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UCL / PETPVC

Partial Volume Correction in PET
Apache License 2.0
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Errors linking to ITK libraries during build on CentOS #27

Closed jeffrey-phillips closed 6 years ago

jeffrey-phillips commented 6 years ago

Hi folks,

We've been having trouble building PETPVC on CentOS--with a couple of different compilers and ITK 4.12.2, we consistently get a bunch of linking errors. We're wondering if you'd recommend particular versions of gcc/g++ or ITK--possibly older than what we have installed here? If you have any suggestions, we'd appreciate them.

Please see below for the full list of errors, as well as details on our OS, ITK version, and compilers. We get similar errors (identical, I think) when compiling with gcc/g++ 4.8.2 and ccmake 2.8.12.2.

Thanks for developing this package--the versatility has been great for our PET processing.

Jeff

OS: Linux version 2.6.32-696.3.2.el6.x86_64 (mockbuild@c1bl.rdu2.centos.org) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Tue Jun 20 01:26:55 UTC 2017

ITK: ITK release 4.12.2 (95f0bb0b264aa131f92db5992d649c4627301efc) Module_ITKReview is ON.

Our default versions of gcc/g++:

gcc -v

Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux Thread model: posix gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC)

g++ -v

g++ -v Using built-in specs. Target: x86_64-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux Thread model: posix gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC)

Trying to build PETPVC under these conditions gives the following errors:

