[Mrtrix-discussion] MRtrix building issue Mac OS X 10.8.5

[Donald Tournier]

Hi Stephan,

Sounds like your compiler is stricter than most... Can I ask what version
of g++ you're running (g++ --version), and if this is the latest version of
macosx? Is this version of g++ the standard one that was installed along
with xcode?

The reason I ask is that solving this problem is going to require some
changes to the code. I wanted to know whether this is specific to your
installation, or whether a lot of users will soon be affected by the same
problem...

I'll start making the required changes in the meantime.

Cheers,
Donald.

--
Dr J-Donald Tournier (PhD)

Senior Lecturer, Biomedical Engineering
Division of Imaging Sciences & Biomedical Engineering
King's College London

A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH
T: +44 (0)20 7188 7118 ext 53613
W:
http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering

On 4 Oct 2013 15:20, <s070439 at student.dtu.dk> wrote:

> Hi,
>
> I have some problems at "The compilation step" and "Installation of
> executables" step. Could you possibly help?
>
> In Installing dependencies step:
> First I tried installing dependencies with MacPorts (recommended) method
> as on http://www.brain.org.au/software/mrtrix/install/macosx.html, but it
> failed.
>
> So I tried Homebrew method and succeeded in Get and build the
> dependencies, i.e.
> when I typed in "brew install python glib gtk+ glibmm gtkmm gtkglext gsl".
> I got:
> Warning: python-2.7.5 already installed
> Warning: glib-2.38.0 already installed
> Warning: gtk+-2.24.21 already installed
> Warning: glibmm-2.36.2 already installed
> Warning: gtkmm-2.24.4 already installed
> Warning: gtkglext-1.2.0 already installed
> Warning: gsl-1.16 already installed
>
> In Compile MRtrix step:
> 1. $ cd /Users/Stephan/Documents/MSc_Thesis/mrtrix-0.2.11
> 2. then when I tried: "./build"
> and I got:
> -bash: ./build: /usr/bin/python2: bad interpreter: No such file or
> directory
>
> so I tried: "python2.7 ./build" and got:
> Package xcb-shm was not found in the pkg-config search path.
> Perhaps you should add the directory containing `xcb-shm.pc'
> to the PKG_CONFIG_PATH environment variable
> Package 'xcb-shm', required by 'cairo', not found
> WARNING: unable to find gtkmm-2.4 configuration
> Package xcb-shm was not found in the pkg-config search path.
> Perhaps you should add the directory containing `xcb-shm.pc'
> to the PKG_CONFIG_PATH environment variable
> Package 'xcb-shm', required by 'cairo', not found
> WARNING: unable to find gtkmm-2.4 configuration
> Traceback (most recent call last):
>   File "./build", line 980, in <module>
>     [ Entry(item) for item in targets ]
>   File "./build", line 253, in __init__
>     [ Entry(item) for item in self.deps ]
>   File "./build", line 250, in __init__
>     elif is_object (self.name): self.set_object()
>   File "./build", line 305, in set_object
>     '$src$': [ cc_file ] })
>   File "./build", line 379, in fillin
>     if item in keyvalue: cmd += keyvalue[item]
> TypeError: 'NoneType' object is not iterable
>
> So, I read some discussions on your forum and tried:
> i. export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig
> ii. python2.7 ./build
> and I got:
> [CC] cmd/gen_ROI.o[CC] cmd/mradd.o
>
>
> ERROR: [CC] cmd/gen_ROI.o
>
> g++ -c -Wall -mtune=native -fPIC -fno-strict-aliasing
> -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -O2 -D_REENTRANT
> -I/usr/local/Cellar/glibmm/2.36.2/include/glibmm-2.4
> -I/usr/local/Cellar/glibmm/2.36.2/lib/glibmm-2.4/include
> -I/usr/local/Cellar/libsigc++/2.2.11/include/sigc++-2.0
> -I/usr/local/Cellar/libsigc++/2.2.11/lib/sigc++-2.0/include
> -I/usr/local/Cellar/glib/2.38.0/include/glib-2.0
> -I/usr/local/Cellar/glib/2.38.0/lib/glib-2.0/include
> -I/usr/local/opt/gettext/include -Ilib -Isrc cmd/gen_ROI.cpp -o
> cmd/gen_ROI.o
>
> failed with output:
>
> cmd/gen_ROI.cpp:89:23: error: variable length array of non-POD element
> type 'std::vector<int>'
>   std::vector<int> pos[in_obj.ndim()];
>                       ^
> 1 error generated.
>
> STOP
>
> ERROR: [CC] cmd/mradd.o
>
> g++ -c -Wall -mtune=native -fPIC -fno-strict-aliasing
> -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -O2 -D_REENTRANT
> -I/usr/local/Cellar/glibmm/2.36.2/include/glibmm-2.4
> -I/usr/local/Cellar/glibmm/2.36.2/lib/glibmm-2.4/include
> -I/usr/local/Cellar/libsigc++/2.2.11/include/sigc++-2.0
> -I/usr/local/Cellar/libsigc++/2.2.11/lib/sigc++-2.0/include
> -I/usr/local/Cellar/glib/2.38.0/include/glib-2.0
> -I/usr/local/Cellar/glib/2.38.0/lib/glib-2.0/include
> -I/usr/local/opt/gettext/include -Ilib -Isrc cmd/mradd.cpp -o cmd/mradd.o
>
> failed with output:
>
> cmd/mradd.cpp:56:27: error: variable length array of non-POD element type
> 'RefPtr<Image::Object>'
>   RefPtr<Image::Object> in[num_images];
>                           ^
> 1 error generated.
>
> STOP
>
> I also tried:
> 1. export PATH=/Users/Stephan/Documents/MSc_Thesis/mrtrix-0.2.11/bin:$PATH
> 2. export
> LD_LIBRARY_PATH=/Users/Stephan/Documents/MSc_Thesis/mrtrix-0.2.11/lib
> 3. python2.7 ./build install
> and I got:
> installing executables to "/usr/local/mrtrix/bin" and dynamic library to
> "/usr/local/mrtrix/lib"...
> Traceback (most recent call last):
>   File "./build", line 925, in <module>
>     apply_recursive (install, os.path.join (lib_dir, libname),
> os.path.join (dest_lib, libname))
>   File "./build", line 747, in apply_recursive
>     action (source, destination)
>   File "./build", line 764, in install
>     shutil.copy (source, destination)
>   File
>
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py",
> line 116, in copy
>     copyfile(src, dst)
>   File
>
> "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py",
> line 81, in copyfile
>     with open(src, 'rb') as fsrc:
> IOError: [Errno 2] No such file or directory: 'lib/libmrtrix-0_2_11.dylib'
>
> Best,
> Stephan
>
>
>
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