[Mrtrix-discussion] Linking error

[Jon Clayden]

Hi Donald,

Thanks for the quick reply. Unfortunately I've already tried cleaning up first, and it doesn't help.

Clang is now the default compiler on OS X, and I think Homebrew uses it by default too. So the only other thing I can think of is that Clang uses different name-mangling to GCC and therefore that the symbols don't match up. They're definitely there in some form:

$ nm -arch x86_64 -g /usr/local/Cellar/glibmm/2.38.0/lib/libglibmm-2.4.dylib | grep build_filename
0000000000017261 T __ZN4Glib14build_filenameERKNS_11ArrayHandleINSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEENS_17Container_Helpers10TypeTraitsIS7_EEEE
00000000000172ce T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_
000000000001735d T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_
00000000000173fd T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_
00000000000174b0 T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_
0000000000017575 T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_S8_
000000000001765c T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_S8_S8_
000000000001775a T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_S8_S8_S8_
000000000001786f T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_S8_S8_S8_S8_
                 U _g_build_filename
                 U _g_build_filenamev

Unfortunately MRtrix won't build out of the box with Clang, so I can't quickly try that. I'll keep plugging away at it.

All the best,
Jon


On 28 Oct 2013, at 15:25, Donald Tournier <jdtournier at gmail.com> wrote:

