[Mrtrix-discussion] installation error
Zhuang Song
zhuang.song at gmail.com
Tue Mar 12 10:30:33 PDT 2013
Hi Donald,
Thank you so much for the advices and pointing out the conflicts between
fink installations and the 64-bit system. I did use fink to install some
packages a few months ago. But recently I only used MacPorts to install all
the dependencies (64-bit) by following the instructions in your webpage. It
looks like that MRtrix couldn't be built with coexisting 64-bit and 32-bit
versions of those GTK dependencies.
By simply deleting the fink folder /sw, MRtrix has been installed
beautifully in my 2nd Mac. It seems to me the build program of MRtrix would
first look for the 32-bit version of Glib/GTK and then the 64-bit version
even in a 64-bit environment of MacOSX. Maybe this is something you may
like to look into.
Many thanks and cheers,
Zhuang
On Mon, Mar 11, 2013 at 4:18 PM, Donald Tournier <d.tournier at brain.org.au>wrote:
> 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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