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Tasklist

FS#21708 - [openbabel] python bindings does not work properly

Attached to Project: Arch Linux
Opened by Hector Mtz-Seara Monne (hseara) - Monday, 15 November 2010, 22:04 GMT
Last edited by Andrea Scarpino (BaSh) - Wednesday, 17 November 2010, 10:47 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To Andrea Scarpino (BaSh)
Architecture All
Severity High
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 1
Private No

Details

Description:

Openbabel package fails to use properly the python bindings. See the error message when importing the pybel package in idle (same in openbabel):

#############################
Python 3.1.2 (r312:79147, Oct 4 2010, 12:35:40)
[GCC 4.5.1] on linux2
Type "copyright", "credits" or "license()" for more information.
>>> import pybel
Traceback (most recent call last):
File "<pyshell#0>", line 1, in <module>
import pybel
File "/usr/lib/python3.1/site-packages/pybel.py", line 16, in <module>
import openbabel as ob
File "/usr/lib/python3.1/site-packages/openbabel.py", line 56, in <module>
_openbabel = swig_import_helper()
File "/usr/lib/python3.1/site-packages/openbabel.py", line 52, in swig_import_helper
_mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError: /usr/lib/python3.1/site-packages/_openbabel.so: undefined symbol: _ZTVN9OpenBabel22OBEnergyConformerScoreE
###################

The python bindings installation seems okay (python-openbabel and python2-openbabel). Just reinstalling openbabel using the PKGBUILD of abs solves the problem with further modification in my computer.

Additional info:
* package version(s)
openbabel 3.2.0-1
* config and/or log files etc.


Steps to reproduce:
It happens alway to me. If you need any further information please let me know.
This task depends upon

Closed by  Andrea Scarpino (BaSh)
Wednesday, 17 November 2010, 10:47 GMT
Reason for closing:  Fixed
Additional comments about closing:  openbabel 2.3.0-2
Comment by Andrea Scarpino (BaSh) - Monday, 15 November 2010, 22:32 GMT
openbabel is built using python2, maybe python-openbabel cannot be used with it
Comment by Hector Mtz-Seara Monne (hseara) - Tuesday, 16 November 2010, 09:39 GMT
No, This does not influence. I'm aware that cmake detects python 2.7 but if -DPYTHON_BINDINGS=ON option is not used is not use for anything. The prove is that I have it running nicely in my computer, both python2 and 3, and I only recompile openbabel where cmake also detected python 2.7. Aside I got the same error with python2 bindings as I say and both get corrected simultaneously when openbabel is installed from the sources using the abs PKGBUILD method. I don't know which is the problem of the binaries of openbabel, but something is wrong.
Comment by Andrea Scarpino (BaSh) - Tuesday, 16 November 2010, 21:29 GMT
I rebuilt python2-openbabel, but I get the same error. Didn't test with Python3.
Comment by Hector Mtz-Seara Monne (hseara) - Tuesday, 16 November 2010, 22:12 GMT
As I say in my previous comment the problem in not in the bindings. It is in the openbabel package itself. I do not understand what is wrong with it, maybe the computer where the package was build have some environmental variable that makes this problem appear. When I upgrade ONLY the openbabel package in my computer from the sources using the PKGBUILD in abs, I only change the release number, the plugings start working correctly. I repeat: I didn't need to install/reinstall/upgrade/recompile at all python2-openbabel and python-openbabel( python3 version) packages.
Comment by Andrea Scarpino (BaSh) - Wednesday, 17 November 2010, 09:20 GMT
We build packages in clean chroot, so there was no environment variables set.
I rebuilt only openbabel and this does not help here. I am using python2.
Comment by Hector Mtz-Seara Monne (hseara) - Wednesday, 17 November 2010, 10:16 GMT
In my case after rebuilding openbabel package both python2-openbabel and python-openbabel start working correctly. I'm not sure if that means that I have something installed that you don't have. I have checked if the package swig was needed but do not seem so. In principle, openbabel people already compile these part of the code so no need of swig. Any idea of what I can check in my system to guess what's going on? I have archlinux in 32bits only.
Comment by Andrea Scarpino (BaSh) - Wednesday, 17 November 2010, 10:20 GMT
I built again openbabel on my system and now it works. This time I have both eigen and swig. I am doing some test.

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