make

make [ 6%] Building CXX object test/CMakeFiles/pvc_compareImages.dir/CompareImages.cxx.o Linking CXX executable pvc_compareImages /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkDynamicLoader.cxx.o): In function itk::DynamicLoader::GetSymbolAddress(void*, char const*)': itkDynamicLoader.cxx:(.text+0xfa): undefined reference toitksys::DynamicLoader::GetSymbolAddress(void, std::basic_string<char, std::char_traits, std::allocator > const&)' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkDynamicLoader.cxx.o): In function `itk::DynamicLoader::OpenLibrary(char const)': itkDynamicLoader.cxx:(.text+0x18e): undefined reference to itksys::DynamicLoader::OpenLibrary(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkDynamicLoader.cxx.o): In functionitk::DynamicLoader::LastError()': itkDynamicLoader.cxx:(.text+0x51): undefined reference to itksys::DynamicLoader::LastError()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkDynamicLoader.cxx.o): In functionitk::DynamicLoader::CloseLibrary(void)': itkDynamicLoader.cxx:(.text+0x61): undefined reference to `itksys::DynamicLoader::CloseLibrary(void)' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOGDCM-4.12.a(itkGDCMImageIO.cxx.o): In function itk::GDCMImageIO::Write(void const*)': itkGDCMImageIO.cxx:(.text+0x4598): undefined reference toitksysBase64_Decode' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOGDCM-4.12.a(itkGDCMImageIO.cxx.o): In function itk::GDCMImageIO::InternalReadImageInformation()': itkGDCMImageIO.cxx:(.text+0x9c24): undefined reference toitksysBase64_Encode' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In function bool itk::HDF5ImageIO::WriteMetaArray<char>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIcEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray<char>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)]+0x4e): undefined reference tovnl_vector::vnl_vector(vnl_vector const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIcEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0xfb): undefined reference to `vnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIcEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x15c): undefined reference to vnl_vector<char>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionbool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIhEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x47): undefined reference to vnl_vector<unsigned char>::vnl_vector(vnl_vector<unsigned char> const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIhEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray<unsigned char>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)]+0xf3): undefined reference tovnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIhEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x15c): undefined reference to vnl_vector<unsigned char>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIhEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayIhEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned char>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIsEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayIsEEED5Ev]+0x29): undefined reference to vnl_vector<short>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayItEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayItEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned short>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIjEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayIjEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned int>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayImEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayImEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned long>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIxEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayIxEEED5Ev]+0x29): undefined reference to vnl_vector<long long>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIyEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayIyEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned long long>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionbool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayItEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x49): undefined reference to `vnl_vector::vnl_vector(vnl_vector const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayItEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x1a7): undefined reference to vnl_vector<unsigned short>::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayItEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray<unsigned short>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)]+0x20b): undefined reference tovnl_vector::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In function bool itk::HDF5ImageIO::WriteMetaArray<unsigned int>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIjEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray<unsigned int>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)]+0x49): undefined reference tovnl_vector::vnl_vector(vnl_vector const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIjEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x1b5): undefined reference to `vnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIjEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x21b): undefined reference to vnl_vector<unsigned int>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionbool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIfEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x50): undefined reference to vnl_vector<float>::vnl_vector(vnl_vector<float> const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIfEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray<float>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)]+0x1b5): undefined reference tovnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIfEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x21b): undefined reference to vnl_vector<float>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionbool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIiEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x50): undefined reference to `vnl_vector::vnl_vector(vnl_vector const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIiEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x1b5): undefined reference to vnl_vector<int>::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIiEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray<int>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)]+0x21b): undefined reference tovnl_vector::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In function bool itk::HDF5ImageIO::WriteMetaArray<short>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIsEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray<short>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)]+0x49): undefined reference tovnl_vector::vnl_vector(vnl_vector const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIsEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x1a7): undefined reference to `vnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayIsEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x20b): undefined reference to vnl_vector<short>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayItEEED0Ev[_ZN3itk14MetaDataObjectINS_5ArrayItEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned short>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIsEEED0Ev[_ZN3itk14MetaDataObjectINS_5ArrayIsEEED5Ev]+0x29): undefined reference to vnl_vector<short>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIxEEED0Ev[_ZN3itk14MetaDataObjectINS_5ArrayIxEEED5Ev]+0x29): undefined reference to vnl_vector<long long>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayImEEED0Ev[_ZN3itk14MetaDataObjectINS_5ArrayImEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned long>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIjEEED0Ev[_ZN3itk14MetaDataObjectINS_5ArrayIjEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned int>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIyEEED0Ev[_ZN3itk14MetaDataObjectINS_5ArrayIyEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned long long>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkHDF5ImageIO.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIhEEED0Ev[_ZN3itk14MetaDataObjectINS_5ArrayIhEEED5Ev]+0x29): undefined reference to vnl_vector<unsigned char>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionbool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayImEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x49): undefined reference to vnl_vector<unsigned long>::vnl_vector(vnl_vector<unsigned long> const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayImEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray<unsigned long>(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, itk::MetaDataObjectBase*)]+0x199): undefined reference tovnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO14WriteMetaArrayImEEbRKSsPNS_18MetaDataObjectBaseE[bool itk::HDF5ImageIO::WriteMetaArray(std::basic_string<char, std::char_traits, std::allocator > const&, itk::MetaDataObjectBase)]+0x203): undefined reference to vnl_vector<unsigned long>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionvoid itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIjEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x41): undefined reference to `vnl_vector::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIjEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xe5): undefined reference to vnl_vector<unsigned int>::set_size(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIjEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<unsigned int>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0xf4): undefined reference tovnl_vector::operator=(vnl_vector const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIjEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x136): undefined reference to `vnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIjEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x26a): undefined reference to vnl_vector<unsigned int>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionvoid itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIxEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x41): undefined reference to vnl_vector<long long>::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIxEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<long long>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0xe7): undefined reference tovnl_vector::set_size(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIxEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xf6): undefined reference to `vnl_vector::operator=(vnl_vector const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIxEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x138): undefined reference to vnl_vector<long long>::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIxEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<long long>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x266): undefined reference tovnl_vector::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In function void itk::HDF5ImageIO::StoreMetaData<unsigned long long>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIyEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<unsigned long long>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x41): undefined reference tovnl_vector::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIyEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xe7): undefined