Console output when the bug occurred is as follows: $ igv INFO [2014-12-09 11:23:41,761] [DirectoryManager.java:149] [main] IGV Directory: /home/gokcen/igv INFO [2014-12-09 11:23:41,771] [Main.java:72] [main] Startup IGV Version 2.3.14 (16)08/05/2013 09:18 PM INFO [2014-12-09 11:23:41,771] [Main.java:73] [main] Java 1.7.0_65 Fetching user directory... INFO [2014-12-09 11:23:41,835] [Main.java:74] [main] Default User Directory: /home/gokcen INFO [2014-12-09 11:23:43,385] [GenomeManager.java:960] [main] java.io.FileNotFoundException: /home/gokcen/igv/genomes/user-defined-genomes.txt (No such file or directory) INFO [2014-12-09 11:23:43,422] [GenomeManager.java:120] [main] Loading genome: http://igvdata.broadinstitute.org/genomes/hg18.genome INFO [2014-12-09 11:23:45,356] [GenomeManager.java:164] [main] Genome loaded. id= hg18 ERROR [2014-12-09 11:23:45,387] [CommandListener.java:98] [Thread-6] java.net.BindException: Address already in use
INFO [2014-12-09 11:24:07,890] [IGV.java:1576] [pool-1-thread-6] Loading 2 resources. INFO [2014-12-09 11:24:07,899] [TrackLoader.java:113] [pool-1-thread-6] Loading resource, path http://igvdata.broadinstitute.org/data/hg18/metabric/Metabric_Clinical_IGV.txt INFO [2014-12-09 11:24:08,450] [TrackLoader.java:113] [pool-1-thread-6] Loading resource, path http://igvdata.broadinstitute.org/data/hg18/metabric/Metabric_CN_IGV.seg ERROR [2014-12-09 11:24:29,539] [DefaultExceptionHandler.java:42] [AWT-EventQueue-0] 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:1045) at javax.swing.JComponent.paintChildren(JComponent.java:878) at javax.swing.JComponent.paint(JComponent.java:1054) at javax.swing.JComponent.paintChildren(JComponent.java:878) at javax.swing.JComponent.paint(JComponent.java:1054) at javax.swing.JComponent.paintChildren(JComponent.java:878) at javax.swing.JComponent.paint(JComponent.java:1054) at javax.swing.JViewport.paint(JViewport.java:731) at javax.swing.JComponent.paintChildren(JComponent.java:878) at javax.swing.JComponent.paint(JComponent.java:1054) at javax.swing.JComponent.paintChildren(JComponent.java:878) at javax.swing.JComponent.paint(JComponent.java:1054) at javax.swing.JComponent.paintChildren(JComponent.java:878) at javax.swing.JComponent.paint(JComponent.java:1054) at javax.swing.JComponent.paintChildren(JComponent.java:878) at javax.swing.JComponent.paint(JComponent.java:1054) at javax.swing.JComponent.paintChildren(JComponent.java:878) at javax.swing.JComponent.paint(JComponent.java:1054) at javax.swing.JLayeredPane.paint(JLayeredPane.java:585) at javax.swing.JComponent.paintChildren(JComponent.java:878) at javax.swing.JComponent.paint(JComponent.java:1054) at javax.swing.JComponent.paintToOffscreen(JComponent.java:5210) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1529) at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1452) at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:311) at javax.swing.RepaintManager.paint(RepaintManager.java:1249) at javax.swing.JComponent._paintImmediately(JComponent.java:5158) at javax.swing.JComponent.paintImmediately(JComponent.java:4969) 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.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:796) at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:769) at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:718) at javax.swing.RepaintManager.access$1100(RepaintManager.java:62) at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1677) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:312) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:703) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Caused by: java.lang.ClassNotFoundException: com.google.java.contract.util.Objects at java.net.URLClassLoader$1.run(URLClassLoader.java:366) at java.net.URLClassLoader$1.run(URLClassLoader.java:355) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:354) at java.lang.ClassLoader.loadClass(ClassLoader.java:425) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308) at java.lang.ClassLoader.loadClass(ClassLoader.java:358) ... 58 more -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1400648 Title: igv is unusable since track panel does not refresh properly To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/igv/+bug/1400648/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
