NoClassDefFoundError - can't find bytecode.jar

Hi there!

I have a problem and can't solve ist on my own. I try to start this Java-webstart application. It copies all the files and starts as usual. It's an application for multiple sequence allignment. I started it on 5 different IMacs and all worked fine, but if I start it on my PowerBook it doesn't work. The application starts as usual until I try to load some sequences out of a database. It throws following exception:

$ ant run

Buildfile: build.xml

compile:

build:

run:

[java] Searchingfor existing preferences.../ca/virology/bbb already exists

[java] Checking http://athena.bioc.uvic.ca/ca.virology/xml/BBBPrefs.xml for new preferences...

[java] Prefs XML file version is: 3.0

[java] Client Prefs version is: 3.0

[java] Client has the latest version of the prefs.

[java] Searchingfor existing preferences.../ca/virology/externalapps already exists

[java] Checking http://athena.bioc.uvic.ca/ca.virology/xml/ExternalAppsPrefs.xml for new preferences...

[java] Prefs XML file version is: 1.0

[java] Client Prefs version is: 1.0

[java] Client has the latest version of the prefs.

[java] http://athena.bioc.uvic.ca/ca.virology/xml/ExternalAppsPrefs.xml

[java] ClientHitTracker> ip:athena.bioc.uvic.ca port:4440

[java] No log file specified. Logging to /Users/oli/.vbrc/virology.log

[java] HitTracker: connect to db

[java] HitTracker: send request ...

[java] HitTracker: send request ... done

[java] Utils.Debug: turning DEBUG mode ON

[java] 2007-04-03 15:13:45.104 java[501] Can't open input server /Library/InputManagers/Smart Crash Reports.bundle

[java] Asfarviridae

[java] SELECT [ListMatchSelector.genome_name_id_select]: SELECT genome.genome_name, genome.genome_id FROM genome WHERE (genome.family_id=200) ORDER BY genome.genome_name ASC

[java] SELECT [ListMatchSelector.genome_name_id_select]: SELECT genome.genome_name, genome.genome_id FROM genome WHERE (genome.family_id=200) ORDER BY genome.genome_name ASC

[java] The select statement sent from virusDNASequenceSelect: SELECT genome.genome_abbr, LENGTH(genome.genome_seq) AS virus_bp_size, genome.genome_seq FROM genome WHERE (genome.family_id=200) AND (genome.genome_id = 483)

[java] The select statement sent from geneOrfInfoSelect: SELECT gene.gene_id, gene.gene_abbr, gene_orf.start, gene_orf.stop, gene.strand FROM gene_orf, gene WHERE (gene_orf.family_id=200) AND (gene.family_id=200) AND (gene.gene_id=gene_orf.gene_id) AND ((gene.genome_id = 483) AND (gene.molecule_type ='protein') AND (gene_orf.position = 1)) ORDER BY gene_orf.start ASC

[b] [java] Exception in thread"AWT-EventQueue-0" java.lang.NoClassDefFoundError: org/biojava/utils/bytecode/CodeException[/b]

[java]at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(FeatureFilter.java:1270)

[java]at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)

[java]at org.biojava.bio.seq.impl.SimpleSequence.getFeatureHolder(SimpleSequence.java:144)

[java]at org.biojava.bio.seq.impl.SimpleSequence.createFeature(SimpleSequence.java:224)

[java]at ca.virology.lib.io.sequenceData.FeaturedSequence.createFeature(FeaturedSequence.java:165)

[java]at ca.virology.lib.io.tools.FeatureTools.createGeneFeature(FeatureTools.java:402)

[java]at ca.virology.baseByBase.io.VocsTools.getGenomeData(VocsTools.java:108)

[java]at ca.virology.baseByBase.gui.AppendDBAction$2.actionPerformed(AppendDBAction.java:154)

[java]at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)

[java]at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)

[java]at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)

[java]at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)

[java]at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:234)

[java]at java.awt.Component.processMouseEvent(Component.java:5554)

