External Email - Use Caution
Hi Freesurfer developers
I’m trying to install the development package from github on my mac running osx
10.14.6. I ran CMake with the OSX package without any issue, although when I
ran make I got the following error:
[ 28%] Linking CXX executable surf2vol
ld: warning: could not create compact unwind for _MatSetValuesLocal: stack subq
instruction is too different from dwarf stack size
…
"vnl_nonlinear_minimizer::is_a() const", referenced from:
vtable for fs_powell in libutils.a(numerics.cpp.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [fem_elastic/surf2vol] Error 1
make[1]: *** [fem_elastic/CMakeFiles/surf2vol.dir/all] Error 2
make: *** [all] Error 2
The full error is copied in the attached text file. I have not been able to
find anything useful on google so please let me know if you have any ideas. I
don’t necessarily need MRI_surf2vol so I could exclude it from the install but
I’m guessing that there are other programs that rely on it?
Best,
Jon
:~/freesurfer$ make
[ 3%] Built target jpeg
[ 3%] Built target expat
[ 5%] Built target tiff
[ 8%] Built target glut
[ 10%] Built target xml2
[ 11%] Built target minc
[ 12%] Built target dicom
[ 13%] Built target cephes
[ 13%] Built target netcdf
[ 13%] Built target tetgen
[ 15%] Built target nrrdio
[ 16%] Built target nifti
[ 16%] Built target gifti
[ 17%] Built target svm
[ 17%] Built target fsPrintHelp
[ 27%] Built target utils
[ 28%] Built target vtkutils
[ 28%] Built target lineprof
[ 28%] Linking CXX executable surf2vol
ld: warning: could not create compact unwind for _MatSetValuesLocal: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _MatSetValuesBlockedLocal:
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscFinalize: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscError: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscOptionsInsertFile: stack
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscSynchronizedFlush: stack
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscViewerDestroy_Binary:
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for
_PetscViewerFileSetName_Binary: stack subq instruction is too different from
dwarf stack size
ld: warning: could not create compact unwind for _VecViewFromOptions: stack
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for
_PetscLogOpenHistoryFile.part.1: stack subq instruction is too different from
dwarf stack size
ld: warning: could not create compact unwind for
_PetscOptionsCheckInitial_Private: stack subq instruction is too different from
dwarf stack size
ld: warning: could not create compact unwind for _MatMult_SeqCSRPERM: stack
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _MatMultAdd_SeqCSRPERM: stack
subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscLogDump: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscSharedTmp: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscFileRetrieve: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscInfo_Private: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscFOpen: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscPOpen: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscRandomViewFromOptions:
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscViewerDestroy_ASCII:
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _PetscViewerStringSPrintf:
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _VecStrideNormAll: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for
_MPIDI_CH3I_VC_post_sockconnect: stack subq instruction is too different from
dwarf stack size
ld: warning: could not create compact unwind for _connToStringKVS: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _MatSetValues_IS: stack subq
instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for _MPIDI_CH3_Get_parent_port:
stack subq instruction is too different from dwarf stack size
ld: warning: could not create compact unwind for
__ZN6itksys31SystemInformationImplementation27GetFullyQualifiedDomainNameERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE:
stack subq instruction is too different from dwarf stack size
Undefined symbols for architecture x86_64:
"std::_Rb_tree_insert_and_rebalance(bool, std::_Rb_tree_node_base*,
std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)", referenced from:
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::pair<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
>, std::_Select1st<std::pair<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> > >,
std::allocator<std::pair<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
> > >::_M_insert_unique(std::pair<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
> const&) in libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::_M_replace_aux(unsigned long, unsigned long, unsigned
long, char)", referenced from:
itksys::SystemTools::GetFilenamePath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) in
libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::reserve(unsigned long)", referenced from:
itksys::SystemTools::JoinPath(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >,
__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >) in
libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::push_back(char)", referenced from:
itksys::SystemTools::SplitPathRootComponent(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>*) in libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::AddTranslationPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::resize(unsigned long, char)", referenced from:
itksys::SystemTools::ConvertToUnixSlashes(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::SplitPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > >&, bool) in
libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::find_first_of(char const*, unsigned long, unsigned
long) const", referenced from:
itksys::SystemTools::ConvertToUnixSlashes(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) in
libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::assign(char const*)", referenced from:
itksys::SystemTools::ConvertToUnixSlashes(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::SplitPathRootComponent(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>*) in libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::SplitPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > >&, bool) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::ClassInitialize() in
libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::find(char const*, unsigned long, unsigned long) const",
referenced from:
itksys::SystemTools::CheckTranslationPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) (.part.83) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::AddTranslationPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::_M_append(char const*, unsigned long)", referenced from:
itksys::SystemTools::CheckTranslationPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) (.part.83) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::ReplaceString(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&, char const*, unsigned long,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::FileIsDirectory(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::JoinPath(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >,
__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >) in
libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::_M_erase(unsigned long, unsigned long)", referenced
from:
itksys::SystemTools::CheckTranslationPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) (.part.83) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::ReplaceString(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&, char const*, unsigned long,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libitksys-4.13.a(SystemTools.cxx.o)
"std::ostream::flush()", referenced from:
vnl_svd<float>::vnl_svd(vnl_matrix<float> const&, double) in
libitkvnl_algo-4.13.a(vnl_svd+float-.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::~basic_string()", referenced from:
vnl_nonlinear_minimizer::is_a[abi:cxx11]() const in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
vnl_nonlinear_minimizer::is_class(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
itksys::SystemToolsAppendComponents(std::vector<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >,
std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> > > >&,
__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >,
__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >) in
libitksys-4.13.a(SystemTools.cxx.o)
"std::__throw_length_error(char const*)", referenced from:
itksys::SystemTools::CheckTranslationPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) (.part.83) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::ReplaceString(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&, char const*, unsigned long,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::FileIsDirectory(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::JoinPath(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >,
__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >) in
libitksys-4.13.a(SystemTools.cxx.o)
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > >
>::_M_fill_insert(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >, unsigned long,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libitksys-4.13.a(SystemTools.cxx.o)
"std::ostream::put(char)", referenced from:
vnl_svd<float>::vnl_svd(vnl_matrix<float> const&, double) in
libitkvnl_algo-4.13.a(vnl_svd+float-.cxx.o)
"std::cerr", referenced from:
vnl_nonlinear_minimizer::report_iter() in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
vnl_qr<float>::inverse() const in
libitkvnl_algo-4.13.a(vnl_qr+float-.cxx.o)
vnl_svd<float>::vnl_svd(vnl_matrix<float> const&, double) in
libitkvnl_algo-4.13.a(vnl_svd+float-.cxx.o)
"std::ostream& std::ostream::_M_insert<long>(long)", referenced from:
vnl_nonlinear_minimizer::report_iter() in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
vnl_qr<float>::inverse() const in
libitkvnl_algo-4.13.a(vnl_qr+float-.cxx.o)
vnl_svd<float>::vnl_svd(vnl_matrix<float> const&, double) in
libitkvnl_algo-4.13.a(vnl_svd+float-.cxx.o)
"std::ostream& std::ostream::_M_insert<double>(double)", referenced from:
vnl_nonlinear_minimizer::report_iter() in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*,
unsigned long)", referenced from:
Realpath(std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&, std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>*) (.constprop.155) in libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::CheckTranslationPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) (.part.83) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::ConvertToUnixSlashes(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::SplitPathRootComponent(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>*) in libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::ClassInitialize() in
libitksys-4.13.a(SystemTools.cxx.o)
"std::__throw_logic_error(char const*)", referenced from:
vnl_nonlinear_minimizer::is_a[abi:cxx11]() const in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
vnl_nonlinear_minimizer::is_class(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > >
>::_M_insert_aux(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libITKCommon-4.13.a(itkMetaDataDictionary.cxx.o)
void std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::_M_construct<char*>(char*, char*,
std::forward_iterator_tag) (.isra.98) in libitksys-4.13.a(SystemTools.cxx.o)
std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >*
std::__uninitialized_copy<false>::__uninit_copy<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >*,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>*>(std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >*, std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >*,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>*) in libitksys-4.13.a(SystemTools.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::_M_create(unsigned long&, unsigned long)", referenced
from:
vnl_nonlinear_minimizer::is_a[abi:cxx11]() const in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
vnl_nonlinear_minimizer::is_class(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > >
>::_M_insert_aux(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libITKCommon-4.13.a(itkMetaDataDictionary.cxx.o)
void std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::_M_construct<char*>(char*, char*,
