Hi Donald, <div><br></div><div>Thank you for looking into this problem. It is really helpful to know the problem is related to the setting of the environment variable PKG_CONFIG_PATH. It is certainly a better solution than deleting the fink libraries. In one of my Mac OSX Lion computer after using MacPorts, the GTK package is installed in /opt/local/lib/pkgconfig/, but it may be different in other computers. The PKG_CONFIG_PATH didn't show up with the command 'evn' in the unix shell of my Mac (haven't tested in the other), but I agree it will be effective if this environment variable is set as you suggested. </div>
<div><br></div><div>Thanks again for your kind help. </div><div><br></div><div>Zhuang</div><div><br><br><div class="gmail_quote">On Tue, Mar 12, 2013 at 4:18 PM, Donald Tournier <span dir="ltr"><<a href="mailto:d.tournier@brain.org.au" target="_blank">d.tournier@brain.org.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Zhuang,<div><br></div><div>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. <a href="http://hints.cross-lfs.org/index.php/Basics_of_Multilib#PKG_CONFIG_PATH" target="_blank">this page</a>). 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. </div>
<div><br></div><div>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. </div>
<div><br></div><div>For reference, the way to sort this out in your case (without deleting the 32-bit Fink libraries) would probably be:</div><div><br></div><div>$ export PKG_CONFIG_PATH=/opt/lib64/pkgconfig</div><div>$ ./build</div>
<div><br></div><div>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. </div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div class="HOEnZb"><div class="h5"><div><br><br><div class="gmail_quote">On 13 March 2013 04:30, Zhuang Song <span dir="ltr"><<a href="mailto:zhuang.song@gmail.com" target="_blank">zhuang.song@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Donald, <div><br></div><div>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. </div>
<div><br></div><div>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. </div>
<div><br></div><div>Many thanks and cheers,</div><div>Zhuang </div><div><div>
<div><br></div><div><br></div><div><br></div><div><div> </div><div class="gmail_quote">On Mon, Mar 11, 2013 at 4:18 PM, Donald Tournier <span dir="ltr"><<a href="mailto:d.tournier@brain.org.au" target="_blank">d.tournier@brain.org.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Zhuang,<div><br></div><div>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).</div>
<div><br></div><div>I guess you have two options:</div><div><ul><li>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...</li>
<li>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 <a href="http://www.brain.org.au/software/mrtrix/install/macosx.html" target="_blank">listed in the documentation</a> (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).</li>
</ul><div>Hope this helps.</div></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br><br><div class="gmail_quote"><div><div>On 12 March 2013 04:42, Zhuang Song <span dir="ltr"><<a href="mailto:zhuang.song@gmail.com" target="_blank">zhuang.song@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div>Hi all, </div><div><br></div><div>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? </div>
<div> </div><div>------------------------------------------------------------------------------------------</div><div>ERROR: [LD] lib/libmrtrix-0_2_10.dylib</div><div><br>
</div><div>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</div>
<div><br></div><div>failed with output:</div><div><br></div><div>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:</div>
<div>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</div>
<div>ld: warning:</div><div>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</div>
<div>Undefined symbols for architecture x86_64:</div><div> "_g_ascii_table", referenced from:</div><div> MR::File::Dicom::select_cmdline(MR::File::Dicom::Tree const&)in select_cmdline.o</div><div> 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</div>
<div> "_g_snprintf", referenced from:</div><div> MR::Image::Header::description() constin header.o</div><div> "_g_sprintf", referenced from:</div><div> MR::Image::NameParser::name(std::vector<int, std::allocator<int> > const&)in name_parser.o</div>
<div> "_g_unlink", referenced from:</div><div> MR::File::MMap::Base::~Base()in mmap.o</div><div> "_g_vsnprintf", referenced from:</div><div> MR::printf(char const*, ...)in matrix.o</div><div>
MR::printf(char const*, ...)in patient.o</div><div> MR::printf(char const*, ...)in study.o</div><div> MR::printf(char const*, ...)in element.o</div><div> MR::printf(char const*, ...)in series.o</div>
<div>
"_glib_major_version", referenced from:</div><div> MR::App::sort_arguments(int, char**)in app.o</div><div> "_glib_micro_version", referenced from:</div><div> MR::App::sort_arguments(int, char**)in app.o</div>
<div> "_glib_minor_version", referenced from:</div><div> MR::App::sort_arguments(int, char**)in app.o</div><div>ld: symbol(s) not found for architecture x86_64</div><div>collect2: ld returned 1 exit status</div>
<div><br></div><div>Thanks, </div><span><font color="#888888"><div>Zhuang</div>
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<br></blockquote></div><span><font color="#888888"><br><br clear="all"><div><br></div>-- <br><font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br></b></font><div><font color="#ff6600" size="1">Research Fellow</font></div>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br></b></font><div><font color="#ff6600" size="1">Research Fellow</font></div><div><font size="1"><br>
</font></div><div><font size="1">The Florey Institute of Neuroscience and Mental Health</font></div><div><font size="1">Melbourne Brain Centre - Austin Campus</font></div><div><font size="1">245 Burgundy Street</font></div>
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