problem with BN in OSX

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klafka
2009-10-14
2013-05-20
  • klafka
    klafka
    2009-10-14

    Hey I am trying to use the Bayesian Networks feature in MeV. After loading in a dataset and clicking on the Bayesian Network icon, nothing happens. Any reason as to why it not be loading or how I can work around this would be really appreciated

    Thanks,
    Justin

     
  • raktim
    raktim
    2009-10-14

    Justin,

    Please let the know the following:
    Version of OSX
    Version of Java
    Open console (type console in FInder) then launch MeV and try to do BN. Send us anything you see in the console window.

    Thanks,
    Raktim

     
  • klafka
    klafka
    2009-10-15

    I am using OSX 10.5.8 as to which version of Java Open console that's tricky here is what was used to run the web start version of MeV

    Java Web Start 1.5.0_20
    Using JRE version 1.5.0_20-b02-315 Java HotSpot(TM) Client VM

    here is an exception thrown when I click on the Bayesian Network icon

    Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedClassVersionError: Bad version number in .class file
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
    at com.sun.jnlp.JNLPClassLoader.findClass(JNLPClassLoader.java:257)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
    at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:242)
    at org.tigr.microarray.mev.MultipleArrayViewer.onAnalysis(MultipleArrayViewer.java:2630)
    at org.tigr.microarray.mev.MultipleArrayViewer.access$5400(MultipleArrayViewer.java:229)
    at org.tigr.microarray.mev.MultipleArrayViewer$EventListener.actionPerformed(MultipleArrayViewer.java:5256)
    at org.tigr.microarray.mev.action.ActionManager.forwardAction(ActionManager.java:68)
    at org.tigr.microarray.mev.MultipleArrayToolbar$ComboListener.actionPerformed(MultipleArrayToolbar.java:280)
    at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1197)
    at javax.swing.JComboBox.setSelectedItem(JComboBox.java:561)
    at javax.swing.JComboBox.setSelectedIndex(JComboBox.java:597)
    at javax.swing.plaf.basic.BasicComboPopup$Handler.mouseReleased(BasicComboPopup.java:808)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:232)
    at java.awt.Component.processMouseEvent(Component.java:5602)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
    at javax.swing.plaf.basic.BasicComboPopup$1.processMouseEvent(BasicComboPopup.java:476)
    at java.awt.Component.processEvent(Component.java:5367)
    at java.awt.Container.processEvent(Container.java:2010)
    at java.awt.Component.dispatchEventImpl(Component.java:4068)
    at java.awt.Container.dispatchEventImpl(Container.java:2068)
    at java.awt.Component.dispatchEvent(Component.java:3903)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
    at java.awt.Container.dispatchEventImpl(Container.java:2054)
    at java.awt.Window.dispatchEventImpl(Window.java:1801)
    at java.awt.Component.dispatchEvent(Component.java:3903)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
    at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

     
  • raktim
    raktim
    2009-10-16

    It was not clear from  your email that you used webstart to launch MeV.

    On the Mac, there is an application called Java Preferences. You can use the Spotlight to find it. Launch the Java Preferences and in the
    Java Application Runtime Settings panel, drag the the JRE/J2SE 6 to the top. Save and restart the application.

    I would be eager to know how this goes. We are having some issues with version mismatch for Mac and your feedback will be very much appreciated.
    Raktim

     
  • klafka
    klafka
    2009-10-16

    hey raktim so I changed the java settings to use JSE 6.0 for both webstart and java applications. The webstart then loaded the bayesian network module. However the local MeV did not. Here is the error message.

