[Mrtrix-discussion] installation error

Donald Tournier d.tournier at brain.org.au
Mon Mar 11 16:18:27 PDT 2013 

Hi Zhuang,

It looks like the computer you're trying to build on has the wrong versions
of the dependencies. The particular dependencies that are failing are
libglib-2.0, libgobject-2.0, and libintl. The error message state that
although these libraries were found, they are not 64-bit versions (i.e. not
x86_64). I assume you're trying to build on a 64-bit system, and on this
system you happen to have the 32-bit version of GTK installed (these
libraries are all related to Glib/GTK). I'm not sure how they got onto your
system, but presumably they were pulled in as part of an earlier install of
some other 32-bit software package (probably using Fink, judging from where
these libraries were installed).

I guess you have two options:

   - compile MRtrix in 32-bit mode. I'm not sure how you'd go about doing
   this in MacOSX, but I'm guessing you'll probably need to set the '-mtune'
   option in sysconf/darwin.py to something like 'i686'. That said, the GCC
   compiler options are subtly different on MacOSX, so this might not work,
   but a quick Google search on compiling 32-bit apps in a 64-bit environment
   on MacOSX should give you the information pretty quickly. Note that for
   this approach you'll also need 32-bit versions of all the other
   dependencies, including GSL and OpenGL; if these are not already installed,
   it'll require more work to get them installed too, in which case you'd be
   better off going for the next option, which is the one I'd recommend
   anyway...
   - The better option would be to compile in 64-bit mode, but in this case
   you'll need to install the 64-bit versions of all the dependencies. This
   shouldn't be too hard, you should be able to use one of the
approaches listed
   in the documentation<http://www.brain.org.au/software/mrtrix/install/macosx.html>(which
you've obviously already done on a different system). My guess is
   you should be able install these dependencies alongside the existing ones,
   without conflict. I think Fink will install in /sw/lib64 or similar, so it
   shouldn't affect existing applications that might rely on the 32-bit
   versions (the other approaches also install in different places, so
   shouldn't conflict either).

Hope this helps.
Cheers,

Donald.



On 12 March 2013 04:42, Zhuang Song <zhuang.song at gmail.com> wrote:

> Hi all,
>
> After I installed MRtrix- 0.2.10 successfully in one Mac OSX
> Lion computer, I got the following error when I tried to install it (by
> running ./build) in another Mac OSX Lion computer. It seems to relate to
> Xcode. Could you give me any clue how to fix it?
>
>
> ------------------------------------------------------------------------------------------
> ERROR: [LD] lib/libmrtrix-0_2_10.dylib
>
> g++ -shared -L/sw/lib 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/opt/local/lib -lglibmm-2.4 -lgobject-2.0
> -lsigc-2.0 -lgthread-2.0 -lglib-2.0 -lintl -lgsl -lgslcblas -o
> lib/libmrtrix-0_2_10.dylib
>
> failed with output:
>
> ld: warning: ignoring file /sw/lib/libgobject-2.0.dylib, file was built
> for unsupported file format ( 0xfe 0xed 0xfa 0xce 0x 0 0x 0 0x 0 0x12 0x 0
> 0x 0 0x 0 0x a 0x 0 0x 0 0x 0 0x 6 ) which is not the architecture being
> linked (x86_64): /sw/lib/libgobject-2.0.dylibld: warning:
> ld: warning: ignoring file /sw/lib/libgthread-2.0.dylib, file was built
> for unsupported file format ( 0xfe 0xed 0xfa 0xce 0x 0 0x 0 0x 0 0x12 0x 0
> 0x 0 0x 0 0x a 0x 0 0x 0 0x 0 0x 6 ) which is not the architecture being
> linked (x86_64): /sw/lib/libgthread-2.0.dylibignoring file
> /sw/lib/libglib-2.0.dylib, file was built for unsupported file format (
> 0xfe 0xed 0xfa 0xce 0x 0 0x 0 0x 0 0x12 0x 0 0x 0 0x 0 0x a 0x 0 0x 0 0x 0
> 0x 6 ) which is not the architecture being linked (x86_64):
> /sw/lib/libglib-2.0.dylib
> ld: warning:
> ignoring file /sw/lib/libintl.dylib, file was built for unsupported file
> format ( 0xfe 0xed 0xfa 0xce 0x 0 0x 0 0x 0 0x12 0x 0 0x 0 0x 0 0x a 0x 0
> 0x 0 0x 0 0x 6 ) which is not the architecture being linked (x86_64):
> /sw/lib/libintl.dylib
> Undefined symbols for architecture x86_64:
>   "_g_ascii_table", referenced from:
>       MR::File::Dicom::select_cmdline(MR::File::Dicom::Tree const&)in
> select_cmdline.o
>       MR::(anonymous
> namespace)::print_formatted_paragraph(std::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&,
> std::basic_string<char, std::char_traits<char>, std::allocator<char> >
> const&, int, int, int)in app.o
>   "_g_snprintf", referenced from:
>       MR::Image::Header::description() constin header.o
>   "_g_sprintf", referenced from:
>       MR::Image::NameParser::name(std::vector<int, std::allocator<int> >
> const&)in name_parser.o
>   "_g_unlink", referenced from:
>       MR::File::MMap::Base::~Base()in mmap.o
>   "_g_vsnprintf", referenced from:
>       MR::printf(char const*, ...)in matrix.o
>       MR::printf(char const*, ...)in patient.o
>       MR::printf(char const*, ...)in study.o
>       MR::printf(char const*, ...)in element.o
>       MR::printf(char const*, ...)in series.o
>    "_glib_major_version", referenced from:
>       MR::App::sort_arguments(int, char**)in app.o
>   "_glib_micro_version", referenced from:
>       MR::App::sort_arguments(int, char**)in app.o
>   "_glib_minor_version", referenced from:
>       MR::App::sort_arguments(int, char**)in app.o
> ld: symbol(s) not found for architecture x86_64
> collect2: ld returned 1 exit status
>
> Thanks,
> Zhuang
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>


-- 
*Dr Jacques-Donald Tournier
*
Research Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg  Vic  3084
Ph:  +61 3 9035 7033
Fax:  +61 3 9035 7307
www.florey.edu.au
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