[Debichem-devel] Bug#865085: Bug#865085: avogadro: doesn't display molecules

[Michael Banck]

Hi,

On Mon, Jun 19, 2017 at 05:04:09PM +1000, Stuart Prescott wrote:
> Package: avogadro
> Version: 1.2.0-1+b1
> Severity: serious
> Justification: package is useless
> 
> Dear Maintainer,
> 
> Avogadro in stretch appears to be unable to display any molecules. It only
> displays the background colour fill. Picking any molecule should be enough
> to reproduce this:
> 
> $ avogadro /usr/share/avogadro/fragments/alkanes/hexane.cml
> 
> or
> 
> $ avogadro
> 
>    File → Import → Fetch by chemical name → hexane
> 
> The debug view shows that avogadro has imported the right number of atoms
> and bonds, but nothing is displayed no matter what settings are chosen for
> the viewer.
> 
> (checked across 3 computers including one on which avogadro had never been
> installed before just in case it was a local config problem. Old discussions
> on the avogadro development lists around such problems frequently implicate
> compositing, but I this under Xvfb and various WMs and is, in any case, a
> regression since jessie.)

This has also been filed in Ubuntu and upstream:

https://bugs.launchpad.net/ubuntu/+source/avogadro/+bug/1640171
https://sourceforge.net/p/avogadro/bugs/783/

It seems to be an issue with out eigen3 patch, there's since been a
different commit upstream, and Khanh-Dang Nguyen Thu Lam confirmed this:

22:39 <zooe> compilation just done
22:39 <zooe> it works :)
22:40 <zooe> i did: "apt-get source avogadro", replaced
debian/patches/eigen3.patch by 43af3c117b0b3220b15c2fe2895b94bbd83d3a60,
then compiled it

https://github.com/cryos/avogadro/commit/43af3c117b0b3220b15c2fe2895b94bbd83d3a60
is the relevant changeset.


Michael