Layouts Cyto 2.6.x

[Inti]

Hi,
I am sorry if this has been asked before. I tried to find the asnwer
in google and I could not.
What happend with the Layouts in the last version of Cytoscape? I can
not find any in the menu except the grid layout. Do I need to get some
plugins now?
I look forward you answers!
Best,
Inti

[Scooter Morris]

Hi Inti,
The Cytoscape layouts have always been one of the core plugins. It
sounds like you don't have the AutomaticLayout.jar file in your plugins
directory for some reason. This should have been part of your Cytoscape
download. Can you try re-installing, maybe?

-- scooter

[Inti Pedroso]

Hi,

I do have that file (look at the bottom). I installed version 2.6.1 and 2.6.0 but the same happens in all of them. i did install in in unix and mac and the same as well. See attached picture for an example from mac.

I hope you can suggest a solution.

Cheers,

Inti

[pedrosoi@DL165G5-1-14 Cytoscape_v2.6.2]$ ls plugins/

AutomaticLayout.jar  filters.jar       MetaNodePlugin2.jar

biopax.jar           GLay.jar          psi_mi.jar

browser.jar          GraphMerge.jar    quick_find.jar

cpath2.jar           last.mc           SBMLReader.jar

cPath.jar            linkout.jar       TableImport.jar

CytoscapeEditor.jar  ManualLayout.jar  yLayouts.jar

filter.jar           MCODE.jar

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[Scooter Morris]

Inti Pedroso wrote:
> Hi,
> I do have that file (look at the bottom). I installed version 2.6.1
> and 2.6.0 but the same happens in all of them. i did install in in
> unix and mac and the same as well. See attached picture for an example
> from mac.
> I hope you can suggest a solution.
> Cheers,
> Inti

Hi Inti,
Can you look at Help->Error Console and see if there are any errors
associated with your plugin loading?

-- scooter

[Inti Pedroso]

Hi,

This is the message at the terminal

>java -Xmx27000m -jar cytoscape.jar

cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization

cytoscape.CytoscapeInit[INFO]: Log information can now be found in the Help->Error Console menu

Working directory: /storage/data/pedrosoi/APP/Cytoscape_v2.6.2

Successfully created a client to server with URL = http://err.bio.nyu.edu/bionetserver2

Successfully created a client to server with URL = http://err.bio.nyu.edu/bionetserver2

Successfully created a client to server with URL = http://err.bio.nyu.edu/bionetserver2

MyDataClient.execute(interactions.getSourcesNames, params = [])

Couldn't find a boss, trying to start one....

Failed to start boss process!

java.io.IOException: java.io.IOException: /usr/java/jdk1.5.0_10/jre/bin/javaws: not found

at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)

at java.lang.ProcessImpl.start(ProcessImpl.java:65)

at java.lang.ProcessBuilder.start(ProcessBuilder.java:451)

at java.lang.Runtime.exec(Runtime.java:591)

at java.lang.Runtime.exec(Runtime.java:429)

at java.lang.Runtime.exec(Runtime.java:326)

at org.systemsbiology.gaggle.geese.common.RmiGaggleConnector.tryToStartBoss(RmiGaggleConnector.java:161)

at org.systemsbiology.gaggle.geese.common.RmiGaggleConnector.connectToGaggle(RmiGaggleConnector.java:101)

at org.isb.bionet.gui.BuilderGoose.connectToGaggle(BuilderGoose.java)

at org.isb.bionet.gui.BuilderGoose.<init>(BuilderGoose.java)

at org.isb.bionet.BioNetPlugin.prepare(BioNetPlugin.java)

at org.isb.bionet.BioNetPlugin.<init>(BioNetPlugin.java)

at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)

at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)

at java.lang.reflect.Constructor.newInstance(Constructor.java:494)

at java.lang.Class.newInstance0(Class.java:350)

at java.lang.Class.newInstance(Class.java:303)

at cytoscape.plugin.CytoscapePlugin.loadPlugin(CytoscapePlugin.java:146)

at cytoscape.plugin.PluginManager.loadPlugin(PluginManager.java:947)

at cytoscape.plugin.PluginManager.loadURLPlugins(PluginManager.java:863)

at cytoscape.plugin.PluginManager.loadPlugins(PluginManager.java:796)

at cytoscape.CytoscapeInit.init(CytoscapeInit.java:259)

at cytoscape.CyMain.<init>(CyMain.java:158)

at cytoscape.CyMain.main(CyMain.java:122)

Boss isn't quite ready yet, trying again...

Failed to connect.