[java]at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)

[java]at java.awt.Component.processEvent(Component.java:5319)

[java]at java.awt.Container.processEvent(Container.java:2010)

[java]at java.awt.Component.dispatchEventImpl(Component.java:4021)

[java]at java.awt.Container.dispatchEventImpl(Container.java:2068)

[java]at java.awt.Component.dispatchEvent(Component.java:3869)

[java]at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)

[java]at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)

[java]at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)

[java]at java.awt.Container.dispatchEventImpl(Container.java:2054)

[java]at java.awt.Window.dispatchEventImpl(Window.java:1774)

[java]at java.awt.Component.dispatchEvent(Component.java:3869)

[java]at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)

[java]at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)

[java]at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)

[java]at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:180)

[java]at java.awt.Dialog$1.run(Dialog.java:517)

[java]at java.awt.Dialog$2.run(Dialog.java:545)

[java]at java.security.AccessController.doPrivileged(Native Method)

[java]at java.awt.Dialog.show(Dialog.java:543)

[java]at java.awt.Component.show(Component.java:1300)

[java]at java.awt.Component.setVisible(Component.java:1253)

[java]at ca.virology.baseByBase.gui.AppendDBAction.actionPerformed(AppendDBAction.java:193)

[java]at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1882)

[java]at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2202)

[java]at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)

[java]at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)

[java]at javax.swing.AbstractButton.doClick(AbstractButton.java:334)

[java]at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1000)

[java]at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1041)

[java]at java.awt.Component.processMouseEvent(Component.java:5554)

[java]at javax.swing.JComponent.processMouseEvent(JComponent.java:3126)

[java]at java.awt.Component.processEvent(Component.java:5319)

[java]at java.awt.Container.processEvent(Container.java:2010)

[java]at java.awt.Component.dispatchEventImpl(Component.java:4021)

[java]at java.awt.Container.dispatchEventImpl(Container.java:2068)

[java]at java.awt.Component.dispatchEvent(Component.java:3869)

[java]at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4256)

[java]at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3936)

[java]at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3866)

[java]at java.awt.Container.dispatchEventImpl(Container.java:2054)

[java]at java.awt.Window.dispatchEventImpl(Window.java:1774)

[java]at java.awt.Component.dispatchEvent(Component.java:3869)

[java]at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)

[java]at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:269)

[java]at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)

[java]at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)

[java]at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)

[java]at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)

as far, as I understand, the application can't find the class "CodeException" in the file bytecode-0.92.jar. The file is in the right directory and I checked the .jar - it contains this class.

It's really a mystery, because all other Macs in the laboratory don't have this problem.

I don't know if it might have to do with it, but the PowerBook was installed in Germany and all preferences where changed to "English" - all the other Macs are installed in Canada ...

Please, HELP ME!!!

I don't know what else to try ...

Best regards!

Susanne

[8786 byte] By [Susanne81a] at [2007-11-26 23:55:19]
# 1
Check 1. What is the classpath that the program is using?2. That the jar is listed there.3. That the class CodeException resides in the following directory structure within the jar:org/biojava/utils/bytecode
ChuckBinga at 2007-7-11 15:39:00 > top of Java-index,Java Essentials,Java Programming...
# 2

Check

1. What is the classpath that the program is using?

<path id="runclasspath">

<path refid="classpath" />

<pathelement location="${jar}/bytecode-0.92.jar" />

<pathelem...

The jar files will be copied to a cache-Folder at the first start.

2. That the jar is listed there.

On my Powerbook all the file are @ the right place - besides - all other classes and jar-files (which are in the same directory) will be found.

3. That the class CodeException resides in the following directory structure within the jar:

org/biojava/utils/bytecode

I have checked this - the bytecode-0.92.jar file contains it and should be loaded ...

Thank you for your fast reply!>

Susanne81a at 2007-7-11 15:39:00 > top of Java-index,Java Essentials,Java Programming...