[Mrtrix-discussion] Problems (again) compiling MRTrix on OSX 10.9

Tue Nov 5 06:40:18 PST 2013

Dear Ivan,

By running the ./build on the mrtrix-read-only/ directory I got quite some warnings but no errors. Now it seems to work.

Thanks and great newsletter,

Valerio

________________________________
From: mrtrix-discussion-bounces at www.nitrc.org [mrtrix-discussion-bounces at www.nitrc.org] on behalf of Ivan Alvarez [ivan.alvarez.11 at ucl.ac.uk]
Sent: 05 November 2013 14:54
To: mrtrix-discussion at www.nitrc.org
Subject: Re: [Mrtrix-discussion] Problems (again) compiling MRTrix on OSX 10.9

Dear Valerio,

I had the same problem recently, and Jon Clayden kindly provided a fix in the latest development version of MRtrix. Try with this binary:

https://code.google.com/p/mrtrix/source/checkout

Kind regards,
Ivan Alvarez

PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH

On 05/11/13 13:47, Valerio.Zerbi at radboudumc.nl<mailto:Valerio.Zerbi at radboudumc.nl> wrote:
Dear Donald,

after a clean install of all the dependences required via PORT (port install glib2 glibmm libpng gtk2 gtkmm gtkglext gsl pkgconfig) I am now stuck in the way of compiling MRTrix. When I say ./build I got this error:

bash-3.2$ cd mrtrix-0.2.11

bash-3.2$ ./build

[CC] lib/file/dicom/quick_scan.o[CC] cmd/streamtrack.o

[CC] lib/file/dicom/study.o

[CC] src/mrview/sidebar/orientation_plot.o

[CC] lib/file/dicom/patient.o

[CC] lib/image/header.o

[CC] cmd/mrabs.o

 [CC] src/mrview/sidebar/overlay.o

ERROR: [CC] lib/file/dicom/quick_scan.o

g++ -c -Wall -mtune=native -fPIC -fno-strict-aliasing -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -I/opt/local/include -O2 -D_REENTRANT -I/opt/local/include/glibmm-2.4 -I/opt/local/lib/glibmm-2.4/include -I/opt/local/include/sigc++-2.0 -I/opt/local/lib/sigc++-2.0/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -Ilib -Isrc lib/file/dicom/quick_scan.cpp -o lib/file/dicom/quick_scan.o

failed with output:

In file included from lib/file/dicom/quick_scan.cpp:32:

In file included from lib/file/dicom/element.h:30:

lib/hash_map.h:35:12: fatal error: 'tr1/unordered_map' file not found

#  include <tr1/unordered_map>

           ^

1 error generated.

STOP

ERROR: [CC] lib/file/dicom/study.o

g++ -c -Wall -mtune=native -fPIC -fno-strict-aliasing -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -I/opt/local/include -O2 -D_REENTRANT -I/opt/local/include/glibmm-2.4 -I/opt/local/lib/glibmm-2.4/include -I/opt/local/include/sigc++-2.0 -I/opt/local/lib/sigc++-2.0/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -Ilib -Isrc lib/file/dicom/study.cpp -o lib/file/dicom/study.o

failed with output:

In file included from lib/file/dicom/study.cpp:27:

In file included from lib/file/dicom/patient.h:27:

In file included from lib/file/dicom/study.h:27:

In file included from lib/file/dicom/series.h:27:

In file included from lib/file/dicom/image.h:35:

In file included from lib/file/dicom/element.h:30:

lib/hash_map.h:35:12: fatal error: 'tr1/unordered_map' file not found

#  include <tr1/unordered_map>

           ^

1 error generated.

STOP

ERROR: [CC] cmd/streamtrack.o

g++ -c -Wall -mtune=native -fPIC -fno-strict-aliasing -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -I/opt/local/include -O2 -D_REENTRANT -I/opt/local/include/glibmm-2.4 -I/opt/local/lib/glibmm-2.4/include -I/opt/local/include/sigc++-2.0 -I/opt/local/lib/sigc++-2.0/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -Ilib -Isrc cmd/streamtrack.cpp -o cmd/streamtrack.o

failed with output:

cmd/streamtrack.cpp:262:18: error: call to 'round' is ambiguous

      min_size = round (to<float> (properties["min_dist"]) / to<float> (properties["step_size"]));

                 ^~~~~

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1552:46: note: candidate function

inline _LIBCPP_INLINE_VISIBILITY float       round(float __x) _NOEXCEPT       {return roundf(__x);}

                                             ^

lib/mrtrix.h:383:14: note: candidate function

  inline int round (float x) { return (int (x + (x > 0.0 ? 0.5 : -0.5))); }

             ^

/usr/include/math.h:490:15: note: candidate function

extern double round(double);

              ^

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1553:46: note: candidate function

inline _LIBCPP_INLINE_VISIBILITY long double round(long double __x) _NOEXCEPT {return roundl(__x);}

                                             ^

1 error generated.

