<div dir="ltr">Hi Ben,<div><br></div><div>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.</div><div><br></div><div>All the best,</div>
<div>Jon</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 28 October 2013 23:06, Jeurissen Ben <span dir="ltr"><<a href="mailto:ben.jeurissen@uantwerpen.be" target="_blank">ben.jeurissen@uantwerpen.be</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Jon,<br>
<br>
Thanks for your patch! I came across the same issues and had to apply similar patches.<br>
<br>
One thing that I'm not sure of in your patch is the removal of -DUSE_TR1 in the CPP flags.<br>
<br>
While this fixes the compile error of tr1/unordered_map not being found, it instead defaults to the older hash_map.<br>
Using clang, unordered_map seems to live in the root of the standard library and directly in the std namespace.<br>
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.<br>
<br>
Cheers,<br>
Ben<br>
<br>
<br>
________________________________________<br>
From: <a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a> [<a href="mailto:mrtrix-discussion-bounces@public.nitrc.org">mrtrix-discussion-bounces@public.nitrc.org</a>] on behalf of Jon Clayden [<a href="mailto:jon.clayden@gmail.com">jon.clayden@gmail.com</a>]<br>
Sent: 28 October 2013 17:54<br>
To: Donald Tournier<br>
Cc: mrtrix mailinglist<br>
Subject: Re: [Mrtrix-discussion] Linking error<br>
<div class="HOEnZb"><div class="h5"><br>
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.<br>
<br>
All the best,<br>
Jon<br>
<br>
--<br>
diff --git a/cmd/mrtransform.cpp b/cmd/mrtransform.cpp<br>
index d09d78b..2862667 100644<br>
--- a/cmd/mrtransform.cpp<br>
+++ b/cmd/mrtransform.cpp<br>
@@ -147,9 +147,9 @@ EXECUTE {<br>
opt = get_options (6); // upsample<br>
if (opt.size()) {<br>
float factor = opt[0][0].get_float();<br>
- header.axes.dim[0] = round (header.axes.dim[0] * factor);<br>
- header.axes.dim[1] = round (header.axes.dim[1] * factor);<br>
- header.axes.dim[2] = round (header.axes.dim[2] * factor);<br>
+ header.axes.dim[0] = MR::round (header.axes.dim[0] * factor);<br>
+ header.axes.dim[1] = MR::round (header.axes.dim[1] * factor);<br>
+ header.axes.dim[2] = MR::round (header.axes.dim[2] * factor);<br>
header.axes.vox[0] /= factor;<br>
header.axes.vox[1] /= factor;<br>
header.axes.vox[2] /= factor;<br>
diff --git a/cmd/streamtrack.cpp b/cmd/streamtrack.cpp<br>
index 61e45f1..1b08ed7 100644<br>
--- a/cmd/streamtrack.cpp<br>
+++ b/cmd/streamtrack.cpp<br>
@@ -259,7 +259,7 @@ class Threader {<br>
max_num_attempts = to<guint> (properties["max_num_attempts"]);<br>
<br>
unidirectional = to<int> (properties["unidirectional"]);<br>
- min_size = round (to<float> (properties["min_dist"]) / to<float> (properties["step_size"]));<br>
+ min_size = MR::round (to<float> (properties["min_dist"]) / to<float> (properties["step_size"]));<br>
<br>
writer.create (output_file, properties);<br>
}<br>
diff --git a/sysconf/darwin.py b/sysconf/darwin.py<br>
index a675462..9f62666 100644<br>
--- a/sysconf/darwin.py<br>
+++ b/sysconf/darwin.py<br>
@@ -5,14 +5,14 @@ exe_suffix = ''<br>
lib_prefix = 'lib'<br>
lib_suffix = '.dylib'<br>
<br>
-cpp = [ 'g++', '-c', '$flags$', '$gtk$', '$path$', '$src$', '-o', '$obj$' ]<br>
-cpp_flags = [ '-Wall', '-mtune=native', '-fPIC', '-fno-strict-aliasing', '-DGL_GLEXT_PROTOTYPES', '-DUSE_TR1' ]<br>
+cpp = [ 'clang++', '-c', '$flags$', '$gtk$', '$path$', '$src$', '-o', '$obj$' ]<br>
+cpp_flags = [ '-Wall', '-mtune=native', '-fPIC', '-fno-strict-aliasing', '-DGL_GLEXT_PROTOTYPES' ]<br>
<br>
-ld = [ 'g++', '$flags$', '$path$', '$obj$', '$mrtrix$', '$gsl$', '$gtk$', '$lz$', '-o', '$bin$' ]<br>
+ld = [ 'clang++', '$flags$', '$path$', '$obj$', '$mrtrix$', '$gsl$', '$gtk$', '$lz$', '-o', '$bin$' ]<br>
ld_flags = []<br>
ld_flags_lib_prefix = '-l'<br>
<br>
-ld_lib = [ 'g++', '-shared', '$flags$', '$obj$', '-o', '$lib$' ]<br>
+ld_lib = [ 'clang++', '-shared', '$flags$', '$obj$', '-o', '$lib$' ]<br>
ld_lib_flags = []<br>
<br>
