[Mrtrix-discussion] Problems (again) compiling MRTrix on OSX 10.9
Ivan Alvarez
ivan.alvarez.11 at ucl.ac.uk
Tue Nov 5 05:54:25 PST 2013
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 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
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
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