Problem with libpng

Benjamin_ABEL · March 30, 2013, 9:40pm

Hi all,

and first thanks for this software really impressing.

I’ve build avogadro from source on a linux 64bits machine(ubuntu 12.10),
and I canno’t display any molecule or crystal, the display remains
empty, here’s what i get on the terminal when i run avogadro in a terminal:

"Avogadro version:    1.1.0    Git:    c95020e
LibAvogadro version:    1.1.0    Git:    c95020e"
Locale:  "fr_FR"
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: "/usr/local/bin/../lib/avogadro/1_1"
Searching for plugins in "/usr/local/lib/avogadro/1_1"
Searching for plugins in "/usr/local/lib/avogadro/1_1/colors"
Searching for plugins in "/usr/local/lib/avogadro/1_1/engines"
Searching for plugins in "/usr/local/lib/avogadro/1_1/extensions"
Searching for plugins in "/usr/local/lib/avogadro/1_1/tools"
Loading plugins: "/media/home/ben/.avogadro/1_1/plugins"
Settings are missing for the next engines: ()
QStackedLayout::setCurrentWidget: Widget 0x268bfa0 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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The problem seem to come with libpng...

Does anyone know how can I fix this problem.

In advance, thanks

Benjamin ABEL
Chemistry teacher in Nice(France)

ghutchis · April 1, 2013, 8:03pm

The problem seem to come with libpng…

I wish I knew exactly where this libpng error came from, but it’s innocuous.

If you aren’t seeing anything, I’d first check your video driver. I’d also go under “View → Debug Information” and see that Avogadro is actually creating / moving atoms.

If that’s fine, click on the “Display Settings” button and make sure at least one display type is picked.

Hope that helps,
-Geoff

fredrik_haeffner · April 3, 2013, 2:51pm

Hi!
We are several users of Avogadro 1.0.3 running the application on Mac OS-X 10.7. It keeps crashing every time you copy-paste the coordinates into some other editor, vi, emacs, Word… or anything.
Restarting the computer doesn’t help. Reinstallation doesn’t help. What to do?
Fredrik

ghutchis · April 3, 2013, 3:37pm

We are several users of Avogadro 1.0.3 running the application on Mac OS-X 10.7. It keeps crashing every time you copy-paste the coordinates into some other editor, vi, emacs, Word… or anything.

Try Avogadro 1.1.0 or a nightly build:

http://avogadro.openmolecules.net/nightly/mac/unstable/

Hope that helps,
-Geoff

fredrik_haeffner · April 3, 2013, 3:49pm

Thanks! We will try it out this afternoon.

fredrik_haeffner · April 3, 2013, 9:13pm

The problem with Avogadro is a following:

pasting a structure into Avogadro and then doing select all and copy makes Avogadro crash.
loading a structure via File-Open and then select all and copy makes Avogadro crash
doing the above operations, but instead of select-all and copy, save to file works.

This is when running Avogadro 1.1.0 on a Mac OS X running 10.6.8.

Running Avogadro 1.0.3 runs fine on a machine at work. I will try to install 1.0.3 on this machine (where Avogadro 1.1.0 keeps crashing) to see if that verison is stable.

ghutchis · April 4, 2013, 11:09pm

This is when running Avogadro 1.1.0 on a Mac OS X running 10.6.8.

Huh. I don’t have a 10.6.8 machine around to test. If I send you a “debug” version can you send me back the text that appears in Apple’s crash dialog?

Thanks very much,
-Geoff

fredrik_haeffner · April 5, 2013, 12:16pm

Hi Geoff!

As I said, we are 3 people having the same problem; same Mac’s and same version of Avogadro. I got suspicious to why Avogadro on the Mac desktop at work (which I use all the time) is stable and doesn’t crash when copying coordinates from Avogadro into an editor. That version is 1.0.3. So, I reinstalled that version on my Mac laptop at home. Problem fixed!

If you tell me how to retrieve Apple’s crash dialog I am happy to help!

Fredrik

Fred_Ziegler · April 5, 2013, 7:21pm

Fredrik:

Solved the problem the same way. Back to 1.0.3. Fred Ziegler

On Apr 5, 2013, at 8:16 AM, fredrik haeffner jfhaeffner@hotmail.com wrote:

Hi Geoff!

As I said, we are 3 people having the same problem; same Mac’s and same version of Avogadro. I got suspicious to why Avogadro on the Mac desktop at work (which I use all the time) is stable and doesn’t crash when copying coordinates from Avogadro into an editor. That version is 1.0.3. So, I reinstalled that version on my Mac laptop at home. Problem fixed!

If you tell me how to retrieve Apple’s crash dialog I am happy to help!

Fredrik

From: geoff.hutchison@gmail.com
Date: Thu, 4 Apr 2013 19:09:35 -0400
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Avogadro crashing when copying-pasting

This is when running Avogadro 1.1.0 on a Mac OS X running 10.6.8.

Huh. I don’t have a 10.6.8 machine around to test. If I send you a “debug” version can you send me back the text that appears in Apple’s crash dialog?

Thanks very much,
-Geoff

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Sterling Chemistry Laboratory 
225 Prospect Street
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ghutchis · April 5, 2013, 11:17pm

Fred,

I can’t remember. Are you also using Mac OS X 10.6.x?

I’m wondering if, now that Avogadro 1.1 is compiled on 10.7, if I’m missing some backwards-compatibility issues.

Thanks very much,
-Geoff

Fred_Ziegler · April 5, 2013, 11:57pm

Geoff:

No. OS X 10.8.3. Fred

On Apr 5, 2013, at 7:17 PM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

Fred,

I can’t remember. Are you also using Mac OS X 10.6.x?

I’m wondering if, now that Avogadro 1.1 is compiled on 10.7, if I’m missing some backwards-compatibility issues.

Thanks very much,
-Geoff

Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

Professor Frederick E. Ziegler, Emeritus
Sterling Chemistry Laboratory 
225 Prospect Street
Yale University         	
P.O. Box 208107  	  
New Haven, Connecticut 06520-8107	   	
E-mail: frederick.ziegler@yale.edu 	
Telephone: (203) 432-3959             	
Fax: (203) 432-6144

fredrik_haeffner · April 6, 2013, 12:42am

I’m using Mac OS X 10.6.8

From: geoff.hutchison@gmail.com
Date: Fri, 5 Apr 2013 19:17:28 -0400
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] Avogadro crashing when copying-pasting

Fred,

I can’t remember. Are you also using Mac OS X 10.6.x?

I’m wondering if, now that Avogadro 1.1 is compiled on 10.7, if I’m missing some backwards-compatibility issues.

Thanks very much,
-Geoff

Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html

Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

Problem with libpng

Thanks very much, -Geoff

Thanks very much, -Geoff

Thanks very much,
-Geoff

Thanks very much,
-Geoff