Installation problem on Mac OSX Lion 2.7

Questions about BrainVisa usage and installation

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Dominique Geffroy
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Installation problem on Mac OSX Lion 2.7

Post by Dominique Geffroy »

Hello,

Users reported problem when trying to use Brainvisa/Anatomist on a Mac (Mac OX X 10.7.1, OSX Lion 2.7 GhZ IntelCore i5).

Here is the error when trying to start Anatomist:

./anatomist
dyld: Symbol not found: _sqlite3_wal_checkpoint
Referenced from: /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork
Expected in: /Users/mdojat/Soft/brainvisa-MacOS-10.5-i386-4.1.0-2011_05_16/lib/libsqlite3.dylib
in /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/CFNetwork

Does anyone succeeded in using Brainvisa on this type of Mac ?
We don't have such a system in our lab so it is difficult for us to investigate the problem.

Dominique
jjwisco
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Re: Installation problem on Mac OSX Lion 2.7

Post by jjwisco »

I had BrainVISA working in Snow Leopard, but ever since upgrading to Lion, I haven't been able to get BrainVISA to work. I had to abandon it. I would really like to know if there's a fix, though.
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riviere
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Re: Installation problem on Mac OSX Lion 2.7

Post by riviere »

Hi,

We do not have a MacOS 10.7 machine to do any test or porting for now (we have _one_ Mac and it's a 10.5 system), so we'll not be able to do much if there is a serious problem.
However the error reported here seems to be due to the fact that we ship in brainvisa a libsqlite that is probably too old for your system.
You can try removing (or renaming it) from the brainvisa package, so the sqlite lib from your system will be used instead. No guarantee but you can try it, it's easy: just move out the libsqlite3* files in the lib/ directory of the brainvisa package, and try again.
Please tell us if it helps...

Denis
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Re: Installation problem on Mac OSX Lion 2.7

Post by mdojat »

It seems working if:
- all libsqlite3* files in the lib/ directory are moved
- file libBLAS.dylib in the lib/directory is moved

Best
Michel
Dominique Geffroy
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Re: Installation problem on Mac OSX Lion 2.7

Post by Dominique Geffroy »

Good news !
Thank you for the feedback.

Dominique
ericbarnhill
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Re: Installation problem on Mac OSX Lion 2.7

Post by ericbarnhill »

Hello, just letting you know that this solution worked for me too. It did not run at first and gave me a similar error. I just had to rm libsqlite3* from the lib folder. Now it runs.

Thanks,
Eric
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Re: Installation problem on Mac OSX Lion 2.7

Post by qcai »

Just to know whether there is a solution for Snow Leopard? it doesn't work on mine without any error message / feedback.
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riviere
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Re: Installation problem on Mac OSX Lion 2.7

Post by riviere »

What is Snow Leopard ? Sorry, not a Mac addict, I only understand the OS versions numbers, not the little names. Is it 10.6 ? It should work. Have you tried the above workarounds ?

Denis
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Yann Cointepas
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Re: Installation problem on Mac OSX Lion 2.7

Post by Yann Cointepas »

The snow leopard (Uncia uncia or Panthera uncia) is a moderately large cat native to the mountain ranges of South Asia and Central Asia.
Sorry for the bad joke. According to Google results it is MacOS 10.6.
synic
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Re: Installation problem on Mac OSX Lion 2.7

Post by synic »

mdojat wrote:It seems working if:
- all libsqlite3* files in the lib/ directory are moved
- file libBLAS.dylib in the lib/directory is moved

Best
Michel
Hey Guys,

I tried to do this on my 10.7 OSX and BV 4.3 but I can't find libsqlite3* files neither libBLAS.dylib files in the lib directory.
Brainvisa is not launching but anatomist is working fine.

Thanks for advices and solutions.
Kind regards,

michel
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riviere
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Re: Installation problem on Mac OSX Lion 2.7

Post by riviere »

Hi,
Well, actually I think we removed libsqlite and libBLAS from the binary package since they seemed to be provided on Mac systems and cause trouble if we shipped them. But we could not actually test it since we don't have a MacOS 10.7 machine - we are working almost blindly on that: Mac is not our primary development system, we have just one for porting, it is installed in 10.5 and has many development libs installed so we do not see if there are missing libs in the packages, or incompatibilities with newer systems. We just have users feedback to adapt the packages...
Did you try running brainvisa from a terminal so that you see error messages related to libraries finding / loading ? Could you copy/paste the messages there please ?
Denis
synic
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Re: Installation problem on Mac OSX Lion 2.7

Post by synic »

I completely understand your point on BV not beeing natively developed on MacOS and I am very thanks full that a MacOS version of BV exists!

Having said that the error message I've got is
LSOpenURLsWithRole() failed with error -10810 for the file /brainvisa/BrainVISA.app.

Thanks for your help.
mich
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riviere
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Re: Installation problem on Mac OSX Lion 2.7

Post by riviere »

Hi,
Well, the message doesn't say much... Maybe if you used the "open" command outputs are hidden.
Could you try, in a terminal, running the script directly:

Code: Select all

/brainvisa/bin/brainvisa
I hope it will be a bit more verbose.
Denis
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Re: Installation problem on Mac OSX Lion 2.7

Post by synic »

Here you go!
Traceback (most recent call last):
File "<string>", line 27, in <module>
File "/brainvisa/brainvisa/neuro.py", line 71, in <module>
from brainvisa.toolboxes import readToolboxes, allToolboxes
File "/brainvisa/python/brainvisa/toolboxes.py", line 33, in <module>
import brainvisa.processes
File "/brainvisa/python/brainvisa/processes.py", line 187, in <module>
from brainvisa.data.neuroData import *
File "/brainvisa/python/brainvisa/data/neuroData.py", line 75, in <module>
from brainvisa.processing.neuroException import HTMLMessage
File "/brainvisa/python/brainvisa/processing/neuroException.py", line 50, in <module>
from brainvisa.processing.qtgui.neuroExceptionGUI import ShowException
File "/brainvisa/python/brainvisa/processing/qtgui/neuroExceptionGUI.py", line 33, in <module>
from brainvisa.processing.qt4gui.neuroExceptionGUI import *
File "/brainvisa/python/brainvisa/processing/qt4gui/neuroExceptionGUI.py", line 34, in <module>
from soma.qtgui.api import TextEditWithSearch
File "/brainvisa/python/soma/qtgui/api.py", line 46, in <module>
from soma.qt4gui.api import *
File "/brainvisa/python/soma/qt4gui/api.py", line 72, in <module>
from soma.qt4gui.text import TextEditWithSearch, TextBrowserWithSearch, WebBrowserWithSearch
File "/brainvisa/python/soma/qt4gui/text.py", line 42, in <module>
from PyQt4 import QtWebKit
ImportError: dlopen(/brainvisa/lib/python2.6/site-packages/PyQt4/QtWebKit.so, 2): Library not loaded: QtDBus.framework/Versions/4/QtDBus
Referenced from: /brainvisa/lib/python2.6/site-packages/PyQt4/QtWebKit.so
Reason: image not found
BTW, I installed 4.2.1 removing the lib and it does work very well. It must be something which changed between 4.2.1 and 4.3
Thanks for your help,

mich
Dominique Geffroy
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Re: Installation problem on Mac OSX Lion 2.7

Post by Dominique Geffroy »

Hello,

It seems a Qt library is missing in the 4.3 package. Indeed, we use QtWebKit only since the 4.3 version, so maybe we forgot to put in the package a dependency of this library (QtDBus ?).
Maybe you could install Qt4 (4.6.2) on your system to workaround the problem or wait for a next package...

Dominique
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