WordCloud fails to start

[Florian Duclot]

Hello,

I'm trying to run the WordCloud app on Cytoscape 3.2, but cannot seem to figure out how to install it. I tried to install it directly from Cytoscape via the App Manager, or copying the WordCloud.jar into my Cytoscape_configuration/3/apps/installed folder, or even installing an older version of the plugin, nothing fixes the issue.

I'm running Ubuntu 14.10, with Java 8:

java version "1.8.0_25"

Java(TM) SE Runtime Environment (build 1.8.0_25-b17)

Java HotSpot(TM) 64-Bit Server VM (build 25.25-b02, mixed mode)

Here's the error I found in framework-cytoscape.log:

2014-12-03 19:54:19,776 [fileinstall-/home/florian/CytoscapeConfiguration/3/apps/installed] WARN  org.apache.felix.fileinstall - Error while starting bundle: file:/home/florian/CytoscapeConfiguration/3/apps/installed/wordcloud-3.0.0.jar

org.osgi.framework.BundleException: Activator start error in bundle wordcloud [108].

at org.apache.felix.framework.Felix.activateBundle(Felix.java:2027)

at org.apache.felix.framework.Felix.startBundle(Felix.java:1895)

at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:944)

at org.apache.felix.fileinstall.internal.DirectoryWatcher.startBundle(DirectoryWatcher.java:1263)

at org.apache.felix.fileinstall.internal.DirectoryWatcher.startBundles(DirectoryWatcher.java:1235)

at org.apache.felix.fileinstall.internal.DirectoryWatcher.process(DirectoryWatcher.java:524)

at org.apache.felix.fileinstall.internal.DirectoryWatcher.run(DirectoryWatcher.java:308)

Caused by: java.lang.NullPointerException

at org.baderlab.wordcloud.internal.ui.cloud.CloudDisplayPanel.setDocker(CloudDisplayPanel.java:123)

at org.baderlab.wordcloud.internal.ui.UIManager.show(UIManager.java:102)

at org.baderlab.wordcloud.internal.ui.UIManager.setCurrentCloud(UIManager.java:194)

at org.baderlab.wordcloud.internal.ui.UIManager.setCurrentCloud(UIManager.java:184)

at org.baderlab.wordcloud.internal.ui.UIManager.setCurrentCloud(UIManager.java:172)

at org.baderlab.wordcloud.internal.ui.UIManager.setCurrentCloud(UIManager.java:153)

at org.baderlab.wordcloud.internal.ui.UIManager$1.actionPerformed(UIManager.java:79)

at org.baderlab.wordcloud.internal.CyActivator.start(CyActivator.java:99)

at org.apache.felix.framework.util.SecureAction.startActivator(SecureAction.java:645)

at org.apache.felix.framework.Felix.activateBundle(Felix.java:1977)

... 6 more

This error keeps repeating itself indefinitively.

Any idea on how to fix this issue?

Thanks a lot for the help,

Florian.

[Florian Duclot]

I realized I forgot to include the following additional information about my setup:

Cytoscape 3.2.0> info
Karaf
  Karaf version               2.3.5
  Karaf home                  /home/florian/Tools/Cytoscape_v3.2.0/framework
  Karaf base                  /home/florian/Tools/Cytoscape_v3.2.0/framework
  OSGi Framework              org.apache.felix.framework - 4.0.3


JVM
  Java Virtual Machine        Java HotSpot(TM) 64-Bit Server VM version 25.25-b02
  Version                     1.8.0_25
  Vendor                      Oracle Corporation
  Pid                         6073
  Uptime                      58.178 seconds
  Total compile time          20.537 seconds
Threads
  Live threads                35
  Daemon threads              27
  Peak                        37
  Total started               43
Memory
  Current heap size           181,592 kbytes
  Maximum heap size           5,050,368 kbytes
  Committed heap size         3,124,224 kbytes
  Pending objects             0
  Garbage collector           Name = 'PS Scavenge', Collections = 3, Time = 0.149 seconds
  Garbage collector           Name = 'PS MarkSweep', Collections = 3, Time = 0.496 seconds
Classes
  Current classes loaded      9,633
  Total classes loaded        9,635
  Total classes unloaded      2
Operating system
  Name                        Linux version 3.16.0-25-generic
  Architecture                amd64
  Processors                  2

[Mike Kucera]

Hi Florian,

You discovered a bug in wordcloud. I will start working on a fix.

Thanks.

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[Mike Kucera]

I have uploaded a new version of WordCloud (3.0.1) to the App Store that fixes this bug.

Thanks.