Your message dated Tue, 18 Mar 2014 07:33:28 +0000
with message-id <[email protected]>
and subject line Bug#741052: fixed in igv 2.3.14+dfsg-2
has caused the Debian Bug report #741052,
regarding [igv] Unhandled exception java.lang.NoClassDefFoundError:
com/google/java/contract/util/Objects
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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misconfiguration somewhere. Please contact [email protected]
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--
741052: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=741052
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: igv
Source-Version: 2.3.14+dfsg-2
We believe that the bug you reported is fixed in the latest version of
igv, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated igv package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 17 Mar 2014 20:22:24 +0100
Source: igv
Binary: igv
Architecture: source all
Version: 2.3.14+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
igv - Integrative Genomics Viewer
Closes: 741052
Changes:
igv (2.3.14+dfsg-2) unstable; urgency=medium
.
* debian/upstream -> debian/upstream/metadata
* (Build-)Depends: libcofoja-java
Closes: #741052
* cme fix dpkg-control
* Add missing default-jdk in Build-Depends and use ${java:Depends}
instead of repeating dependencies manually
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Files:
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