Problem with libpng(no atom display)

Hi,

I believe I am having the same problem. While I could get avogadro working nicely on my mac, an ubuntu 12.04 installation either from the ubuntu-repo or compiling from source-code from https://github.com/dlonie/avogadro (needed for installing xtalopt. I followed the installation directions in http://xtalopt.openmolecules.net/wiki/index.fcgi/wiki/Installation and all dependencies were installed using ‘sudo apt-get’) without any errors gives me an executable which prints the following lines when run, and doesn’t pop-up a GUI window. I do see a avogadro thumbnail on the launcher in ubuntu, but clicking it doesn’t produce a GUI window. The execution hangs in the terminal after printing the lines below. Same happens when run as root except for a few less errors printed to terminal.

I have nvidia video card, and I have updated all drivers as well as programs installed in the computer using apt-get upgrade.

Does anyone have any suggestions? Also, I see that some folks have successfully installed in ubuntu, can they say if they did that in v12.04 and if their video card is nvidia? For Qt I installed version 4 using apt-get install qt4* . Is there anyone with a successful recent ubuntu installation who can post the installation ‘recipe’ ? (again, I used the one from here http://xtalopt.openmolecules.net/wiki/index.fcgi/wiki/Installation and didn’t get any errors during compilation/installation.) .

Thank you for your suggestions.

Text printed to terminal before hanging without a GUI window:

"Avogadro version: 1.1.0 Git:
LibAvogadro version: 1.1.0 Git: "
Locale: "en_US"
Libavogadro translations not found.
System has OpenGL support.
About to test OpenGL capabilities.
OpenGL capabilities found:
Double Buffering.
Direct Rendering.
Antialiasing.
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action “” under id 62
void DBusMenuExporterPrivate::addAction(QAction*, int): Already tracking action “” under id 63
Loading plugins: "/home/g5q/bin/…/lib/avogadro/1_1"
Searching for plugins in "/home/g5q/lib/avogadro/1_1"
Searching for plugins in "/home/g5q/lib/avogadro/1_1/colors"
Searching for plugins in "/home/g5q/lib/avogadro/1_1/engines"
Searching for plugins in "/home/g5q/lib/avogadro/1_1/extensions"
Searching for plugins in "/home/g5q/lib/avogadro/1_1/tools"
Searching for plugins in "/home/g5q/lib/avogadro/1_1/contrib"
Loading plugins: "/home/g5q/.avogadro/1_1/plugins"
Settings are missing for the next engines: (“Ball and Stick”, “Axes”, “Cartoon”, “Dipole”, “Force”, “Hydrogen Bond”, “Label”, “Polygon”, “QTAIM”, “Ribbon”, “Ring”, “Simple Wireframe”, “Van der Waals Spheres”, “Stick”, “Surfaces”, “Wireframe”)
QStackedLayout::setCurrentWidget: Widget 0x292af60 not contained in stack
dev warning: Extension “GAMESS” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Orbitals” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
dev warning: Extension “Vibration” is using a deprecated DockWidget loading method. See Extension::dockWidgets() documentation.
GLWidget initialisation…
GLWidget initialised…
createObjects()
libpng warning: Ignoring attempt to set cHRM RGB triangle with zero area

Thanks for your answer Geoff,

I don’t think it’s my video driver because when I install avogadro from
the repository with apt-get, it works fine (except that avogadro crash
when I want to save).

You’re right, the problem don’t come from libpng because I’ve got the
same message when I run the fonctionnal avogadro 1.0.3 caught with
apt-get.(libpng warning: Ignoring attempt to set cHRM RGB triangle with
zero area)

The atoms are really created but not displayed(seen from the cartesian
editor)

The display is checked.

I’ve also tried to use the avogadro-squared git but there’s a problem
cloning the openbabel git

Cloning into 'openbabel'...
remote: Counting objects: 39465, done.
remote: Compressing objects: 100% (7170/7170), done.
remote: Total 39465 (delta 32101), reused 39412 (delta 32066)
Receiving objects: 100% (39465/39465), 30.23 MiB | 3.43 MiB/s, done.
Resolving deltas: 100% (32101/32101), done.
fatal: reference is not a tree: 2d41e95c6c94d8eab39ddc3459f990b47fcf2e51

Remark: you may need to add the “make” line in the wiki page
http://avogadro.openmolecules.net/wiki/Compiling_on_Linux_and_Mac_OS_X
for beginners like me!

Thanks for your help.

Benjamin ABEL
Chemistry teacher in Nice(France)

On Thu, Apr 18, 2013 at 12:31 PM, Ganesh, Panchapakesan
ganeshp@ornl.gov wrote:

I believe I am having the same problem. While I could get avogadro working nicely on my mac, an ubuntu 12.04 installation either from the ubuntu-repo or compiling from source-code from https://github.com/dlonie/avogadro.

I didn’t catch this earlier, but those instructions were a bit out of
date. Can you try installing from https://github.com/cryos/avogadro?
My fork is probably out of date – I’ve updated the instructions to
point at cryos’s repo.

Dave