Problem Installing Brainvisa (binary package) on MAC OS 10.6

[yo_el]

Hello,

Someone have installed it successfully?
I have installed Brainvisa 4.0 in CENTOS 5, and it worked fine.
I try to install Brainvisa 4.0 (binary package) on my laptop (new MacBookPro) but I have a problem. I get the same problem with Brainvisa 3.2 (binary package too).

I have no problem in the installation step (no error message) but when I run this line:
/usr/local/cartopack-MacOS-10.5-i386-3.2.1-2010_01_27/bin/brainvisa
I get this message:
in the Traceback (most recent call last):
File "<string>", line 27, in <module>
File "/usr/local/cartopack-MacOS-10.5-i386-3.2.1-2010_01_27/brainvisa/neuro.py", line 46, in <module>
import site
File "/usr/local/cartopack-MacOS-10.5-i386-3.2.1-2010_01_27/bin/../lib/python2.6/site-packages/site.py", line 74, in <module>
del __boot
NameError: name '__boot' is not defined

Thanks in advance for your help...

Sara

[yo_el]

I don't have this problem when I am in bash shell .

Although I have get some errors when I run anatomist, some modules seem to be missing ...

Starting Anatomist.....
config file : /Users/sara/.anatomist/config/settings.cfg
PyAnatomist Module present
global modules: /usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/bin/../share/anatomist-4.0/python_plugins
home modules: /Users/sara/.anatomist/python_plugins
loading module anacontrolmenu
loading module foldsplit
loading module gradientpalette
loading module histogram

loading of module histogram failed:
IOError : [Errno 4] Interrupted system call
traceback:
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/python/anatomist/cpp/__init__.py ( 336 ) in __init__ :
exec( 'import ' + x )
<string> ( 1 ) in <module> :
?
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/bin/../share/anatomist-4.0/python_plugins/histogram.py ( 45 ) in <module> :
from matplotlib import pyplot
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/pyplot.py ( 6 ) in <module> :
from matplotlib.figure import Figure, figaspect
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/figure.py ( 19 ) in <module> :
from axes import Axes, SubplotBase, subplot_class_factory
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/axes.py ( 12 ) in <module> :
import matplotlib.axis as maxis
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/axis.py ( 10 ) in <module> :
import matplotlib.font_manager as font_manager
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 1301 ) in <module> :
_rebuild()
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 1292 ) in _rebuild :
fontManager = FontManager()
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 984 ) in __init__ :
self.ttffiles = findSystemFonts(paths) + findSystemFonts()
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 341 ) in findSystemFonts :
for f in get_fontconfig_fonts(fontext):
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 303 ) in get_fontconfig_fonts :
status, output = commands.getstatusoutput("fc-list file")
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/commands.py ( 56 ) in getstatusoutput :
text = pipe.read()

loading module intermeas
loading module meshsplit
loading module modelGraphs
loading module palettecontrols
<H1>Anatomist launched</H1>
loading module paletteViewer

loading of module paletteViewer failed:
IOError : [Errno 4] Interrupted system call
traceback:
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/python/anatomist/cpp/__init__.py ( 336 ) in __init__ :
exec( 'import ' + x )
<string> ( 1 ) in <module> :
?
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/bin/../share/anatomist-4.0/python_plugins/paletteViewer.py ( 64 ) in <module> :
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg \
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/backends/backend_qt4agg.py ( 9 ) in <module> :
from matplotlib.figure import Figure
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/figure.py ( 19 ) in <module> :
from axes import Axes, SubplotBase, subplot_class_factory
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/axes.py ( 12 ) in <module> :
import matplotlib.axis as maxis
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/axis.py ( 10 ) in <module> :
import matplotlib.font_manager as font_manager
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 1301 ) in <module> :
_rebuild()
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 1292 ) in _rebuild :
fontManager = FontManager()
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 984 ) in __init__ :
self.ttffiles = findSystemFonts(paths) + findSystemFonts()
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 341 ) in findSystemFonts :
for f in get_fontconfig_fonts(fontext):
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/site-packages/matplotlib/font_manager.py ( 303 ) in get_fontconfig_fonts :
status, output = commands.getstatusoutput("fc-list file")
/usr/local/brainvisa-MacOS-10.5-i386-4.0-2010_06_16/lib/python2.6/commands.py ( 56 ) in getstatusoutput :
text = pipe.read()

loading module selection
loading module volumepalettes
all python modules loaded
^

[riviere]

Hi Sara,

I don't have this problem when I am in bash shell

Then when did the problem occur ?

From the error messages, it seems that Matplotlib doesn't initialize correctly, so all plugins using Matplotlib are out of order. I'm not a specialist of MacOS (especially 10.6 which I have never used), nor of Matplotlib internals. The error line

status, output = commands.getstatusoutput("fc-list file")

sugests that perhaps a "fc-list" command is used and might not be present on your system. It seems to be related to fontconfig, which I am not familiar with, too... I have to check if fontconfig is part of MacOS systems or if we have installed it afterwards (actually I don't remember).

Denis

[riviere]

Hi,
I have checked on MacOS 10.5. fontconfig, and the fc-list program, seem to be part of the system on 10.5, they are part of the X server. Maybe the X server is not installed systematically on 10.6 ? Or it's simply a PATH problem: fc-list is located in /usr/X11/bin/fc-list, so /usr/X11/bin should be in the PATH.
Denis