Unable to launch IGV 2.1.20

[ymc]

I am running it on Ubuntu 12.04. My Java version is 1.7.0_03. Thanks in advance!

user@HPC:/tank/igvtools/IGV_2.1.20$ java -Xmx10g -jar igv.jar
INFO [2012-06-30 18:24:26,856]  [DirectoryManager.java:149] [main]  IGV Directory: /home/user/igv
INFO [2012-06-30 18:24:26,859]  [Main.java:77] [main]  Startup  IGV Version 2.1.20 (2537)06/26/2012 11:15 PM
Fetching user directory... INFO [2012-06-30 18:24:26,878]  [Main.java:78] [main]  Default User Directory: /home/user
ERROR [2012-06-30 18:24:26,881]  [DefaultExceptionHandler.java:42] [main]  Unhandled exception
java.awt.HeadlessException
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:197)
    at java.awt.Window.<init>(Window.java:534)
    at java.awt.Frame.<init>(Frame.java:420)
    at java.awt.Frame.<init>(Frame.java:385)
    at javax.swing.JFrame.<init>(JFrame.java:174)
    at org.broad.igv.ui.Main.main(Main.java:69)
ERROR [2012-06-30 18:24:26,894]  [DefaultExceptionHandler.java:42] [Thread-2]  Unhandled exception
java.lang.RuntimeException: IGV has not been initialized.  Must call createInstance(Frame) first
    at org.broad.igv.ui.IGV.getInstance(IGV.java:148)
    at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:46)

[ymc]

Oh well, it works after I ran sudo apt-get install openjdk-7-jre

[Jim Robinson]

OK,  it looks like you did not have the Java X-windows support installed before.

[Sara Monzón]

Hi,

I have exactly the same issue, but i have openjdk-7-jre correctly installed. I have being using IGV without problems for years, but suddenly I cannot open it, any idea?

Thanks for your attention,

Sara

[Jim Robinson]

Hi,

You say exactly the same issue, are you getting the exception below  (" Unhandled exception  java.awt.HeadlessException")?

--
 
---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/3aBWNNsY9B0/unsubscribe?hl=en.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[Sara Monzón]

Ups, I'm sorry, you are right it is not the exactly same issue. I only read the begining of the error.

I got this:

ERROR [2013-05-28 13:46:30,986]  [DefaultExceptionHandler.java:42] [AWT-EventQueue-0]  Unhandled exception
java.lang.NoSuchMethodError: sun.reflect.Reflection.getCallerClass(I)Ljava/lang/Class;
        at com.jidesoft.plaf.UIDefaultsLookup.getCallerClassLoader(Unknown Source)
        at com.jidesoft.plaf.UIDefaultsLookup.get(Unknown Source)
        at com.jidesoft.plaf.basic.BasicJideButtonUI.installDefaults(Unknown Source)
        at com.jidesoft.plaf.basic.BasicJideButtonUI.installUI(Unknown Source)
        at javax.swing.JComponent.setUI(JComponent.java:664)
        at com.jidesoft.swing.JideButton.updateUI(Unknown Source)
        at javax.swing.AbstractButton.init(AbstractButton.java:2176)
        at javax.swing.JButton.<init>(JButton.java:137)
        at javax.swing.JButton.<init>(JButton.java:91)
        at com.jidesoft.swing.JideButton.<init>(Unknown Source)
        at com.jidesoft.swing.JideButton.<init>(Unknown Source)
        at org.broad.igv.ui.IGVCommandBar.initComponents(IGVCommandBar.java:784)
        at org.broad.igv.ui.IGVCommandBar.<init>(IGVCommandBar.java:100)
        at org.broad.igv.ui.IGVContentPane.<init>(IGVContentPane.java:74)
        at org.broad.igv.ui.IGV.<init>(IGV.java:232)
        at org.broad.igv.ui.IGV.createInstance(IGV.java:126)
        at org.broad.igv.ui.Main.open(Main.java:182)
        at org.broad.igv.ui.Main$1.run(Main.java:80)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251)
        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:726)
        at java.awt.EventQueue.access$200(EventQueue.java:103)
        at java.awt.EventQueue$3.run(EventQueue.java:687)
        at java.awt.EventQueue$3.run(EventQueue.java:685)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:696)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:220)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:135)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:123)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:119)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:111)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:97)

Thanks a lot and sorry for any inconvenience,

Sara

2013/5/28 Jim Robinson <jrob...@broadinstitute.org>

--
Sara Monzón Fernández
M.Sc. in Bioinformatics and Computational Biology. Complutense University of Madrid
B.Sc. in Biotechnology, University of Leon.

Telf: 677753470
e-mail: sara.mo...@gmail.com
linkedin:es.linkedin.com/pub/sara-monzón-fernández/39/6b5/655