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[melchiaros <melchiaros@xxxxxxx>]

Public bug reported:

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)

** Affects: openjdk-7 (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: amd64 apport-bug quantal running-unity

-- 
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:
  New

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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