Bugzilla – Bug 1093037
Avogadro 1.2.0 crashes on startup: undefined symbol _ZN9OpenBabel5OBMol8NextBondERN9__gnu_cxx17__normal_iteratorIPPNS_6OBBondESt6vectorIS4_SaIS4_EEEE
Last modified: 2018-05-26 05:07:22 UTC
Created attachment 769990 [details]
LD_DEBUG=libs avogadro output
Avogadro 1.2.0 crashes on startup on openSUSE Tumbleweed 20180502, giving the error:
avogadro: symbol lookup error: /usr/lib64/libavogadro.so.1: undefined symbol: _ZN9OpenBabel5OBMol8NextBondERN9__gnu_cxx17__normal_iteratorIPPNS_6OBBondESt6vectorIS4_SaIS4_EEEE
which to me indicates a rebuild may be needed for Avogadro against a new build of OpenBabel. My OpenBabel version is 2.4.1-18.5. I should mention I have the Education repository enabled and both Avogadro and Openbabel packages seems to be from this repository (precise package revision is 1.2.0-5.3). As this seems like too little information to provide I ran:
and that gave the attached output. Likewise strace avogadro gave: https://gist.github.com/231f06f4de25f9d91286b6bd643b17a7.
Created attachment 769991 [details]
strace avogadro output
On the most recent version of tumbleweed:
avogadro crashes right away, and when running from terminal:
avogadro: symbol lookup error: /usr/lib64/libavogadro.so.1: undefined symbol: _ZN9OpenBabel5OBMol12SetConformerEi
Here is a link to the output of "ldd /usr/bin/avogadro" http://paste.opensuse.org/43054496
I've removing the avogadro package (including libavogadro1 which provides libavogadro.so.1) and re-installing without any luck.
So I think I have the same problem.
Not sure what fixed it, but a dup (# VERSION="20180521") and re-install fixed it for me.
Didn't fix it for me.