[Mrtrix-discussion] Linking error

[Donald Tournier]

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
*
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