Bug#865085: [Debichem-devel] 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  compilation just done
22:39  it works :)
22:40  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

Bug#865085: avogadro: doesn't display molecules

[Stuart Prescott]

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.)

cheers
Stuart


-- System Information:
Debian Release: 9.0
  APT prefers proposed-updates
  APT policy: (550, 'proposed-updates'), (500, 'stable-debug'), (500, 
'stable'), (60, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.9.0-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), 
LANGUAGE=en_AU:en (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages avogadro depends on:
ii  libavogadro1 1.2.0-1+b1
ii  libc62.24-11
ii  libgcc1  1:6.3.0-18
ii  libopenbabel4v5  2.3.2+dfsg-3
ii  libqt4-opengl4:4.8.7+dfsg-11
ii  libqtcore4   4:4.8.7+dfsg-11
ii  libqtgui44:4.8.7+dfsg-11
ii  libstdc++6   6.3.0-18
ii  libx11-6 2:1.6.4-3

Versions of packages avogadro recommends:
ii  avogadro-data  1.2.0-1

avogadro suggests no packages.

-- no debconf information