Errors when start up cytoscape.

[Jinyan Huang]

It seems after I installed MetaNodePlugin through plugin manager.

files in my plugin directory
------------------------------------------------------------------------------------------------------------------------
AgilentLiteratureSearch.jar
AutomaticLayout.jar
BiNGO.jar
biopax.jar
browser.jar
cPath.jar
cpath2.jar
CytoscapeEditor.jar
filter.jar
filters.jar
GraphMerge.jar
linkout.jar
ManualLayout.jar
netmatch.jar
psi_mi.jar
quick_find.jar
rowan.jar
SBMLReader.jar
TableImport.jar
yLayouts.jar

-----------------------------------------error
messages-------------------------------------------------------------------------------
java.lang.IllegalArgumentException: name
at sun.misc.URLClassPath$Loader.getResource(Unknown Source)
at sun.misc.URLClassPath.getResource(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 java.lang.ClassLoader.loadClassInternal(Unknown Source)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at cytoscape.plugin.PluginManager.loadResourcePlugins(PluginManager.java:922)
at cytoscape.plugin.PluginManager.loadPlugins(PluginManager.java:787)
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)

--
Best regards,
Jinyan Huang (ekeen)
School of Life Sciences and Technology, 1302 Room
Tongji University
Siping Road 1239, Shanghai 200092
P.R. China
Tel :0086-21-65981041
Msn: hie...@hotmail.com
eMail: hie...@gmail.com

[Peng-Liang Wang]

Hi

 

Can you provide more specific information about the error message? Such as on what OS (windows/Linux/Mac?), what Cytoscape version, what version of MetaNodePlugin and what other error messages are.

 

Thanks,

 

Peng

[Jinyan Huang]

I can remove this error by deleting the .cytoscape directory. But next
time running cytoscape, I get the same error.

the error message are:

java.lang.IllegalArgumentException: name
at sun.misc.URLClassPath$Loader.getResource(Unknown Source)
at sun.misc.URLClassPath.getResource(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 java.lang.ClassLoader.loadClassInternal(Unknown Source)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at cytoscape.plugin.PluginManager.loadResourcePlugins(PluginManager.java:922)
at cytoscape.plugin.PluginManager.loadPlugins(PluginManager.java:787)
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)

OS:windows xp
Cytoscape version:2.6.0
MetaNodePlugin2 version: 1.1

[Peng-Liang Wang]

I tested Cytoscape 2.6 on Win XP and installed the same plugin, it is just fine. I can not reproduce the error message you got.

 

Peng

[Jinyan Huang]

I also installed the fellow plugins. They all are the newest version.

AgilentLiteratureSearch.jar
AutomaticLayout.jar
BiNGO.jar
biopax.jar
browser.jar
cPath.jar
cpath2.jar
CytoscapeEditor.jar
filter.jar
filters.jar
GraphMerge.jar

HyperEdgeEditor.jar
linkout.jar
ManualLayout.jar
metaNodePlugin2.jar
MultilevelLayoutPlugin.jar
ncbiUI.jar
psi_mi.jar
quick_find.jar
SBMLReader.jar
TableImport.jar
yLayouts.jar