    10/16/09 10:18:36 AM .MeV  Java application launched from PPC or bad stub. Relaunching in 32-bit, and tagging sub-processes to prefer 32-bit with $JAVA_ARCH=i386.
    10/16/09 10:18:36 AM .MeV MultiExperimentViewer - version 4.4.1 - Mac OS X
    10/16/09 10:18:36 AM .MeV MultiExperimentViewer - version 4.4.1 - Mac OS X
    10/16/09 10:18:36 AM .MeV Java Runtime Environment version: 1.5.0_20
    10/16/09 10:18:36 AM .MeV Java Runtime Environment vendor: Apple Inc.
    10/16/09 10:18:36 AM .MeV Java Virtual Machine name: Java HotSpot(TM) Client VM
    10/16/09 10:18:36 AM .MeV Java Virtual Machine version: 1.5.0_20-141
    10/16/09 10:18:36 AM .MeV Java Virtual Machine vendor: Apple Inc.
    10/16/09 10:18:36 AM .MeV Java 3D Runtime Environment: Java 3D Core Runtime Environment
    10/16/09 10:18:36 AM .MeV Java 3D Runtime Environment vendor: Apple Computer, Inc.
    10/16/09 10:18:36 AM .MeV Java 3D Runtime Environment version:1.3.1
    10/16/09 10:18:36 AM .MeV Operating System name: Mac OS X
    10/16/09 10:18:36 AM .MeV Operating System version: 10.5.8
    10/16/09 10:18:36 AM .MeV Operating System architecture: i386
    10/16/09 10:18:36 AM .MeV MeV Build: 1836
    10/16/09 10:18:36 AM .MeV MeV Revision Date: 2009/06/30 11:18:56
    10/16/09 10:18:36 AM .MeV MeV Branch: https://mev-tm4.svn.sourceforge.net/svnroot/mev-tm4/branches/MeV_4_4
    10/16/09 10:18:36 AM .MeV MeV Branch: https://mev-tm4.svn.sourceforge.net/svnroot/mev-tm4/branches/MeV_4_4
    10/16/09 10:18:59 AM .MeV Exception in thread "AWT-EventQueue-0" java.lang.UnsupportedClassVersionError: Bad version number in .class file
    10/16/09 10:18:59 AM .MeV  at java.lang.ClassLoader.defineClass1(Native Method)
    10/16/09 10:18:59 AM .MeV  at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
    10/16/09 10:18:59 AM .MeV  at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
    10/16/09 10:18:59 AM .MeV  at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
    10/16/09 10:18:59 AM .MeV  at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
    10/16/09 10:18:59 AM .MeV  at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
    10/16/09 10:18:59 AM .MeV  at java.security.AccessController.doPrivileged(Native Method)
    10/16/09 10:18:59 AM .MeV  at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
    10/16/09 10:18:59 AM .MeV  at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
    10/16/09 10:18:59 AM .MeV  at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:280)
    10/16/09 10:18:59 AM .MeV  at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
    10/16/09 10:18:59 AM .MeV  at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
    10/16/09 10:18:59 AM .MeV  at java.lang.Class.forName0(Native Method)
    10/16/09 10:18:59 AM .MeV  at java.lang.Class.forName(Class.java:242)
    10/16/09 10:18:59 AM .MeV  at org.tigr.microarray.mev.MultipleArrayViewer.onAnalysis(MultipleArrayViewer.java:2630)
    10/16/09 10:18:59 AM .MeV  at org.tigr.microarray.mev.MultipleArrayViewer.access$5400(MultipleArrayViewer.java:229)
    10/16/09 10:18:59 AM .MeV  at org.tigr.microarray.mev.MultipleArrayViewer$EventListener.actionPerformed(MultipleArrayViewer.java:5256)
    10/16/09 10:18:59 AM .MeV  at org.tigr.microarray.mev.action.ActionManager.forwardAction(ActionManager.java:68)
    10/16/09 10:18:59 AM .MeV  at org.tigr.microarray.mev.MultipleArrayToolbar$ComboListener.actionPerformed(MultipleArrayToolbar.java:280)
    10/16/09 10:18:59 AM .MeV  at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1197)
    10/16/09 10:18:59 AM .MeV  at javax.swing.JComboBox.setSelectedItem(JComboBox.java:561)
    10/16/09 10:18:59 AM .MeV  at javax.swing.JComboBox.setSelectedIndex(JComboBox.java:597)
    10/16/09 10:18:59 AM .MeV  at javax.swing.plaf.basic.BasicComboPopup$Handler.mouseReleased(BasicComboPopup.java:808)
    10/16/09 10:18:59 AM .MeV  at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:232)
    10/16/09 10:18:59 AM .MeV  at java.awt.Component.processMouseEvent(Component.java:5602)
    10/16/09 10:18:59 AM .MeV  at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
    10/16/09 10:18:59 AM .MeV  at javax.swing.plaf.basic.BasicComboPopup$1.processMouseEvent(BasicComboPopup.java:476)
    10/16/09 10:18:59 AM .MeV  at java.awt.Component.processEvent(Component.java:5367)
    10/16/09 10:18:59 AM .MeV  at java.awt.Container.processEvent(Container.java:2010)
    10/16/09 10:18:59 AM .MeV  at java.awt.Component.dispatchEventImpl(Component.java:4068)
    10/16/09 10:18:59 AM .MeV  at java.awt.Container.dispatchEventImpl(Container.java:2068)
    10/16/09 10:18:59 AM .MeV  at java.awt.Component.dispatchEvent(Component.java:3903)
    10/16/09 10:18:59 AM .MeV  at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)
    10/16/09 10:18:59 AM .MeV  at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)
    10/16/09 10:18:59 AM .MeV  at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)
    10/16/09 10:18:59 AM .MeV  at java.awt.Container.dispatchEventImpl(Container.java:2054)
    10/16/09 10:18:59 AM .MeV  at java.awt.Window.dispatchEventImpl(Window.java:1801)
    10/16/09 10:18:59 AM .MeV  at java.awt.Component.dispatchEvent(Component.java:3903)

    this is in Console version: Version 10.5.6 (137)

     
  • raktim
    raktim
    2009-10-16

    Justin,

    can you type the following at a terminal prompt and tell me the output:
    java -version

    Also when you launched MeV locally did it not launch at all or the BN module did not start?
    Raktim

     
  • klafka
    klafka
    2009-10-16

    sorry, while MeV launched the BN module did not start.

    java version "1.6.0_15"
    Java(TM) SE Runtime Environment (build 1.6.0_15-b03-226)
    Java HotSpot(TM) 64-Bit Server VM (build 14.1-b02-92, mixed mode)

    is the version