Installation issues on Suse 10 (64-bits) Linux...

Questions about BrainVisa usage and installation

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MichelLeipzig
Posts: 42
Joined: Tue May 29, 2007 8:31 am

Installation issues on Suse 10 (64-bits) Linux...

Post by MichelLeipzig »

Dear members,

I am seeing some installation problems on 64-bits Suse 10, despite setting LD_LIBRARY_PATH to point to 32-bit libraries.

Can anyone spot any glaring omissions on my part, or in my installation?

maudette@icaw164059:~/research/source/SHFJ_pack-stable-linux-3.0.2> ./setup.sh
Building BrainVISA cache
ERROR RuntimeError: Error(s) occured while reading processes, see the log for
details

--------------------------------------------------------------------------------
neuro.py (115) in main:

readProcesses()

neuroProcesses.py (2290) in readProcesses:

raise RuntimeError( _t_( 'Error(s) occured while reading processes, see the log
for details' ) )

SHFJ package is now installed. Enjoy.
maudette@icaw164059:~/research/source/SHFJ_pack-stable-linux-3.0.2> ./BrainVISA
Traceback (most recent call last):
File "/home/maudette/research/source/SHFJ_pack-stable-linux-3.0.2/brainvisa/neuro.py", line 49, in ?
import neuroConfig
File "/home/maudette/research/source/SHFJ_pack-stable-linux-3.0.2/brainvisa/neuroConfig.py", line 36, in ?
from backwardCompatibleQt import *
File "/home/maudette/research/source/SHFJ_pack-stable-linux-3.0.2/brainvisa/backwardCompatibleQt.py", line 35, in ?
from qt import *
ImportError: /home/maudette/research/source/SHFJ_pack-stable-linux-3.0.2/lib/python2.4/site-packages/qt.so: undefined symbol: _ZN13QDateTimeEdit13layoutEditorsEv

Thanks for your kind consideration.

Michel
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riviere
Site Admin
Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Post by riviere »

Hi,
Installation works well for me on 64 bits Fedora core 6.
BrainVisa has an incons display bug (due to Qt we guess) that can be fixed as explained in this post (look for 'ManyColor'). Anatomist icons have also strange colors.
No library problem for me...
The missing symbol is a Qt symbol, but Qt is actually shipped with the binary package, so I don't really know what goes wrong. It looks like a LD_LIBRARY_PATH problem, but this path is set inside our programs, do it should not happen...
Denis
MichelLeipzig
Posts: 42
Joined: Tue May 29, 2007 8:31 am

Post by MichelLeipzig »

riviere wrote:.... It looks like a LD_LIBRARY_PATH problem, but this path is set inside our programs, do it should not happen...
Denis
Dear Denis,

your intuition was bang-on. Thanks for your kind help. I have not played with the sulcal identification yet, and probably questions will arise, but at least the program runs fine now.

Cheers,

Michel
MichelLeipzig
Posts: 42
Joined: Tue May 29, 2007 8:31 am

Post by MichelLeipzig »

Dear All (& Denis),

looks like I jumped the gun a little bit.

The executable Brainvisa runs without errors in the log file, but the small-b brainvisa runs into the following problem:

maudette@icaw164201:~/brainvisa> ./brainvisa/brainvisa
Traceback (most recent call last):
File "/home/maudette/brainvisa/brainvisa/neuro.py", line 49, in ?
import neuroConfig
File "/home/maudette/brainvisa/brainvisa/neuroConfig.py", line 35, in ?
import gettext, sys, __builtin__, os, pickle, string, traceback, htmllib, formatter
File "/home/maudette/brainvisa/lib/python2.4/gettext.py", line 50, in ?
import locale, copy, os, re, struct, sys
ImportError: /home/maudette/brainvisa/lib/python2.4/lib-dynload/struct.so: cannot open shared object file: No such file or directory
yet...
maudette@icaw164201:~/brainvisa> find . -name struct.* -print
./lib/python2.4/lib-dynload/struct.so
and

it appears in the following paths...
maudette@icaw164201:~> grep /home/maudette/brainvisa/lib/python2.4/lib-dynload .bashrc
LD_LIBRARY_PATH=/home/maudette/brainvisa/lib:/home/maudette/brainvisa/lib/python2.4/lib-dynload:/home/maudette/brainvisa/lib/python2.4/site-packages:/usr/lib:/usr/local/vtk4.4/lib/vtk:/home/maudette/research/source/MeVisLab/bin:/home/maudette/research/source/sofa/lib/linux:/usr/lib64:/usr/X11R6/lib64:/var/tmp/dirinstall/usr/X11R6:/var/tmp/dirinstall/usr/lib:/var/tmp/dirinstall/usr/X11R6/lib64:/usr/local/lib/gdcm:$LD_LIBRARY_PATH:
PYTHONPATH=/home/maudette/brainvisa:/home/maudette/brainvisa/brainvisa:/home/maudette/brainvisa/lib:/home/maudette/brainvisa/lib/python2.4:/home/maudette/brainvisa/lib/python2.4/lib-dynload:/home/maudette/brainvisa/lib/python2.4/site-packages:/home/maudette/research/source/atamaiStuff/atamai/classes:/home/maudette/research/source/atamaiStuff/atamai/dicom:/home/maudette/research/source/atamaiStuff/atamai/examples:/home/maudette/research/source/atamaiStuff/atamai/minc:/usr/lib64:/var/tmp/dirinstall/VTK/Wrapping/Python:/var/tmp/dirinstall/VTK:/usr/lib64:/usr/lib64/python2.4:/usr/lib64/python2.4/config:/usr/lib64/python2.4/lib-tk:/usr/lib64/python2.4/site-packages:/usr/lib64/python2.4/site-packages/PIL:/usr/lib64/python2.4/site-packages/Numeric:/usr/local/vtk4.4/lib:/home/maudette/otherSource/VTK4.4/bin:/usr/local/lib:/var/tmp/dirinstall/VTK/bin

Does this look familiiar to anyone? I don't see how it can be a path issue...

Cheers,

Michel
Manik
Posts: 99
Joined: Fri Mar 05, 2004 1:00 pm
Location: INSERM U836, Grenoble

Post by Manik »

Hi,

it seems that BrainVISA just calls brainvisa/brainvisa after setting a lot of environment variables.
The variables you used are not enough to have the proper environment for brainvisa/brainvisa.
Why do you want to use brainvisa/brainvisa, as the standard way to use Brainvisa is to use BrainVISA or bin/brainvisa in the package ?
Manik Bhattacharjee
INSERM U836
MichelLeipzig
Posts: 42
Joined: Tue May 29, 2007 8:31 am

Post by MichelLeipzig »

Hello,

my mistake. I mistook big-B BrainVISA to be just a documentation for some other code. Now I've got it. Thanks for the kind reply.

Michel
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