> Hey Jon,
> 
> Seems odd, but my best guess would be that these functions might have changed from being actual functions calls to now being header-only inline functions, which would therefore not be present in the library. If that's the case, it would only be a problem if you're trying to link already compiled code, which would happen if you're trying to build from your previous installation without issuing a './build clean' first to remove all already compiled object files.
> 
> So in brief, try './build clean', then './build'...
> 
> Cheers,
> Donald.
> 
> 
> 
> On 28 October 2013 15:11, Jon Clayden <jon.clayden at gmail.com> wrote:
> Dear all,
> 
> I know this is tedious--sorry--but I've been struggling to get MRtrix installed on a new computer (Mac OS X Mavericks + Homebrew) and can't find my way past this problem.
> 
> The MRtrix build script fails at link time (see output below). But the library paths look fine, the appropriate libraries are listed in the link command generated by the script, and I see no evidence that the functions in question have moved or been removed in recent versions of glibmm (I'm using 2.38.0).
> 
> Am I missing something obvious here?
> 
> Thanks in advance,
> Jon
> 
> --
> [LD] lib/libmrtrix-0_2_11.dylib
> 
> ERROR: [LD] lib/libmrtrix-0_2_11.dylib
> 
> g++-4.8 -shared lib/math/vector.o lib/math/matrix.o lib/image/format/analyse.o lib/file/dicom/quick_scan.o lib/image/format/list.o lib/file/dicom/image.o lib/file/config.o lib/point.o lib/image/name_parser.o lib/image/format/xds.o lib/data_type.o lib/args.o lib/file/dicom/patient.o lib/file/dicom/tree.o lib/image/fft.o lib/image/header.o lib/file/dicom/mapper.o lib/file/dicom/select_cmdline.o lib/math/linalg.o lib/file/dicom/study.o lib/file/dicom/element.o lib/file/mmap.o lib/image/format/nifti1.o lib/file/dicom/dict.o lib/image/format/mrtrix.o lib/image/format/base.o lib/image/axis.o lib/image/interp.o lib/image/mapper.o lib/file/dicom/series.o lib/mrtrix.o lib/image/format/mri.o lib/image/object.o lib/image/format/dicom.o lib/app.o lib/file/key_value.o -L/usr/local/Cellar/glibmm/2.38.0/lib -L/usr/local/Cellar/glib/2.38.1/lib -L/usr/local/Cellar/libsigc++/2.3.1/lib -L/usr/local/Cellar/glib/2.38.1/lib -L/usr/local/opt/gettext/lib -lglibmm-2.4 -lgobject-2.0 -lsigc-2.0 -lgthre
>  ad-2.0 -lglib-2.0 -lintl -lgsl -lgslcblas -lz -o lib/libmrtrix-0_2_11.dylib
> 
> failed with output:
> 
> Undefined symbols for architecture x86_64:
>  "Glib::build_filename(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
>      MR::File::Config::init()   in config.o
>      MR::Image::NameParser::name(std::vector<int, std::allocator<int> > const&) in name_parser.o
>      MR::Image::NameParser::get_next_match(std::vector<int, std::allocator<int> >&, bool) in name_parser.o
>      MR::File::Dicom::Tree::read_dir(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in tree.o
>      MR::Image::Format::MRtrix::read(MR::Image::Mapper&, MR::Image::Header&) const in mrtrix.o
>  "Glib::str_has_suffix(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
>      MR::Image::Format::Analyse::check(MR::Image::Header&, int) const in analyse.o
>      MR::Image::Format::Analyse::read(MR::Image::Mapper&, MR::Image::Header&) const in analyse.o
>      MR::Image::Format::XDS::check(MR::Image::Header&, int) const in xds.o
>      MR::Image::Format::XDS::read(MR::Image::Mapper&, MR::Image::Header&) const in xds.o
>      MR::File::Dicom::Element::set(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in element.o
>      MR::Image::Format::NIfTI::check(MR::Image::Header&, int) const in nifti1.o
>      MR::Image::Format::NIfTI::create(MR::Image::Mapper&, MR::Image::Header const&) const in nifti1.o
>      ...
>  "Glib::path_get_dirname(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
>      MR::Image::NameParser::parse(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int) in name_parser.o
>      MR::Image::Format::MRtrix::read(MR::Image::Mapper&, MR::Image::Header&) const in mrtrix.o
>  "Glib::path_get_basename(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
>      MR::Image::NameParser::parse(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int) in name_parser.o
>      MR::Image::Format::MRtrix::create(MR::Image::Mapper&, MR::Image::Header const&) const in mrtrix.o
>      MR::Image::Object::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool) in object.o
>      MR::Image::Object::create(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, MR::Image::Header&) in object.o
>      MR::App::App(int, char**, char const**, MR::Argument const*, MR::Option const*, unsigned int const*, char const*, char const*) in app.o
>      MR::App::App(int, char**, char const**, MR::Argument const*, MR::Option const*, unsigned int const*, char const*, char const*) in app.o
>  "Glib::Dir::Dir(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
>      MR::Image::NameParser::get_next_match(std::vector<int, std::allocator<int> >&, bool) in name_parser.o
>      MR::File::Dicom::Tree::read_dir(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in tree.o
>  "Glib::ustring::ustring(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
>      MR::Math::Vector::save(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in vector.o
>      MR::Math::Vector::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in vector.o
>      MR::Math::Matrix::save(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in matrix.o
>      MR::Math::Matrix::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in matrix.o
>      MR::Image::NameParser::get_next_match(std::vector<int, std::allocator<int> >&, bool) in name_parser.o
>      MR::Image::Format::XDS::read(MR::Image::Mapper&, MR::Image::Header&) const in xds.o
>      MR::Image::Format::XDS::create(MR::Image::Mapper&, MR::Image::Header const&) const in xds.o
>      ...
>  "Glib::file_test(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Glib::FileTest)", referenced from:
>      MR::File::Config::init()   in config.o
>      MR::Image::NameParser::parse(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int) in name_parser.o
>      MR::File::Dicom::Tree::read_dir(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in tree.o
>      MR::File::Dicom::Tree::read(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in tree.o
>      MR::Image::Format::MRtrix::create(MR::Image::Mapper&, MR::Image::Header const&) const in mrtrix.o
>  "Glib::operator<<(std::basic_ostream<char, std::char_traits<char> >&, Glib::ustring const&)", referenced from:
>      MR::cmdline_info(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in app.o
>      MR::cmdline_error(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in app.o
>      MR::cmdline_debug(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in app.o
>      MR::operator<<(std::basic_ostream<char, std::char_traits<char> >&, MR::App const&) in app.o
> ld: symbol(s) not found for architecture x86_64
> collect2: error: ld returned 1 exit status
> 
> STOP
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
> 
> 
> 
> -- 
> Dr J-Donald Tournier (PhD)
> 
> Senior Lecturer, Biomedical Engineering
> Division of Imaging Sciences & Biomedical Engineering
> King's College London
> 
> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH
> T: +44 (0)20 7188 7118 ext 53613
> W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering