Dear cytoscape users ,

I’m not new in cytoscape, but I got several troubles

1)      while opening the 2.6.3 version: The first use is ok, but when I
want to re-open cytoscape, then I’m unable to do so and the following error
message appears (I upgraded the java version, but nothing changed):

java.lang.NullPointerException

                at
cytoscape.plugin.PluginTracker.createPluginTable(PluginTracker.java:351)

                at
cytoscape.plugin.PluginTracker.init(PluginTracker.java:114)

                at
cytoscape.plugin.PluginTracker.<init>(PluginTracker.java:76)

                at
cytoscape.plugin.PluginManager.<init>(PluginManager.java:281)

                at
cytoscape.plugin.PluginManager.getPluginManager(PluginManager.java:175)

                at cytoscape.CytoscapeInit.init(CytoscapeInit.java:165)

                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(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)

The only way I found to re-open cytoscape is to delete each time the’
.cytoscape’  file that is created each time cytoscape is opened in my user
directory.

Maybe the problem occurs from the plugins file that I saved from a previous
version and that I paste in the new one: I tried other computers and the
same failure happened when I paste the plugins file.

2)      I’m using the expression correlation network plugin; once network
are calculated and displayed, if I save the corresponding *.cys file, this
latter cannot be re-opened anymore and I have to restart all from scratch to
visualize it again. The designer of the plugin told me that this is a bug
with the latest version of cytoscape . Do somebody fixed that?

Thank you

Jean-Charles Martin
Chargé de Recherches en Nutrition (Nutrition research Scientist)
UMR INRA 1260 / INSERM 476 / Universités AIX-MARSEILLE I & II
Nutriments Lipidiques & Prévention des Maladies Métaboliques
27, Bvd Jean Moulin
faculté de médecine de La Timone
13385 Marseille, FRANCE
 <http://www.inserm476-inra1260.fr/> www.inserm476-inra1260.fr
lab movie at  <http://fr.youtube.com/watch?v=hBipy_mmx0w>
http://fr.youtube.com/watch?v=hBipy_mmx0w
tél : 04 91 29 40 94
portable: 06 64 34 55 88
fax: 04 91 78 21 01
(from abroad) phone:+33 4 91 29 40 94
           cell phone: +33 6 64 34 55 88
                fax: +33 4 91 78 21 01