Re: [Open Babel] python bindings broken in 2.2.1 on 64 bit linux

[Rajiv N. <ask...@gm...>]

Thanks for the suggestion It turns out I was indeed using an outdated
version of SWIG, However switching to the latest version (1.3.39) didnt fix
the problem. I then discovered that the problem occurs only with python2.4
and not python2.5 or python2.6. So I think the issue is python related
rather than swig related. This is not a big deal for me as I can easily
switch to python 2.6, but its worth noting..

-Rajiv



On Mon, Mar 23, 2009 at 5:14 AM, Noel O'Boyle <bao...@gm...> wrote:

> Sorry for the delay in replying. openbabel-scripting is a good place
> to send emails about the Python bindings BTW.
>
> I'm afraid I can't test the problem as I don't have access to a 64 bit
> system. However, it is possible it is due to OpenBabel's use of SWIG
> 1.3.37, which has several changes to how it handles Python in
> particular (some good, some unexpected). You could try recompiling OB
> and its bindings using the very latest version of swig (1.3.39) or the
> earlier one (1.3.36). (Put swig on the path and use ./configure
> --enable-maintainer-mode).
>
> I would be very interested to know if this helps.
>
> - Noel
>
> 2009/3/10 Rajiv Narayan <ask...@gm...>:
> > Python bindings seem partially broken on my 64 bit system. Anyone else
> > experiencing a similar problem?
> > It builds and installs ok, but running
> scripts/python/examples/examples.py
> > segfaults at the following line
> > obConversion = openbabel.OBConversion()
> > It also segfaults when importing pybel. Libopenbabel and the perl
> bindings
> > seem to function ok.
> >
> > -Rajiv
> >
> > SuSE Linux 9.2 (x86-64)
> > Linux foobar 2.6.8-24.25-smp #1 SMP Thu Aug 24 09:57:32 UTC 2006 x86_64
> > x86_64 x86_64 GNU/Linux
> > gcc 3.4.4
> > python 2.4.2
> > openbabel 2.2.1
> >
> >>python examples.py
> >
> > Should print 0 (atoms)
> > 0
> > Should print 2 (atoms)
> > 2
> > Should print 1 (bond)
> > 1
> > *** glibc detected *** double free or corruption: 0x0000000000745450 ***
> > *** glibc detected *** double free or corruption: 0x0000000000747dd8 ***
> > *** glibc detected *** double free or corruption: 0x0000000000748a00 ***
> > ==============================
> > *** Open Babel Error  in OBDefine
> >   Failed to make an instance CompopWtr
> > Segmentation fault
> >
> > Python 2.4.2 (#1, Apr 18 2007, 16:10:26)
> > [GCC 3.3.4 (pre 3.3.5 20040809)] on linux2
> > Type "help", "copyright", "credits" or "license" for more information.
> >>>> import openbabel
> >>>> import pybel
> > *** glibc detected *** double free or corruption: 0x00000000007bd7a0 ***
> > *** glibc detected *** double free or corruption: 0x00000000007c0128 ***
> > *** glibc detected *** double free or corruption: 0x00000000007c0d50 ***
> > ==============================
> > *** Open Babel Error  in OBDefine
> >   Failed to make an instance Compo��{r
> > Segmentation fault
> >
> >
> >
> >
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