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datamind in brainvisa 4.3
Posted: Wed Mar 20, 2013 11:42 am
by guillaume
Hello,
I see that the datamind toolbox is "available" by default in the stable version of brainvisa4.3...
...but have the following error when trying to launch it:
Traceback (most recent call last): File "/home/me/BVs/brainvisa-4.3.0/bin/real-bin/datamind", line 70, in <module> import datamind.gui.MainGui File "/home/me/BVs/brainvisa-4.3.0/python/datamind/gui/MainGui.py", line 46, in <module> from qt3gui.MainGui import * File "/home/me/BVs/brainvisa-4.3.0/python/datamind/gui/MainGui.py", line 34, in <module> ImportError: libqassistantclient.so.1: cannot open shared object file: No such file or directory
So I suspect a missing lib such as pyqt-dev or similar.
I just wonder if it is plausible to make datamind running with acceptable effort or is it still quite complicated?
cheers,
gui
Re: datamind in brainvisa 4.3
Posted: Thu Mar 21, 2013 9:44 am
by riviere
Hi Guillaume,
In your case datamind is trying to load Qt3/PyQt3, which it should not, it should use Qt4/PyQt4, so something is going wrong.
Try to edit the source <brainvisa>/python/datamind/gui/MainGui.py and print if USE_QT4 is correctly set to True, and if the modules importation is OK.
Denis
Re: datamind in brainvisa 4.3
Posted: Fri Mar 22, 2013 2:42 pm
by guillaume
Hi Denis,
in fact the problem seems to be the import of datamind.config.
In the IPyhton shell I can import datamind but not datamind.config, does it make sense for you?
gui
Re: datamind in brainvisa 4.3
Posted: Fri Mar 22, 2013 6:09 pm
by riviere
Hi Guillaume,
That's right, the config.py file seems to me missing in the package, I have to investigate why.
You can recreate it, it should be in
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<brainvisa>/python/datamind/config.py
and contains a single line:
Re: datamind in brainvisa 4.3
Posted: Fri Mar 22, 2013 6:53 pm
by guillaume
Good Denis,
then I had to modify <brainvisa>/python/datamind/gui/MainGui.py like following:
from datamind.config import MAJOR_QT_VERSIONi ==> from datamind.config import MAJOR_QT_VERSION
i.e. just suppress the 'i' and now I have an error that corresponds to a library for R which is missing, but this is related to my install of R.
I will continue the fight on monday...
gui
Re: datamind in brainvisa 4.3
Posted: Sat Mar 23, 2013 1:50 am
by riviere
Strange, I don't know where that "i" comes from...
For datamind, R needs a bunch of modules. Edouard used to have a list somewhere, but I don't know if it is up to date.
Try looking in
ftp://ftp.cea.fr/pub/dsv/anatomist/unreleased/
There is a file "datamind_for_bv.tgz" there, which may contain it.
Denis
Re: datamind in brainvisa 4.3
Posted: Sat Mar 23, 2013 1:28 pm
by guillaume
Denis, in fact I think the "i" was a mistake I personally made, it is not there in another install of bv4.3.0 I have on my laptop, sorry for that.
Thank you for the link to the modules for R, I already have it from an old post on the forum and I'm currently trying to install them all.
I've never been so close to use datamind, I'll tell you if it works.
gui
Re: datamind in brainvisa 4.3
Posted: Wed Mar 27, 2013 10:20 am
by guillaume
Hi Denis,
I've never been so close...
... but it still doesnt work.
Now I'm facing issues in the install of R packages so maybe shoul I contact Edouard...
I've installed the precompiled version of R from the ftp, such that the gui of datamind appears properly however, at the start of datamind I have the following error:
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Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/guillaume/BVs/datamind_for_bv/tmp_install_R/r/lib/R/library/e1071/libs/e1071.so': libstdc++.so.6: wrong ELF class: ELFCLASS64
Error : package/namespace load failed for 'e1071'
while a "locate" shows me several libstdc++.so.6, including the one in brainvisa... so it may just be a path to set properly...
But after that when I try to plot a variable to test (plot1D in plot) I get the following exception:
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Exception in thread Thread-2: Traceback (most recent call last): File "/i2bm/research/Mandriva-2008.0-x86_64/python-2.5.1/lib/python2.5/threading.py", line 460, in __bootstrap self.run() File "/i2bm/research/Mandriva-2008.0-x86_64/python-2.5.1/lib/python2.5/threading.py", line 440, in run self.__target(*self.__args, **self.__kwargs) File "/neurospin/brainvisa/build/Mandriva-2008.0-x86_64/bug_fix/python/datamind/gui/qt4gui/StatGuiUtils.py", line 163, in asyncCallFunc File "/i2bm/research/Mandriva-2008.0-x86_64/python-2.5.1/lib/python2.5/xmlrpclib.py", line 1147, in __call__ return self.__send(self.__name, args) File "/i2bm/research/Mandriva-2008.0-x86_64/python-2.5.1/lib/python2.5/xmlrpclib.py", line 1437, in __request verbose=self.__verbose File "/i2bm/research/Mandriva-2008.0-x86_64/python-2.5.1/lib/python2.5/xmlrpclib.py", line 1201, in request return self._parse_response(h.getfile(), sock) File "/i2bm/research/Mandriva-2008.0-x86_64/python-2.5.1/lib/python2.5/xmlrpclib.py", line 1340, in _parse_response return u.close() File "/i2bm/research/Mandriva-2008.0-x86_64/python-2.5.1/lib/python2.5/xmlrpclib.py", line 787, in close raise Fault(**self._stack[0]) Fault: <Fault 800: 'missing value where TRUE/FALSE needed'>
I would just add a BIG WARNING when trying to install the pre-compiled R from the FTP:
There is a cute "rm -rf ${SRC_R}" in the r/setup.sh that is likely to produce some trouble when trying to install it in /usr/local as suggested in the readme.txt... as I did...
I suggest to comment it!
Re: datamind in brainvisa 4.3
Posted: Wed Mar 27, 2013 1:54 pm
by riviere
Hi Guillaume,
Hm, yes you'd probably rather contact Edouard. The precompiled R and script on the ftp site are probably largely outdated. Actually I don't think datamind is really maintained currently.
Denis