[Mrtrix-discussion] installation error
Donald Tournier
d.tournier at brain.org.au
Tue Mar 12 16:18:48 PDT 2013
Hi Zhuang,
Good to hear you got it to work. It sounds to me like the issue is either
with your pkg-config installation, or with pkg-config itself. The
pkg-config command is a little program whose job it is to tell you what
compiler settings to use for a particular package (GTK or glib in this
instance). I'm not sure how it's supposed to work, but it's disappointing
that it gave you settings for a 32-bit install, when you were running a
64-bit install and clearly the 64-bit versions were available. From a quick
Google search, it seems the way around this is to make sure your desired
versions appear first in the PKG_CONFIG_PATH environment variable (see
e.g. this
page<http://hints.cross-lfs.org/index.php/Basics_of_Multilib#PKG_CONFIG_PATH>).
The correct setup on a 64-bit system would be for the 64-bit versions to
appear first in this variable, and the 32-bit version last. Clearly this
was not the case for you.
I'm not sure I can do anything to help with this issue from my end, since
on MacOSX these are 3rd-party dependencies and could be installed into many
different locations, depending on which installer was used (Fink, Macports
or Homebrew), and the particular preferences of the user (since for most of
these the default installation path can be changed by the user). Besides,
sorting this out is the job pkg-config was designed to do in the first
place, so I should not try to second-guess it - even though it is
disappointing that it failed in this case.
For reference, the way to sort this out in your case (without deleting the
32-bit Fink libraries) would probably be:
$ export PKG_CONFIG_PATH=/opt/lib64/pkgconfig
$ ./build
I'm not sure what the correct location is for PKG_CONFIG_PATH, could
be /opt/lib/pkgconfig, it really depends on how MacPorts works... In any
case, this will hopefully give a hint to anyone else who might come across
this problem.
Cheers,
Donald.
On 13 March 2013 04:30, Zhuang Song <zhuang.song at gmail.com> wrote:
> 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
>>
>>
>
--
*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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