MiSinkConfigAction: edu.ucla.mbi.dip.misink.MiSinkPlugin@64889c4e

PATH: /home/pedrosoi/.cytoscape/2.6/plugins/MiSink-2.04

[LinkOutNetworkListener]: constructor called

MiSink plugin initialized

MiSinkThread: server socket created...

Starting jActiveModules plugin!

[MiSinkNetworkListener]: propertyChange called

[MiSinkContextMenuListener]: Constructor called

[MiSinkContextMenuListener]: Constructor called

On 15 Apr 2009, at 23:08, Scooter Morris wrote:

An this one at the error console when i started it using the binary file

java.lang.UnsupportedClassVersionError: Bad version number in .class file

at java.lang.ClassLoader.defineClass1(Native Method)

at java.lang.ClassLoader.defineClass(ClassLoader.java:620)

at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)

at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)

at java.net.URLClassLoader.access$100(URLClassLoader.java:56)

at java.net.URLClassLoader$1.run(URLClassLoader.java:195)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:188)

at java.lang.ClassLoader.loadClass(ClassLoader.java:306)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)

at java.lang.ClassLoader.loadClass(ClassLoader.java:251)

at cytoscape.plugin.PluginManager.getPluginClass(PluginManager.java:970)

at cytoscape.plugin.PluginManager.loadURLPlugins(PluginManager.java:896)

at cytoscape.plugin.PluginManager.loadPlugins(PluginManager.java:796)

at cytoscape.CytoscapeInit.init(CytoscapeInit.java:259)

at cytoscape.CyMain.<init>(CyMain.java:158)

at cytoscape.CyMain.main(CyMain.java:122)

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

at java.lang.reflect.Method.invoke(Method.java:585)

at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)

at com.install4j.runtime.Launcher.main(Unknown Source)

 

I am starting it using the jar file because I need to use a lot of memory for my analysis.

Any idea what could be going on?

Cheers,

inti

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[Scooter Morris]

Hi Inti,
    The first error you are getting is an error from the CyGoose plugin, which isn't in the plugins list you have, and the second one looks like it's coming from a plugin that was compiled with Java 6 and you are trying to run it in Java 1.5.  I think maybe you have some additional plugins installed in your .cytoscape directory.  I would suggest removing the .cytoscape directory in your home and try again.

-- scooter

[Inti Pedroso]

Hi,

I did remove the .cytoscape folder and re-install but i have the same problem. Below is the message of the error console and then messaged from the terminal.

Any other idea of what the problem may be?

Cheers,

Inti

1 cytoscape[INFO]: starting delete action

2 cytoscape[INFO]: ending delete action

3 cytoscape[INFO]: PreferenceAction()...

4 cytoscape.actions.BookmarkAction[INFO]: BookmarkAction()... 

5 cytoscape.CytoscapeInit[INFO]: init mode: 1

6 cytoscape.CytoscapeInit[INFO]: Updating plugins...

7 cytoscape.CytoscapeInit[INFO]: loading plugins....

8 cytoscape.CytoscapeInit[INFO]: loading session...

9 cytoscape.CytoscapeInit[INFO]: loading networks...

10 cytoscape.CytoscapeInit[INFO]: loading attributes...

11 cytoscape.CytoscapeInit[INFO]: loading expression files...

12 cytoscape.CytoscapeInit[INFO]: Cytoscape initialized successfully in: 3798 ms

>java -Xmx8000M -jar cytoscape.jar 

cytoscape.CytoscapeInit[INFO]: CytoscapeInit static initialization

cytoscape.CytoscapeInit[INFO]: Parent_Dir: /home/pedrosoi/.cytoscape created.

cytoscape.CytoscapeInit[INFO]: Config file: /home/pedrosoi/.cytoscape/cytoscape.props created.

cytoscape.CytoscapeInit[INFO]: Config file: /home/pedrosoi/.cytoscape/vizmap.props created.

libxcb: WARNING! Program tries to unlock a connection without having acquired

        a lock first, which indicates a programming error.

        There will be no further warnings about this issue.

libxcb: WARNING! Program tries to lock an already locked connection,

        which indicates a programming error.

        There will be no further warnings about this issue.

cytoscape.plugin.PluginManager[INFO]: Creating directories for /home/pedrosoi/.cytoscape/2.6/plugins

cytoscape.plugin.PluginTracker[WARN]: Plugin tracker file: /home/pedrosoi/.cytoscape/2.6/track_plugins.xml

cytoscape.CytoscapeInit[INFO]: Log information can now be found in the Help->Error Console menu