reference to `vnl_vector::set_size(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIyEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xf6): undefined reference to vnl_vector<unsigned long long>::operator=(vnl_vector<unsigned long long> const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIyEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<unsigned long long>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x138): undefined reference tovnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIyEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x266): undefined reference to vnl_vector<unsigned long long>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionvoid itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIfEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x3e): undefined reference to `vnl_vector::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIfEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xeb): undefined reference to vnl_vector<float>::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIfEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<float>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x20c): undefined reference tovnl_vector::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In function void itk::HDF5ImageIO::StoreMetaData<unsigned long>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataImEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<unsigned long>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x41): undefined reference tovnl_vector::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataImEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xe0): undefined reference to `vnl_vector::set_size(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataImEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xef): undefined reference to vnl_vector<unsigned long>::operator=(vnl_vector<unsigned long> const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataImEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<unsigned long>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x131): undefined reference tovnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataImEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x245): undefined reference to vnl_vector<unsigned long>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionvoid itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIiEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x3e): undefined reference to `vnl_vector::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIiEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xeb): undefined reference to vnl_vector<int>::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIiEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<int>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x20a): undefined reference tovnl_vector::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In function void itk::HDF5ImageIO::StoreMetaData<char>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIcEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<char>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x3a): undefined reference tovnl_vector::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIcEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xe7): undefined reference to `vnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIcEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x20a): undefined reference to vnl_vector<char>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionvoid itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIhEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x3d): undefined reference to vnl_vector<unsigned char>::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIhEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<unsigned char>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0xe1): undefined reference tovnl_vector::set_size(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIhEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xf0): undefined reference to `vnl_vector::operator=(vnl_vector const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIhEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x132): undefined reference to vnl_vector<unsigned char>::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIhEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<unsigned char>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x262): undefined reference tovnl_vector::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In function void itk::HDF5ImageIO::StoreMetaData<short>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIsEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<short>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x40): undefined reference tovnl_vector::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIsEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xdf): undefined reference to `vnl_vector::set_size(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIsEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xee): undefined reference to vnl_vector<short>::operator=(vnl_vector<short> const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIsEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<short>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0x130): undefined reference tovnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataIsEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x25b): undefined reference to vnl_vector<short>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOHDF5-4.12.a(itkHDF5ImageIO.cxx.o): In functionvoid itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)': itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataItEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x40): undefined reference to `vnl_vector::vnl_vector(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataItEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0xdf): undefined reference to vnl_vector<unsigned short>::set_size(unsigned long)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataItEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData<unsigned short>(itk::MetaDataDictionary*, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)]+0xee): undefined reference tovnl_vector::operator=(vnl_vector const&)' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataItEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x130): undefined reference to `vnl_vector::~vnl_vector()' itkHDF5ImageIO.cxx:(.text._ZN3itk11HDF5ImageIO13StoreMetaDataItEEvPNS_18MetaDataDictionaryERKSsS5_m[void itk::HDF5ImageIO::StoreMetaData(itk::MetaDataDictionary, std::basic_string<char, std::char_traits, std::allocator > const&, std::basic_string<char, std::char_traits, std::allocator > const&, unsigned long)]+0x25b): undefined reference to vnl_vector<unsigned short>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKIOTIFF-4.12.a(itkTIFFImageIO.cxx.o): In functionitk::TIFFImageIO::ReadTIFFTags()': itkTIFFImageIO.cxx:(.text+0x15b6): undefined reference to vnl_vector<float>::vnl_vector(unsigned long)' itkTIFFImageIO.cxx:(.text+0x16b7): undefined reference tovnl_vector::~vnl_vector()' itkTIFFImageIO.cxx:(.text+0x16de): undefined reference to vnl_vector<int>::vnl_vector(unsigned long)' itkTIFFImageIO.cxx:(.text+0x17e7): undefined reference tovnl_vector::~vnl_vector()' itkTIFFImageIO.cxx:(.text+0x1ad9): undefined reference to vnl_vector<unsigned short>::vnl_vector(unsigned long)' itkTIFFImageIO.cxx:(.text+0x1ba7): undefined reference tovnl_vector::set_size(unsigned long)' itkTIFFImageIO.cxx:(.text+0x1bb6): undefined reference to vnl_vector<unsigned short>::operator=(vnl_vector<unsigned short> const&)' itkTIFFImageIO.cxx:(.text+0x1c24): undefined reference tovnl_vector::~vnl_vector()' itkTIFFImageIO.cxx:(.text+0x1d77): undefined reference to vnl_vector<char>::vnl_vector(char const*, unsigned long)' itkTIFFImageIO.cxx:(.text+0x1e4e): undefined reference tovnl_vector::~vnl_vector()' itkTIFFImageIO.cxx:(.text+0x2765): undefined reference to vnl_vector<char>::~vnl_vector()' itkTIFFImageIO.cxx:(.text+0x2847): undefined reference tovnl_vector::~vnl_vector()' itkTIFFImageIO.cxx:(.text+0x29ee): undefined reference to vnl_vector<int>::~vnl_vector()' itkTIFFImageIO.cxx:(.text+0x2a84): undefined reference tovnl_vector::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkMetaDataObject.cxx.o): In function itk::MetaDataObject<itk::Array<float> >::~MetaDataObject()': itkMetaDataObject.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIfEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayIfEEED5Ev]+0x29): undefined reference tovnl_vector::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkMetaDataObject.cxx.o): In function itk::MetaDataObject<itk::Array<float> >::SetMetaDataObjectValue(itk::Array<float> const&)': itkMetaDataObject.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIfEEE22SetMetaDataObjectValueERKS2_[itk::MetaDataObject<itk::Array<float> >::SetMetaDataObjectValue(itk::Array<float> const&)]+0x35): undefined reference tovnl_vector::set_size(unsigned long)' itkMetaDataObject.cxx:(.text._ZN3itk14MetaDataObjectINS5ArrayIfEEE22SetMetaDataObjectValueERKS2[itk::MetaDataObject<itk::Array >::SetMetaDataObjectValue(itk::Array const&)]+0x56): undefined reference to vnl_vector<float>::operator=(vnl_vector<float> const&)' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkMetaDataObject.cxx.o): In functionitk::MetaDataObject<itk::Array >::~MetaDataObject()': itkMetaDataObject.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIiEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayIiEEED5Ev]+0x29): undefined reference to vnl_vector<int>::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkMetaDataObject.cxx.o): In functionitk::MetaDataObject<itk::Array >::SetMetaDataObjectValue(itk::Array const&)': itkMetaDataObject.cxx:(.text._ZN3itk14MetaDataObjectINS5ArrayIiEEE22SetMetaDataObjectValueERKS2[itk::MetaDataObject<itk::Array >::SetMetaDataObjectValue(itk::Array const&)]+0x35): undefined reference to vnl_vector<int>::set_size(unsigned long)' itkMetaDataObject.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIiEEE22SetMetaDataObjectValueERKS2_[itk::MetaDataObject<itk::Array<int> >::SetMetaDataObjectValue(itk::Array<int> const&)]+0x56): undefined reference tovnl_vector::operator=(vnl_vector const&)' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkMetaDataObject.cxx.o): In function itk::MetaDataObject<itk::Array<char> >::~MetaDataObject()': itkMetaDataObject.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIcEEED2Ev[_ZN3itk14MetaDataObjectINS_5ArrayIcEEED5Ev]+0x29): undefined reference tovnl_vector::~vnl_vector()' /data/jet/pcook/bin/petpvc/standardCompiler/itk/lib/libITKCommon-4.12.a(itkMetaDataObject.cxx.o): In function itk::MetaDataObject<itk::Array<char> >::SetMetaDataObjectValue(itk::Array<char> const&)': itkMetaDataObject.cxx:(.text._ZN3itk14MetaDataObjectINS_5ArrayIcEEE22SetMetaDataObjectValueERKS2_[itk::MetaDataObject<itk::Array<char> >::SetMetaDataObjectValue(itk::Array<char> const&)]+0x35): undefined reference tovnl_vector::set_size(unsigned long)' itkMetaDataObject.cxx:(.text._ZN3itk14MetaDataObjectINS5ArrayIcEEE22SetMetaDataObjectValueERKS2[itk::MetaDataObject<itk::Array >::SetMetaDataObjectValue(itk::Array const&)]+0x56): undefined reference to `vnl_vector::operator=(vnl_vector const&)' collect2: ld returned 1 exit status make[2]: [test/pvc_compareImages] Error 1 make[1]: [test/CMakeFiles/pvc_compareImages.dir/all] Error 2 make: *** [all] Error 2

