[Debian-med-packaging] Bug#741052: [igv] Unhandled exception java.lang.NoClassDefFoundError: com/google/java/contract/util/Objects
Diane Trout
diane at ghic.org
Fri Mar 7 22:13:29 UTC 2014
Package: igv
Version: 2.3.14+dfsg-1
Severity: normal
--- Please enter the report below this line. ---
Hi,
In a few different cases I gotten a very similar a java stack trace.
* I tried to download a new genome using the drop down box.
* Hitting the X maximize window decoration
* Several things that trigger tool tip popups.
(Stack trace below)
As far as I can tell IGV 2.3.14 needs Google Contracts for Java.
https://code.google.com/p/cofoja/
(I tried IGV with one of prebuilt jar files from the cofoja project and it
behaved much better).
cofoja appears to be LGPL-2.1+, so I'm assuming the best solution is to
package it for Debian.
Diane
----
Example stack trace.
ERROR [2014-03-07 13:46:08,565] [DefaultExceptionHandler.java:42] [AWT-
EventQueue-1] Unhandled exception
java.lang.NoClassDefFoundError: com/google/java/contract/util/Objects
at org.broad.igv.data.Interval.contains(Interval.java:59)
at
org.broad.igv.track.LoadedDataInterval.contains(LoadedDataInterval.java:46)
at org.broad.igv.track.DataTrack.render(DataTrack.java:83)
at
org.broad.igv.ui.panel.DataPanelPainter.draw(DataPanelPainter.java:260)
at
org.broad.igv.ui.panel.DataPanelPainter.paintFrame(DataPanelPainter.java:234)
at
org.broad.igv.ui.panel.DataPanelPainter.paint(DataPanelPainter.java:176)
at org.broad.igv.ui.panel.DataPanel.paintComponent(DataPanel.java:138)
at javax.swing.JComponent.paint(JComponent.java:1029)
at javax.swing.JComponent.paintChildren(JComponent.java:866)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent.paintChildren(JComponent.java:866)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent.paintChildren(JComponent.java:866)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JViewport.paint(JViewport.java:764)
at javax.swing.JComponent.paintChildren(JComponent.java:866)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent.paintChildren(JComponent.java:866)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent.paintChildren(JComponent.java:866)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent.paintChildren(JComponent.java:866)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent.paintChildren(JComponent.java:866)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JLayeredPane.paint(JLayeredPane.java:581)
at javax.swing.JComponent.paintChildren(JComponent.java:866)
at javax.swing.JComponent.paint(JComponent.java:1038)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5138)
at
javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1483)
at
javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1414)
at
javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:318)
at javax.swing.RepaintManager.paint(RepaintManager.java:1217)
at javax.swing.JComponent._paintImmediately(JComponent.java:5086)
at javax.swing.JComponent.paintImmediately(JComponent.java:4896)
at javax.swing.RepaintManager$3.run(RepaintManager.java:808)
at javax.swing.RepaintManager$3.run(RepaintManager.java:796)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:108)
at
javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:796)
at
javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:765)
at
javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:707)
at javax.swing.RepaintManager.access$1000(RepaintManager.java:62)
at
javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1622)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:226)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:673)
at java.awt.EventQueue.access$300(EventQueue.java:96)
at java.awt.EventQueue$2.run(EventQueue.java:634)
at java.awt.EventQueue$2.run(EventQueue.java:632)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:108)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:643)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)
--- System information. ---
Architecture: amd64
Kernel: Linux 3.12-1-amd64
Debian Release: jessie/sid
500 testing ftp.us.debian.org
500 stable-updates ftp.us.debian.org
500 stable security.debian.org
500 stable ftp.us.debian.org
110 unstable ftp.us.debian.org
110 unstable cdn.debian.net
1 experimental ftp.us.debian.org
--- Package information. ---
Depends (Version) | Installed
===========================================-+-===========
libbatik-java | 1.7+dfsg-4
libcommons-logging-java | 1.1.3-1
libcommons-math-java | 2.2-3
libcommons-net-java | 1.4.1-5
libconcurrent-java | 1.3.4-4
libhttpclient-java (>> 4.1) | 4.3.2-1
libhttpcore-java (>> 4.1) | 4.3.2-1
libjcommon-java | 1.0.16-3
libjfreechart-java | 1.0.13-5
libjhdf5-java | 2.9-1
libjlibeps-java | 0.1+2-2
libjama-java | 1.0.3-1
libjargs-java | 1.0.0-4
libjaxp1.3-java | 1.3.05-2
liblog4j1.2-java | 1.2.17-4
libsam-java (>= 1.89) | 1.105-1
libswing-layout-java | 1.0.4-4
libxml-commons-external-java | 1.4.01-2
libguava-java | 15.0-2
libnb-absolutelayout-java | 7.0.1+dfsg1-5
libbcprov-java (>= 1.47) | 1.49+dfsg-2
libjgrapht0.8-java | 0.8.3-3
libcofoja-java | 1.0~r139-2
libjide-oss-java | 3.5.10+dfsg-1
Package's Recommends field is empty.
Package's Suggests field is empty.
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