# look for MacPorts or FINK dependencies, and act accordingly if found:<br>
<br>
<br>
On 28 Oct 2013, at 16:18, Jon Clayden <<a href="mailto:jon.clayden@gmail.com">jon.clayden@gmail.com</a>> wrote:<br>
<br>
> Hi Donald,<br>
><br>
> Thanks for the quick reply. Unfortunately I've already tried cleaning up first, and it doesn't help.<br>
><br>
> 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:<br>
><br>
> $ nm -arch x86_64 -g /usr/local/Cellar/glibmm/2.38.0/lib/libglibmm-2.4.dylib | grep build_filename<br>
> 0000000000017261 T __ZN4Glib14build_filenameERKNS_11ArrayHandleINSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEENS_17Container_Helpers10TypeTraitsIS7_EEEE<br>
> 00000000000172ce T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_<br>
> 000000000001735d T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_<br>
> 00000000000173fd T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_<br>
> 00000000000174b0 T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_<br>
> 0000000000017575 T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_S8_<br>
> 000000000001765c T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_S8_S8_<br>
> 000000000001775a T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_S8_S8_S8_<br>
> 000000000001786f T __ZN4Glib14build_filenameERKNSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEES8_S8_S8_S8_S8_S8_S8_S8_<br>
> U _g_build_filename<br>
> U _g_build_filenamev<br>
><br>
> 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.<br>
><br>
> All the best,<br>
> Jon<br>
><br>
><br>
> On 28 Oct 2013, at 15:25, Donald Tournier <<a href="mailto:jdtournier@gmail.com">jdtournier@gmail.com</a>> wrote:<br>
><br>
>> Hey Jon,<br>
>><br>
>> 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.<br>
>><br>
>> So in brief, try './build clean', then './build'...<br>
>><br>
>> Cheers,<br>
>> Donald.<br>
>><br>
>><br>
>><br>
>> On 28 October 2013 15:11, Jon Clayden <<a href="mailto:jon.clayden@gmail.com">jon.clayden@gmail.com</a>> wrote:<br>
>> Dear all,<br>
>><br>
>> 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.<br>
>><br>
>> 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).<br>
>><br>
>> Am I missing something obvious here?<br>
>><br>
>> Thanks in advance,<br>
>> Jon<br>
>><br>
>> --<br>
>> [LD] lib/libmrtrix-0_2_11.dylib<br>
>><br>
>> ERROR: [LD] lib/libmrtrix-0_2_11.dylib<br>
>><br>
>> 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<br>
hre<br>
>> ad-2.0 -lglib-2.0 -lintl -lgsl -lgslcblas -lz -o lib/libmrtrix-0_2_11.dylib<br>
>><br>
>> failed with output:<br>
>><br>
>> Undefined symbols for architecture x86_64:<br>
>> "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:<br>
>> MR::File::Config::init() in config.o<br>
>> MR::Image::NameParser::name(std::vector<int, std::allocator<int> > const&) in name_parser.o<br>
>> MR::Image::NameParser::get_next_match(std::vector<int, std::allocator<int> >&, bool) in name_parser.o<br>
>> MR::File::Dicom::Tree::read_dir(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in tree.o<br>
>> MR::Image::Format::MRtrix::read(MR::Image::Mapper&, MR::Image::Header&) const in mrtrix.o<br>
>> "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:<br>
>> MR::Image::Format::Analyse::check(MR::Image::Header&, int) const in analyse.o<br>
>> MR::Image::Format::Analyse::read(MR::Image::Mapper&, MR::Image::Header&) const in analyse.o<br>
>> MR::Image::Format::XDS::check(MR::Image::Header&, int) const in xds.o<br>
>> MR::Image::Format::XDS::read(MR::Image::Mapper&, MR::Image::Header&) const in xds.o<br>
>> MR::File::Dicom::Element::set(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in element.o<br>
>> MR::Image::Format::NIfTI::check(MR::Image::Header&, int) const in nifti1.o<br>
>> MR::Image::Format::NIfTI::create(MR::Image::Mapper&, MR::Image::Header const&) const in nifti1.o<br>
>> ...<br>
>> "Glib::path_get_dirname(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:<br>
