openjdk has become incompatible to Cytoscape2.8.3 with the latest updates

[Sasa Paporovic]

With the latest updates to Ubuntu12.10 Quantal Cytoscape 2.8.3 has become unusable.

You can get Cytoscape from:

http://cytoscape.org/

download it as tar.gz for Linux.

Extract it and run from terminal in the Cytoscape directory:

java -Xmx2000m -Xss500m -jar cytoscape.jar -p plugins

after this you get the error :

cytoscape.CytoscapeInit[ERROR]: Plugin system initialization error: java.lang.NumberFormatException: Cytoscape version numbers must be in the format: "^\d+\.\d+(\.\d+(-[a-zA-Z]+)?)?$"! (Bad version is "".)

Caused by:
Cytoscape version numbers must be in the format: "^\d+\.\d+(\.\d+(-[a-zA-Z]+)?)?$"! (Bad version is "".)
at cytoscape.plugin.DownloadableInfo.addCytoscapeVersion(DownloadableInfo.java:176)
at cytoscape.plugin.PluginTracker.createBasicObject(PluginTracker.java:508)
at cytoscape.plugin.PluginTracker.createPluginObject(PluginTracker.java:600)
at cytoscape.plugin.PluginTracker.getPluginContent(PluginTracker.java:569)
at cytoscape.plugin.PluginTracker.getDownloadableContent(PluginTracker.java:588)
at cytoscape.plugin.PluginTracker.getDownloadableListByStatus(PluginTracker.java:196)
at cytoscape.plugin.PluginManager.getDownloadables(PluginManager.java:313)
at cytoscape.CytoscapeInit.loadPlugins(CytoscapeInit.java:636)
at cytoscape.CytoscapeInit.init(CytoscapeInit.java:209)
at cytoscape.CyMain.(CyMain.java:144)
at cytoscape.CyMain.main(CyMain.java:108)

Some days ago this Cytoscape version was working, so the error must be on Ubuntu.

ProblemType: Bug
DistroRelease: Ubuntu 12.10
Package: openjdk-7-jre 7~u3-2.1.1~pre1-1ubuntu4
ProcVersionSignature: Ubuntu 3.5.0-11.11-generic 3.5.2
Uname: Linux 3.5.0-11-generic x86_64
ApportVersion: 2.5.1-0ubuntu2
Architecture: amd64
Date: Sat Aug 25 14:18:26 2012
InstallationMedia: Ubuntu 12.10 "Quantal Quetzal" - Alpha amd64 (20120722)
ProcEnviron:
 PATH=(custom, no username)
 LANG=de_DE.UTF-8
 SHELL=/bin/bash
SourcePackage: openjdk-7
UpgradeStatus: No upgrade log present (probably fresh install)

[Sasa Paporovic (melchiaros)]

I have seen that the latest openjdk update is month ago, but anyway with today(two days ago all was working) the program has get a broken start.

[Sasa Paporovic (melchiaros)]

This seems to be cuased by a wider system change. I get also by copying the whole cytoscape folder to a usb drive the nautilus message, that the file names are invalid.

[Sasa Paporovic (melchiaros)]

The only big change I have observed within the last upgrade round I have done, was the nautilus downgrade to 3.5.4

[Sasa Paporovic (melchiaros)]

I have tested a swith to oracle jdk 7u6. No difference, so it is not caused specific by openjdk.

[Sasa Paporovic (melchiaros)]

I have found the problem; it was cuased by a corrupted file in a hidden folder; I have searched for this hours; a wasted day.

I close this here as invalid.

[alvaro (alvarolsj)]

Hi,

I'm using Cytoscape 2.8.3 with Ubuntu and found the same error. Can you describe step by step how to resolve this error? I am Ubuntu novice user.

Thank you!

Alvaro