Cytoscape 3.1 consistently crashes immediately after loading

[Neil the Grad Student]

I had no trouble using Cytoscape 2.8.3 (64 bit), but as soon as I loaded 3.1 (64 bit), the program will not stop crashing.  I have tried using the 32 bit version, but that produces the same problems.

Interestingly, it loads just fine the very time you use it.  It presents the message: Allegro Layout:

Added the missing property(sun.*,com.sun.*) in 'org.osgi.framework.bootdelegation' config in 'C:\Program Files\Cytoscape_v3.1.0\framework\etc\custom.properties.'

Please restart Cytoscape to apply the change.

Allegro Layout will start properly after the restart.

The problem is, nothing loads properly following the restart.  I've attached a screenshot of the problem.

I updated my Java RTE (32 and 64 bit) yesterday, so I don't think that is the problem.  I'm attaching one of my error dump files if someone has experience using these to troubleshoot.

I run Windows 7 64 bit, have 8 GB of ram, and a 6-core AMD Phenom II 3.2 ghz processor.

Thanks for the help.

[Tim Hull]

It looks like you installed AllegroLayout. Did you follow the instructions on the App Store site (http://apps.cytoscape.org/apps/allegrolayout) for that? It requires you to make OSGi configuration changes in order to work. If that doesn't resolve the problem, I would try to get in touch with the developer of AllegroLayout (jy...@allegroviva.com) regarding this issue.

In any case, if you just want to get Cytoscape working again without AllegroLayout, I would delete the AllegroLayout JAR file from CytoscapeConfiguration/3/apps/installed (under your home directory) and do a clean reinstall of Cytoscape.

Hope this helps...

Tim

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[Neil the Grad Student]

Well the simple solutions are always the best.  Thank you Tim!

On Thursday, April 10, 2014 4:54:23 PM UTC-5, Tim Hull wrote:

It looks like you installed AllegroLayout. Did you follow the instructions on the App Store site (http://apps.cytoscape.org/apps/allegrolayout) for that? It requires you to make OSGi configuration changes in order to work. If that doesn't resolve the problem, I would try to get in touch with the developer of AllegroLayout (jy...@allegroviva.com) regarding this issue.

In any case, if you just want to get Cytoscape working again without AllegroLayout, I would delete the AllegroLayout JAR file from CytoscapeConfiguration/3/apps/installed (under your home directory) and do a clean reinstall of Cytoscape.

Hope this helps...

Tim

On Thu, Apr 10, 2014 at 9:33 AM, Neil the Grad Student <ntemple...@gmail.com> wrote:

I had no trouble using Cytoscape 2.8.3 (64 bit), but as soon as I loaded 3.1 (64 bit), the program will not stop crashing.  I have tried using the 32 bit version, but that produces the same problems.

Interestingly, it loads just fine the very time you use it.  It presents the message: Allegro Layout:

Added the missing property(sun.*,com.sun.*) in 'org.osgi.framework.bootdelegation' config in 'C:\Program Files\Cytoscape_v3.1.0\framework\etc\custom.properties.'

Please restart Cytoscape to apply the change.

Allegro Layout will start properly after the restart.

The problem is, nothing loads properly following the restart.  I've attached a screenshot of the problem.

I updated my Java RTE (32 and 64 bit) yesterday, so I don't think that is the problem.  I'm attaching one of my error dump files if someone has experience using these to troubleshoot.

I run Windows 7 64 bit, have 8 GB of ram, and a 6-core AMD Phenom II 3.2 ghz processor.

Thanks for the help.

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[Jun Yoon]

Hello Neil,

I am the plugin author of AllegroLayout.

It looks like there is some problem relating to loading OpenCL runtime functions which are included by the graphics driver on your system.

Please try to update your graphics driver to the latest one.

The following are the website links of graphics vendors.

Please download the latest driver and install it

- AMD graphics driver: http://support.amd.com/en-us/download

- NVIDIA graphics driver: http://www.nvidia.co.kr/Download/index.aspx?lang=en-us

If you have the same problem after updating the graphics driver, please let me know that.

I hope it will be helpful to you.

Jun