STOP

ERROR: [CC] src/mrview/sidebar/overlay.o

g++ -c -Wall -mtune=native -fPIC -fno-strict-aliasing -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -I/opt/local/include -O2 -D_REENTRANT -I/opt/local/include/gtkmm-2.4 -I/opt/local/lib/gtkmm-2.4/include -I/opt/local/include/atkmm-1.6 -I/opt/local/include/gtk-unix-print-2.0 -I/opt/local/include/gtk-2.0 -I/opt/local/include/gdkmm-2.4 -I/opt/local/lib/gdkmm-2.4/include -I/opt/local/include/giomm-2.4 -I/opt/local/lib/giomm-2.4/include -I/opt/local/include/pangomm-1.4 -I/opt/local/lib/pangomm-1.4/include -I/opt/local/include/glibmm-2.4 -I/opt/local/lib/glibmm-2.4/include -I/opt/local/include/cairomm-1.0 -I/opt/local/lib/cairomm-1.0/include -I/opt/local/include/sigc++-2.0 -I/opt/local/lib/sigc++-2.0/include -I/opt/local/include/gtkglext-1.0 -I/opt/local/lib/gtkglext-1.0/include -I/opt/local/include -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/pango-1.0 -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/cairo -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/include/libpng15 -I/opt/local/include -I/opt/local/include/gdk-pixbuf-2.0 -I/opt/local/include/libpng15 -I/opt/local/include/pango-1.0 -I/opt/local/include/harfbuzz -I/opt/local/include/pango-1.0 -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/freetype2 -I/opt/local/include -I/opt/local/include/freetype2 -I/opt/local/include -Ilib -Isrc src/mrview/sidebar/overlay.cpp -o src/mrview/sidebar/overlay.o

failed with output:

In file included from src/mrview/sidebar/overlay.cpp:26:

In file included from src/mrview/window.h:36:

In file included from src/mrview/display_area.h:28:

src/mrview/pane.h:66:11: warning: 'gluProject' is deprecated: first deprecated in OS X 10.9 - "Use GLKMathProject" [-Wdeprecated-declarations]

          gluProject (pos[0], pos[1], pos[2], modelview, projection, viewport, &wx, &wy, &wz);

          ^

/System/Library/Frameworks/OpenGL.framework/Headers/glu.h:280:14: note: 'gluProject' declared here

extern GLint gluProject (GLdouble objX, GLdouble objY, GLdouble objZ, const GLdouble *model, const GLdouble *proj, const GLint *view, GLdouble* winX, GLdouble* winY, GLdouble* winZ) OPENGL_DEPRECATED_MSG(10_0, 10_9, "Use GLKMathProject");

             ^

In file included from src/mrview/sidebar/overlay.cpp:26:

In file included from src/mrview/window.h:36:

In file included from src/mrview/display_area.h:28:

src/mrview/pane.h:73:11: warning: 'gluUnProject' is deprecated: first deprecated in OS X 10.9 - "Use GLKMathUnproject" [-Wdeprecated-declarations]

          gluUnProject (pos[0], pos[1], pos[2], modelview, projection, viewport, &wx, &wy, &wz);

          ^

/System/Library/Frameworks/OpenGL.framework/Headers/glu.h:297:14: note: 'gluUnProject' declared here

extern GLint gluUnProject (GLdouble winX, GLdouble winY, GLdouble winZ, const GLdouble *model, const GLdouble *proj, const GLint *view, GLdouble* objX, GLdouble* objY, GLdouble* objZ) OPENGL_DEPRECATED_MSG(10_0, 10_9, "Use GLKMathUnproject");

             ^

In file included from src/mrview/sidebar/overlay.cpp:28:

In file included from src/dialog/file.h:37:

In file included from lib/file/dicom/tree.h:27:

In file included from lib/file/dicom/patient.h:27:

In file included from lib/file/dicom/study.h:27:

In file included from lib/file/dicom/series.h:27:

In file included from lib/file/dicom/image.h:35:

In file included from lib/file/dicom/element.h:30:

lib/hash_map.h:35:12: fatal error: 'tr1/unordered_map' file not found

#  include <tr1/unordered_map>

           ^

2 warnings and 1 error generated.

STOP

ERROR: [CC] src/mrview/sidebar/orientation_plot.o

g++ -c -Wall -mtune=native -fPIC -fno-strict-aliasing -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -I/opt/local/include -O2 -D_REENTRANT -I/opt/local/include/gtkmm-2.4 -I/opt/local/lib/gtkmm-2.4/include -I/opt/local/include/atkmm-1.6 -I/opt/local/include/gtk-unix-print-2.0 -I/opt/local/include/gtk-2.0 -I/opt/local/include/gdkmm-2.4 -I/opt/local/lib/gdkmm-2.4/include -I/opt/local/include/giomm-2.4 -I/opt/local/lib/giomm-2.4/include -I/opt/local/include/pangomm-1.4 -I/opt/local/lib/pangomm-1.4/include -I/opt/local/include/glibmm-2.4 -I/opt/local/lib/glibmm-2.4/include -I/opt/local/include/cairomm-1.0 -I/opt/local/lib/cairomm-1.0/include -I/opt/local/include/sigc++-2.0 -I/opt/local/lib/sigc++-2.0/include -I/opt/local/include/gtkglext-1.0 -I/opt/local/lib/gtkglext-1.0/include -I/opt/local/include -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/pango-1.0 -I/opt/local/include/gtk-2.0 -I/opt/local/lib/gtk-2.0/include -I/opt/local/include/pango-1.0 -I/opt/local/include/gio-unix-2.0/ -I/opt/local/include -I/opt/local/include/cairo -I/opt/local/include/atk-1.0 -I/opt/local/include/cairo -I/opt/local/include/pixman-1 -I/opt/local/include/libpng15 -I/opt/local/include -I/opt/local/include/gdk-pixbuf-2.0 -I/opt/local/include/libpng15 -I/opt/local/include/pango-1.0 -I/opt/local/include/harfbuzz -I/opt/local/include/pango-1.0 -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -I/opt/local/include/freetype2 -I/opt/local/include -I/opt/local/include/freetype2 -I/opt/local/include -Ilib -Isrc src/mrview/sidebar/orientation_plot.cpp -o src/mrview/sidebar/orientation_plot.o

failed with output:

In file included from src/mrview/sidebar/orientation_plot.cpp:40:

In file included from src/dialog/file.h:37:

In file included from lib/file/dicom/tree.h:27:

In file included from lib/file/dicom/patient.h:27:

In file included from lib/file/dicom/study.h:27:

In file included from lib/file/dicom/series.h:27:

In file included from lib/file/dicom/image.h:35:

In file included from lib/file/dicom/element.h:30:

lib/hash_map.h:35:12: fatal error: 'tr1/unordered_map' file not found

#  include <tr1/unordered_map>

           ^

1 error generated.

ERROR: [CC] lib/file/dicom/patient.o

g++ -c -Wall -mtune=native -fPIC -fno-strict-aliasing -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -I/opt/local/include -O2 -D_REENTRANT -I/opt/local/include/glibmm-2.4 -I/opt/local/lib/glibmm-2.4/include -I/opt/local/include/sigc++-2.0 -I/opt/local/lib/sigc++-2.0/include -I/opt/local/include/glib-2.0 -I/opt/local/lib/glib-2.0/include -I/opt/local/include -Ilib -Isrc lib/file/dicom/patient.cpp -o lib/file/dicom/patient.o

STOP

failed with output:

In file included from lib/file/dicom/patient.cpp:27:

In file included from lib/file/dicom/patient.h:27:

In file included from lib/file/dicom/study.h:27:

In file included from lib/file/dicom/series.h:27:

In file included from lib/file/dicom/image.h:35:

In file included from lib/file/dicom/element.h:30:

lib/hash_map.h:35:12: fatal error: 'tr1/unordered_map' file not found

#  include <tr1/unordered_map>

           ^

1 error generated.

STOP

Any clue how to solve this??

thank you,

Valerio

Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.
The Radboud university medical centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

_______________________________________________
Mrtrix-discussion mailing list
Mrtrix-discussion at www.nitrc.org<mailto:Mrtrix-discussion at www.nitrc.org>
http://www.nitrc.org/mailman/listinfo/mrtrix-discussion

Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629.
The Radboud university medical centre is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20131105/af13756a/attachment-0001.html>