std::forward_iterator_tag) (.isra.98) in libitksys-4.13.a(SystemTools.cxx.o)
std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >*
std::__uninitialized_copy<false>::__uninit_copy<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >*,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>*>(std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >*, std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >*,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>*) in libitksys-4.13.a(SystemTools.cxx.o)
"std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)",
referenced from:
itk::ObjectFactoryBase::UnRegisterAllFactories() in
libITKCommon-4.13.a(itkObjectFactoryBase.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)", referenced from:
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > >
>::_M_insert_aux(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libITKCommon-4.13.a(itkMetaDataDictionary.cxx.o)
Realpath(std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&, std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>*) (.constprop.155) in libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::CheckTranslationPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) (.part.83) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::SplitPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > >&, bool) in
libitksys-4.13.a(SystemTools.cxx.o)
itksys::SystemTools::ClassInitialize() in
libitksys-4.13.a(SystemTools.cxx.o)
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > >
>::_M_fill_insert(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >*,
std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > >, unsigned long,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
const&) in libitksys-4.13.a(SystemTools.cxx.o)
"std::basic_ostream<char, std::char_traits<char> >&
std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char,
std::char_traits<char> >&, char const*, long)", referenced from:
vnl_nonlinear_minimizer::report_iter() in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
vnl_qr<float>::inverse() const in
libitkvnl_algo-4.13.a(vnl_qr+float-.cxx.o)
vnl_svd<float>::vnl_svd(vnl_matrix<float> const&, double) in
libitkvnl_algo-4.13.a(vnl_svd+float-.cxx.o)
std::ostream& vnl_matlab_print<float>(std::ostream&, float const*,
unsigned int, vnl_matlab_print_format) in
libitkvnl-4.13.a(vnl_matlab_print+float-.cxx.o)
std::ostream& vnl_matlab_print<float>(std::ostream&,
vnl_matrix_ref<float> const&, char const*, vnl_matlab_print_format) in
libitkvnl-4.13.a(vnl_matlab_print+float-.cxx.o)
"vnl_nonlinear_minimizer::is_class(std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> > const&) const",
referenced from:
vtable for fs_powell in libutils.a(numerics.cpp.o)
"std::ios_base::Init::Init()", referenced from:
__GLOBAL__sub_I_vnl_matrix_double_.cxx in
libitkvnl-4.13.a(vnl_matrix+double-.cxx.o)
__GLOBAL__sub_I_vnl_vector_double_.cxx in
libitkvnl-4.13.a(vnl_vector+double-.cxx.o)
__GLOBAL__sub_I_vnl_c_vector_double_.cxx in
libitkvnl-4.13.a(vnl_c_vector+double-.cxx.o)
__GLOBAL__sub_I_itkDataObject.cxx in
libITKCommon-4.13.a(itkDataObject.cxx.o)
__GLOBAL__sub_I_itkLightObject.cxx in
libITKCommon-4.13.a(itkLightObject.cxx.o)
__GLOBAL__sub_I_itkExceptionObject.cxx in
libITKCommon-4.13.a(itkExceptionObject.cxx.o)
__GLOBAL__sub_I_itkObjectFactoryBase.cxx in
libITKCommon-4.13.a(itkObjectFactoryBase.cxx.o)
...
"std::_Rb_tree_increment(std::_Rb_tree_node_base const*)", referenced from:
itksys::SystemTools::CheckTranslationPath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) (.part.83) in
libitksys-4.13.a(SystemTools.cxx.o)
"std::__throw_bad_cast()", referenced from:
vnl_svd<float>::vnl_svd(vnl_matrix<float> const&, double) in
libitkvnl_algo-4.13.a(vnl_svd+float-.cxx.o)
"std::ostream& std::ostream::_M_insert<unsigned long>(unsigned long)",
referenced from:
vnl_nonlinear_minimizer::report_iter() in
libitkvnl-4.13.a(vnl_nonlinear_minimizer.cxx.o)
vnl_svd<float>::vnl_svd(vnl_matrix<float> const&, double) in
libitkvnl_algo-4.13.a(vnl_svd+float-.cxx.o)
"std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::rfind(char const*, unsigned long, unsigned long)
const", referenced from:
itksys::SystemTools::GetFilenamePath(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) in
libitksys-4.13.a(SystemTools.cxx.o)
"std::ctype<char>::_M_widen_init() const", referenced from:
vnl_svd<float>::vnl_svd(vnl_matrix<float> const&, double) in
libitkvnl_algo-4.13.a(vnl_svd+float-.cxx.o)
"std::_Rb_tree_decrement(std::_Rb_tree_node_base*)", referenced from:
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::pair<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
>, std::_Select1st<std::pair<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> > >,
std::allocator<std::pair<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
> > >::_M_insert_unique(std::pair<std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const,
std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >
> const&) in libitksys-4.13.a(SystemTools.cxx.o)
"std::__throw_out_of_range_fmt(char const*, ...)", referenced from:
itksys::SystemTools::ConvertToUnixSlashes(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&) in
libitksys-4.13.a(SystemTools.cxx.o)
"std::ios_base::Init::~Init()", referenced from:
__GLOBAL__sub_I_vnl_matrix_double_.cxx in
libitkvnl-4.13.a(vnl_matrix+double-.cxx.o)
__GLOBAL__sub_I_vnl_vector_double_.cxx in
libitkvnl-4.13.a(vnl_vector+double-.cxx.o)
__GLOBAL__sub_I_vnl_c_vector_double_.cxx in
libitkvnl-4.13.a(vnl_c_vector+double-.cxx.o)
__GLOBAL__sub_I_itkDataObject.cxx in
libITKCommon-4.13.a(itkDataObject.cxx.o)
__GLOBAL__sub_I_itkLightObject.cxx in
libITKCommon-4.13.a(itkLightObject.cxx.o)
__GLOBAL__sub_I_itkExceptionObject.cxx in
libITKCommon-4.13.a(itkExceptionObject.cxx.o)
__GLOBAL__sub_I_itkObjectFactoryBase.cxx in
libITKCommon-4.13.a(itkObjectFactoryBase.cxx.o)
...
"vnl_nonlinear_minimizer::is_a() const", referenced from:
vtable for fs_powell in libutils.a(numerics.cpp.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [fem_elastic/surf2vol] Error 1
make[1]: *** [fem_elastic/CMakeFiles/surf2vol.dir/all] Error 2
make: *** [all] Error 2_______________________________________________
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