startup error after installing plugins

[nattha]

Hi I just installed Cytoscape 2.6 (after uninstalling other versions
and deleting ._cytoscape folder in my home directory) and copied and
paste the plugins that I downloaded for 2.5. Then, when I started
Cytoscape again, I got this error message. This didn't happen when I
used the same set of plugins with Cytoscape 2.6 beta 2. Could it be
because of the plugins? There's an "OK" button underneath this error
message and once I clicked on it, Cytoscape just closed.
java.lang.NoClassDefFoundError: org/apache/xmlbeans/XmlCursor
$XmlBookmark
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
at java.security.SecureClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.access$000(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at cytoscape.plugin.PluginManager.getPluginClass(PluginManager.java:
963)
at cytoscape.plugin.PluginManager.loadURLPlugins(PluginManager.java:
884)
at cytoscape.plugin.PluginManager.loadPlugins(PluginManager.java:786)
at cytoscape.CytoscapeInit.init(CytoscapeInit.java:236)
at cytoscape.CyMain.<init>(CyMain.java:154)
at cytoscape.CyMain.main(CyMain.java:119)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
at com.exe4j.runtime.WinLauncher.main(Unknown Source)

[nattha]

And I actually tried to uninstalled, deleted the ._cytoscape folder in
my home directory and reinstalled it 2 - 3 times.

[alan lerner]

I got the same error going from cytoscape 5.2 to 6.0 and not doing anything about the directories.
I am running windows vista and have updated my java as well. what's going on?
alan lerner

[Mike Smoot]

I'm guessing that a plugin is failing to initialize correctly, but I can't quite tell from the output.

  

Could one of you run the cytoscape.bat file from the terminal (the .bat file is found in the directory where Cytoscape was installed) and then capture the full output and send it to me?  

thanks,

Mike

--
____________________________________________________________
Michael Smoot, Ph.D. Bioengineering Department
tel: 858-822-4756 University of California San Diego

[alan lerner]

Hi Mike - this is the output. it opens cytoscape and the file command/open works but plugins don't load. when I run cytoscape.jar neither happens.
alan

C:\Program Files\Cytoscape_v2.4.1>REM Simple Cytoscape batch script for windows/
dos

C:\Program Files\Cytoscape_v2.4.1>REM (c) Trey Ideker June 21, 2002; Owen Ozier
March 06, 2003

C:\Program Files\Cytoscape_v2.4.1>REM

C:\Program Files\Cytoscape_v2.4.1>REM Runs Cytoscape from its jar file with GO d
ata loaded

C:\Program Files\Cytoscape_v2.4.1>java -Dswing.aatext=true -Xss5M -Xmx512M -jar
cytoscape.jar cytoscape.CyMain -p plugins
CytoscapeInit static initialization
init mode: 1
starting delete action
ending delete action
PreferenceAction()...
BookmarkAction()...
Updating plugins...
loading plugins....
 - directory: C:\Program Files\Cytoscape_v2.4.1\plugins
C:\Users\alan\.cytoscape\2.4\plugins\APID2NET-1.51
 - directory: C:\Users\alan\.cytoscape\2.4\plugins\APID2NET-1.51
C:\Users\alan\.cytoscape\2.4\plugins\structureViz-1.2
 - directory: C:\Users\alan\.cytoscape\2.4\plugins\structureViz-1.2
C:\Users\alan\.cytoscape\2.4\plugins\MetaNodePlugin2-1.1
 - directory: C:\Users\alan\.cytoscape\2.4\plugins\MetaNodePlugin2-1.1

attempting to load plugin url:
jar:file:C:\Program Files\Cytoscape_v2.4.1\plugins\activation.jar!/
No plugin found in specified jar - assuming it's a library.

attempting to load plugin url:
jar:file:C:\Program Files\Cytoscape_v2.4.1\plugins\AgilentLiteratureSearch.jar!/

Successfully loaded: class com.agilent.labs.lsplugin.LitSearchPlugin
Registering com.agilent.labs.lsplugin.LitSearchPlugin@146b6db
     Registering com.agilent.labs.lsplugin.LitSearchPlugin
ERROR registering plugin: Unable to load plugin.props. File is not in the expect
ed location: com/agilent/labs/lsplugin
com.agilent.labs.lsplugin.LitSearchPlugin loaded but not registered, this will n
ot affect the operation of the plugin
Track plugin: true
Adding plugin com.agilent.labs.lsplugin.LitSearchPlugin status CURRENT

attempting to load plugin url:
jar:file:C:\Program Files\Cytoscape_v2.4.1\plugins\AutomaticLayout.jar!/
Loading from manifest
Successfully loaded: class csplugins.layout.LayoutPlugin
Registering csplugins.layout.LayoutPlugin@7ff5b6
     Registering csplugins.layout.LayoutPlugin
Track plugin: true

attempting to load plugin url:
jar:file:C:\Program Files\Cytoscape_v2.4.1\plugins\axis.jar!/
Exception in thread "main" java.lang.NoClassDefFoundError: javax/servlet/http/Ht
tpServlet

        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClass(Unknown Source)
        at java.security.SecureClassLoader.defineClass(Unknown Source)
        at java.net.URLClassLoader.defineClass(Unknown Source)
        at java.net.URLClassLoader.access$000(Unknown Source)
        at java.net.URLClassLoader$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at cytoscape.plugin.PluginManager.getPluginClass(PluginManager.java:963)

        at cytoscape.plugin.PluginManager.loadURLPlugins(PluginManager.java:884)

        at cytoscape.plugin.PluginManager.loadPlugins(PluginManager.java:786)
        at cytoscape.CytoscapeInit.init(CytoscapeInit.java:236)
        at cytoscape.CyMain.<init>(CyMain.java:154)
        at cytoscape.CyMain.main(CyMain.java:119)

Caused by: java.lang.ClassNotFoundException: javax.servlet.http.HttpServlet

        at java.net.URLClassLoader$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)
        at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
        at java.lang.ClassLoader.loadClass(Unknown Source)

        at java.lang.ClassLoader.loadClassInternal(Unknown Source)
        ... 17 more
Errors on close, closed anyways.

[alan lerner]

any ideas re:ho to get plugins to load properly?
alan

[Mike Smoot]

Sorry for the slow response.  It's not clear to me from the output what version of Cytoscape you're dealing with.  2.4.1 or 2.6.0? 

In any case, the first step should be to remove your .cytoscape directory and start with a fresh install of 2.6.  Then, add plugins one by one to see what breaks.  From the output you've got, somehow an axis jar file wound up in the plugins dir and it seems to be requiring an xml api that isn't in the classpath, hence the exception.  Sooo, I'd figure out where the axis jar comes from.   I'm guessing it's coming from a plugin that requires it, but doesn't wrap the axis jar into the plugin jar (which we recommend for 2.6).


Mike

[alan lerner]

thanks!

alan

[Ofir]

I had the same thing happen with 2.6.0 and nothing worked except
deleting the installation folder and re-installing.

[hgrabner]

Hello Ofir!

I had exactly the same problem. However: As you said, when you hit
"ok", cytoscape exits. Don't hit ok. Just close the window (I am using
a mac, and I have to press that tiny little red icon on the upper left
of the window). That way cytoscape did not exit.
I got rid of all the plugins and reinstalled only the absolute
necessary for me and it worked. No error messages anymore. I guess,
one of the plugins is causing this problem. I have no clue which one
though...

Cheers,

Henrik