>> MR::Image::NameParser::parse(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int) in name_parser.o<br>
>> MR::Image::Format::MRtrix::read(MR::Image::Mapper&, MR::Image::Header&) const in mrtrix.o<br>
>> "Glib::path_get_basename(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:<br>
>> MR::Image::NameParser::parse(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int) in name_parser.o<br>
>> MR::Image::Format::MRtrix::create(MR::Image::Mapper&, MR::Image::Header const&) const in mrtrix.o<br>
>> MR::Image::Object::open(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool) in object.o<br>
>> MR::Image::Object::create(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, MR::Image::Header&) in object.o<br>
>> MR::App::App(int, char**, char const**, MR::Argument const*, MR::Option const*, unsigned int const*, char const*, char const*) in app.o<br>
>> MR::App::App(int, char**, char const**, MR::Argument const*, MR::Option const*, unsigned int const*, char const*, char const*) in app.o<br>
>> "Glib::Dir::Dir(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:<br>
>> MR::Image::NameParser::get_next_match(std::vector<int, std::allocator<int> >&, bool) in name_parser.o<br>
>> MR::File::Dicom::Tree::read_dir(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in tree.o<br>
>> "Glib::ustring::ustring(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:<br>
>> MR::Math::Vector::save(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in vector.o<br>
>> MR::Math::Vector::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in vector.o<br>
>> MR::Math::Matrix::save(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const in matrix.o<br>
>> MR::Math::Matrix::load(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in matrix.o<br>
>> MR::Image::NameParser::get_next_match(std::vector<int, std::allocator<int> >&, bool) in name_parser.o<br>
>> MR::Image::Format::XDS::read(MR::Image::Mapper&, MR::Image::Header&) const in xds.o<br>
>> MR::Image::Format::XDS::create(MR::Image::Mapper&, MR::Image::Header const&) const in xds.o<br>
>> ...<br>
>> "Glib::file_test(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Glib::FileTest)", referenced from:<br>
>> MR::File::Config::init() in config.o<br>
>> MR::Image::NameParser::parse(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int) in name_parser.o<br>
>> MR::File::Dicom::Tree::read_dir(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in tree.o<br>
>> MR::File::Dicom::Tree::read(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in tree.o<br>
>> MR::Image::Format::MRtrix::create(MR::Image::Mapper&, MR::Image::Header const&) const in mrtrix.o<br>
>> "Glib::operator<<(std::basic_ostream<char, std::char_traits<char> >&, Glib::ustring const&)", referenced from:<br>
>> MR::cmdline_info(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in app.o<br>
>> MR::cmdline_error(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in app.o<br>
>> MR::cmdline_debug(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) in app.o<br>
>> MR::operator<<(std::basic_ostream<char, std::char_traits<char> >&, MR::App const&) in app.o<br>
>> ld: symbol(s) not found for architecture x86_64<br>
>> collect2: error: ld returned 1 exit status<br>
>><br>
>> STOP<br>
>> _______________________________________________<br>
>> Mrtrix-discussion mailing list<br>
>> <a href="mailto:Mrtrix-discussion@www.nitrc.org">Mrtrix-discussion@www.nitrc.org</a><br>
>> <a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
>><br>
>><br>
>><br>
>> --<br>
>> Dr J-Donald Tournier (PhD)<br>
>><br>
>> Senior Lecturer, Biomedical Engineering<br>
>> Division of Imaging Sciences & Biomedical Engineering<br>
>> King's College London<br>
>><br>
>> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
>> T: <a href="tel:%2B44%20%280%2920%207188%207118%20ext%2053613" value="+442071887118">+44 (0)20 7188 7118 ext 53613</a><br>
>> W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
><br>
<br>
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