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[alvaro <alvarolsj@xxxxxxxxxxx>]

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

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You received this bug notification because you are a member of OpenJDK,
which is subscribed to openjdk-7 in Ubuntu.
https://bugs.launchpad.net/bugs/1041543

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

Status in openjdk-7 package in Ubuntu:
  Invalid

Bug description:
  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)

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