ZN3itk5ArrayIdEaSERKS1_[itk::Array<double>::operator=(itk::Array<double>
> const&)]+0x41): undefined reference to
> `vnl_vector<double>::operator=(vnl_vector<double> const&)'
> ../../bin/libITKIO.a(itkGDCMImageIO.cxx.o): In function
> `vnl_vector<double> vnl_cross_3d<double>(vnl_vector<double> const&,
> vnl_vector<double> const&)':
> itkGDCMImageIO.cxx:(.text._Z12vnl_cross_3dIdE10vnl_vectorIT_ERKS2_S4_[vnl_vector<double>
> vnl_cross_3d<double>(vnl_vector<double> const&, vnl_vector<double>
> const&)]+0x54): undefined reference to
> `vnl_vector<double>::vnl_vector(unsigned int)'
> collect2: ld returned 1 exit status
> make[2]: *** [bin/itkTestDriver] Error 1
> make[1]: *** [Code/IO/CMakeFiles/itkTestDriver.dir/all] Error 2
> make: *** [all] Error 2
>
>
> Some other useful information on the computing environment:
>
> krm15 at bassoon000-219:~/bin/GITROOT/itk$ ~/bin/cmake-2.8.2/bin/ccmake --version
> ccmake version 2.8.2
>
> krm15 at bassoon000-219:~/bin/GITROOT/itk$ uname -a
> Linux bassoon000-219 2.6.32-bpo.5-ritg-amd64 #1 SMP Mon Nov 8 10:36:12
> EST 2010 x86_64 GNU/Linux
>
> krm15 at bassoon000-219:~/bin/GITROOT/itk$ gcc --version
> gcc (Debian 4.3.2-1.1) 4.3.2
>
> krm15 at bassoon000-219:~/bin/GITROOT/itk$ c++ --version
> c++ (Debian 4.3.2-1.1) 4.3.2
>
>
> Let me know if you need any other information in identifying the problem.
>
>
> Kishore
>