problem with installing cytoscape plugins

[pooja mandaviya]

hello,

 

     I am new to cytoscape. I have installed the new version of it. Inorder to install plugins, i tried clicking on the "plugins" on the menu and selected "install plugin from file" and then i select the plugin "jar" file i want to install (biopax or psi-nl).. but it gives the following error.

 

plugin install error:

unable to install plugin: java.lang.NullPointerException

 

cytoscape.actions.PluginInstallAction[ERROR]: Unable to install plugin: null Caused by: java.lang.NullPointerException at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at cytoscape.plugin.PluginManager.getPluginClass(PluginManager.java:1006) at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:709) at cytoscape.actions.PluginInstallAction.actionPerformed(PluginInstallAction.java:70) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)
1	cytoscape.actions.PluginInstallAction[ERROR]: Unable to install plugin: null Caused by: java.lang.NullPointerException at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at cytoscape.plugin.PluginManager.getPluginClass(PluginManager.java:1006) at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:709) at cytoscape.actions.PluginInstallAction.actionPerformed(PluginInstallAction.java:70) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.awt.EventQueue$2.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)

can anyone please suggest me. I hav also installled jdk. Or is there any other way to install plugins ?  I have also tried extracting the jar files in the "plugins" directory. but still it didnt work.

[Ankush Sharma]

Hi
Remove .cytoscape  (dot cytoscape)folder from library --> documents if you are using Windows.

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Regards
Ankush Sharma

Doctoral student in Computational Biology

Second University of Naples & Centro Ricerche Oncologiche
di Mercogliano

Email ID : ankush...@unina2.it
Phone: +39 331 831 6370

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[Komal]

Hi Pooja,

Don't extract the jar file. Just put it in the plugins directory.

Komal

On Mar 22, 4:15 am, pooja mandaviya <pooja.mandav...@gmail.com> wrote:
> hello,
>
>      I am new to cytoscape. I have installed the new version of it. Inorder
> to install plugins, i tried clicking on the "plugins" on the menu and
> selected "install plugin from file" and then i select the plugin "jar" file
> i want to install (biopax or psi-nl).. but it gives the following error.
>
> plugin install error:
> unable to install plugin: java.lang.NullPointerException
>
>   cytoscape.actions.PluginInstallAction[ERROR]: Unable to install plugin:
> null
>
> Caused by:
> java.lang.NullPointerException
> at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at cytoscape.plugin.PluginManager.getPluginClass(PluginManager.java:1006)
> at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:709)
> at

> cytoscape.actions.PluginInstallAction.actionPerformed(PluginInstallAction.j ava:70)

>  ------------------------------

>  1 cytoscape.actions.PluginInstallAction[ERROR]: Unable to install plugin:
> null
>
> Caused by:
> java.lang.NullPointerException
> at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at cytoscape.plugin.PluginManager.getPluginClass(PluginManager.java:1006)
> at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:709)
> at

> cytoscape.actions.PluginInstallAction.actionPerformed(PluginInstallAction.j ava:70)

>  ------------------------------

[Komal]

Hi Pooja,

Don't extract the .jar file; directly paste it into the plugins
directory.

On Mar 22, 4:15 am, pooja mandaviya <pooja.mandav...@gmail.com> wrote:

> hello,
>
>      I am new to cytoscape. I have installed the new version of it. Inorder
> to install plugins, i tried clicking on the "plugins" on the menu and
> selected "install plugin from file" and then i select the plugin "jar" file
> i want to install (biopax or psi-nl).. but it gives the following error.
>
> plugin install error:
> unable to install plugin: java.lang.NullPointerException
>
>   cytoscape.actions.PluginInstallAction[ERROR]: Unable to install plugin:
> null
>
> Caused by:
> java.lang.NullPointerException
> at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at cytoscape.plugin.PluginManager.getPluginClass(PluginManager.java:1006)
> at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:709)
> at

> cytoscape.actions.PluginInstallAction.actionPerformed(PluginInstallAction.j ava:70)

>  ------------------------------

>  1 cytoscape.actions.PluginInstallAction[ERROR]: Unable to install plugin:
> null
>
> Caused by:
> java.lang.NullPointerException
> at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
> at java.lang.ClassLoader.loadClass(Unknown Source)
> at cytoscape.plugin.PluginManager.getPluginClass(PluginManager.java:1006)
> at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:709)
> at

> cytoscape.actions.PluginInstallAction.actionPerformed(PluginInstallAction.j ava:70)

>  ------------------------------

[pooja mandaviya]

Thank u komal n ankush..

i have tried even wihout extracting the jar files. they r in the plugins dir as it is.

 

But ankush, could u please tell me about the "dot cytoscape" folder.. i dont find it in the documents or the cytoscape installed folders...

[Peng-Liang Wang]

".cytoscape" should be in your home directory. On Win7, it is "C:\users\YourLoginID", on WinXP, it should be in "c:\Documents\YourLoginID". I am not sure the folder name "Documents" or something else. Look at the top level folder of your driver  "C:\" .

 

Peng

[pooja mandaviya]

Hey ankush..

 

     well yes , i jus did that.. i removed the ".cytoscape" folder from the library and put it in documents , but again now i get a different error saying :

 

Unable to install plugin: java.io.FileNotFoundException: C:\Users\user\.cytoscape\2.8\plugins\biopax-2.8.1-jar-with-dependencies.jar (The system cannot find the path specified)

[pooja mandaviya]

Hey thanks Peng,

 

    I will just try out again..

[pooja mandaviya]

when i have the ".cytoscape" file as it is in the C:/Users/user/ (home) , it gives me an error :

 

plugin install error:
unable to install plugin: java.lang.NullPointerException

 

 

but when i try n replace it in documents or as any other C:users dir ,  i get the following error :

 

Unable to install plugin: java.io.FileNotFoundException: C:\Users\user\.cytoscape\2.8\plugins\biopax-2.8.1-jar-with-dependencies.jar (The system cannot find the path specified)

 

 

 

 

[Ankush Sharma]

hi pooja,
Are you using Biopax 0.3 version if so then then you have to resolve  a conflict between BioPAX Plugin v0.3 and the CytoscapeEditor.jar that shipped with Cytoscape was discovered. To resolve this conflict, replace Cytoscape-v2.3.1/plugins/CytoscapeEditor.jar with the following CytoscapeEditor.jar.

 if you have resolved it then revert back to the last Java version as i was also having the same problem with some other plugins but when i reverted back to older version of java , it worked fine for me

Regards
Ankush

[pooja mandaviya]

Hi ankush,

 

       Im using the latest cytoscape 2.8.1. and also all the plugins already came with it are 2.8.1..

 

       and i also tried what u said by replacing the cytoscape editor.. it still didnt work.. I think i shoud switch to the older versions.. ?

      
Regards,

Pooja