bathomas commented 6 years ago

HI Jeff,

Good to hear that you're finding the toolbox useful!

As for your errors, the first thing that I would highly recommend doing is updating your CMake version. The latest is 3.9 and you appear to be using 2.8.12.2. You'll probably need to recompile ITK. I have successfully built with ITK 4.10 and 4.11 (Ubuntu) and recently built PETPVC with ITK=4.12.1 under Alpine (see https://hub.docker.com/r/benthomas1984/petpvc/). You seem to be getting lots of dynamic linker errors; are you sure ITK is built correctly? Does make test complete successfully for ITK?

bathomas commented 6 years ago

Hi Jeff,

Did you manage to sort this issue out?

Kind regards,

Ben

jeffrey-phillips commented 6 years ago

Hi Ben,

Sorry to be so slow in replying. Yes, it turned out that updating our cmake to version 3.6.1 allowed us to install successfully. Our tau PET imaging manuscript, which uses the PETPVC package (RVC and DIY methods) for supplementary analyses is now online at HBM, here:

http://onlinelibrary.wiley.com/doi/10.1002/hbm.23874/full

Thanks for all your help!

Jeff

On Mon, Nov 13, 2017 at 8:23 AM, Ben Thomas notifications@github.com wrote:

Hi Jeff,

Did you manage to sort this issue out?

Kind regards,

Ben

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/UCL/PETPVC/issues/27#issuecomment-343917393, or mute the thread https://github.com/notifications/unsubscribe-auth/AFPWEvqb85W8tDuaGKHa_-uaIWB--ktdks5s2ELXgaJpZM4Pn3QZ .