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. 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