[Mrtrix-discussion] Linking error
Jon Clayden
jon.clayden at gmail.com
Tue Oct 29 07:38:48 PDT 2013
Hi Ben,
Thanks for the heads-up. I did look into this, but it didn't sound as
simple as you say. I'll try it locally in the first instance.
All the best,
Jon
On 28 October 2013 23:06, Jeurissen Ben <ben.jeurissen at uantwerpen.be> wrote:
> Hi Jon,
>
> Thanks for your patch! I came across the same issues and had to apply
> similar patches.
>
> One thing that I'm not sure of in your patch is the removal of -DUSE_TR1
> in the CPP flags.
>
> While this fixes the compile error of tr1/unordered_map not being found,
> it instead defaults to the older hash_map.
> Using clang, unordered_map seems to live in the root of the standard
> library and directly in the std namespace.
> So you can keep using the unordered_map with clang by removing the "tr1"
> path from the include and removing tr1:: from the HASH_MAP_TYPE define in
> case __clang__ is defined.
>
> Cheers,
> Ben
>
>
> ________________________________________
> From: mrtrix-discussion-bounces at public.nitrc.org [
> mrtrix-discussion-bounces at public.nitrc.org] on behalf of Jon Clayden [
> jon.clayden at gmail.com]
> Sent: 28 October 2013 17:54
> To: Donald Tournier
> Cc: mrtrix mailinglist
> Subject: Re: [Mrtrix-discussion] Linking error
>
> It looks like that instinct was correct. Tweaking the code to get it to
> compile with Clang seems to have done the job. FWIW, the patch is below:
> Clang is picky about "ambiguous" calls to round(), which can be fixed
> easily by adding an explicit scope. This may be useful to others building
> on recent versions of OS X.
>
> All the best,
> Jon
>
> --
> diff --git a/cmd/mrtransform.cpp b/cmd/mrtransform.cpp
> index d09d78b..2862667 100644
> --- a/cmd/mrtransform.cpp
> +++ b/cmd/mrtransform.cpp
> @@ -147,9 +147,9 @@ EXECUTE {
> opt = get_options (6); // upsample
> if (opt.size()) {
> float factor = opt[0][0].get_float();
> - header.axes.dim[0] = round (header.axes.dim[0] * factor);
> - header.axes.dim[1] = round (header.axes.dim[1] * factor);
> - header.axes.dim[2] = round (header.axes.dim[2] * factor);
> + header.axes.dim[0] = MR::round (header.axes.dim[0] * factor);
> + header.axes.dim[1] = MR::round (header.axes.dim[1] * factor);
> + header.axes.dim[2] = MR::round (header.axes.dim[2] * factor);
> header.axes.vox[0] /= factor;
> header.axes.vox[1] /= factor;
> header.axes.vox[2] /= factor;
> diff --git a/cmd/streamtrack.cpp b/cmd/streamtrack.cpp
> index 61e45f1..1b08ed7 100644
> --- a/cmd/streamtrack.cpp
> +++ b/cmd/streamtrack.cpp
> @@ -259,7 +259,7 @@ class Threader {
> max_num_attempts = to<guint> (properties["max_num_attempts"]);
>
> unidirectional = to<int> (properties["unidirectional"]);
> - min_size = round (to<float> (properties["min_dist"]) / to<float>
> (properties["step_size"]));
> + min_size = MR::round (to<float> (properties["min_dist"]) /
> to<float> (properties["step_size"]));
>
> writer.create (output_file, properties);
> }
> diff --git a/sysconf/darwin.py b/sysconf/darwin.py
> index a675462..9f62666 100644
> --- a/sysconf/darwin.py
> +++ b/sysconf/darwin.py
> @@ -5,14 +5,14 @@ exe_suffix = ''
> lib_prefix = 'lib'
> lib_suffix = '.dylib'
>
> -cpp = [ 'g++', '-c', '$flags$', '$gtk$', '$path$', '$src$', '-o', '$obj$'
> ]
> -cpp_flags = [ '-Wall', '-mtune=native', '-fPIC', '-fno-strict-aliasing',
> '-DGL_GLEXT_PROTOTYPES', '-DUSE_TR1' ]
> +cpp = [ 'clang++', '-c', '$flags$', '$gtk$', '$path$', '$src$', '-o',
> '$obj$' ]
> +cpp_flags = [ '-Wall', '-mtune=native', '-fPIC', '-fno-strict-aliasing',
> '-DGL_GLEXT_PROTOTYPES' ]
>
> -ld = [ 'g++', '$flags$', '$path$', '$obj$', '$mrtrix$', '$gsl$', '$gtk$',
> '$lz$', '-o', '$bin$' ]
> +ld = [ 'clang++', '$flags$', '$path$', '$obj$', '$mrtrix$', '$gsl$',
> '$gtk$', '$lz$', '-o', '$bin$' ]
> ld_flags = []
> ld_flags_lib_prefix = '-l'
>
> -ld_lib = [ 'g++', '-shared', '$flags$', '$obj$', '-o', '$lib$' ]
> +ld_lib = [ 'clang++', '-shared', '$flags$', '$obj$', '-o', '$lib$' ]
> ld_lib_flags = []
>
> # look for MacPorts or FINK dependencies, and act accordingly if found:
>
>
> On 28 Oct 2013, at 16:18, Jon Clayden <jon.clayden at gmail.com> wrote:
>
> > 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 -lgt
> hre
> >> 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
> >
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20131029/1def1623/attachment-0001.html>
More information about the Mrtrix-discussion
mailing list