[Insight-users] itk compilation problem

[Kishore Mosaliganti]

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