Problem with libpng

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)

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

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

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

Thanks! We will try it out this afternoon.

The problem with Avogadro is a following:

  1. pasting a structure into Avogadro and then doing select all and copy makes Avogadro crash.

  2. loading a structure via File-Open and then select all and copy makes Avogadro crash

  3. 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.

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

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

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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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 	
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Fax: (203) 432-6144                   	

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

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
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss


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                   	

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
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss