MeV unable to launch appplication ... class not found exception

[Jari Häkkinen]

I cannot launch MeV with the BASE 2.11.0. I have pasted the stack trace and the jnlp below.

I note that there is a commented out reference to goose.jar in the jnlp

<!--jar href="goose.jar"/> -->

maybe this is cause the trouble since the class not found references to goose?

Shouldn't the version in the jnlp be changed to 4.3 or maybe 4.3.1?

Jari

Stack trace:

java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at com.sun.javaws.Launcher.executeApplication(Launcher.java:1332)
	at com.sun.javaws.Launcher.executeMainClass(Launcher.java:1270)
	at com.sun.javaws.Launcher.doLaunchApp(Launcher.java:1117)
	at com.sun.javaws.Launcher.run(Launcher.java:105)
	at java.lang.Thread.run(Thread.java:637)
Caused by: java.lang.NoClassDefFoundError: org/systemsbiology/gaggle/core/Goose
	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$000(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:256)
	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 org.tigr.microarray.mev.TMEV.main(TMEV.java:185)
	... 9 more
Caused by: java.lang.ClassNotFoundException: org.systemsbiology.gaggle.core.Goose
	at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at com.sun.jnlp.JNLPClassLoader.findClass(JNLPClassLoader.java:256)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:374)
	... 22 more

JNLP file:

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE jnlp PUBLIC "-//Sun Microsystems, Inc.//DTD JNLP 1.5//EN" "http://www.netbeans.org/jnlp/DTD/jnlp.dtd">
<jnlp spec="1.0"
	codebase="http://base.onk.lu.se:80/onk/extensions/mev-launcher.jar/jar"
	version="4.0">

	<information>
		<title>MeV: MultiExperiment Viewer</title>
		<vendor>http://www.tm4.org</vendor>
		<homepage href="http://www.tm4.org"/>
	</information>

	<security>
		<all-permissions/>
	</security>

	<resources>
		<jar href="mev-base.jar"/> <!-- must be first since main class is here -->
		<jar href="mev-algorithm-impl.jar"/>
		<jar href="mev-algorithm-support.jar"/>
		<jar href="mev-gui-impl.jar"/>
		<jar href="mev-gui-support.jar"/>
		<jar href="mev-util.jar"/>

		<jar href="args4j-2.0.9.jar"/>
		<jar href="base64.jar"/>
		<jar href="colt.jar"/>
		<jar href="comcgh.jar"/>
		<jar href="commons-net-1.4.1.jar"/>
		<jar href="dialogHelp.jar"/>
		<jar href="educgh.jar"/>
		<jar href="ftpbean.jar"/>
		<!--jar href="goose.jar"/> -->
		<jar href="HTTPClient.jar"/>
		<jar href="images.jar"/>
		<jar href="j3daudio.jar"/>
		<jar href="j3dcore.jar"/>
 		<jar href="j3dutils.jar"/>
		<jar href="jai_codec.jar"/>
		<jar href="jai_core.jar"/>
		<jar href="jama.jar"/>
		<jar href="jaxp.jar"/>
		<jar href="jbcl.jar"/>
		<jar href="jconn2.jar"/>
		<jar href="jdom-1.0.jar"/>
		<jar href="jfreechart-0.9.20.jar"/>
		<jar href="jfreechart-common-0.9.5.jar"/>
		<jar href="jsch-0.1.39.jar"/>
		<jar href="JSciCore.jar"/>
		<jar href="JSciPartial.jar"/>
		<!--jar href="mail.jar"/> -->
		<jar href="normalization.jar"/>
		<jar href="piccolo.jar"/>
		<jar href="piccolox.jar"/>
		<jar href="servlet.jar"/>
		<jar href="soap.jar"/>
		<jar href="swing-layout-1.0.1.jar"/>
		<jar href="swingx-2006_10_27.jar"/>
		<jar href="tar.jar"/>
		<jar href="Text_JDBC30.jar"/>
		<jar href="vecmath.jar"/>
		<jar href="weka.jar"/>
		<jar href="xerces.jar"/>
		<jar href="xml-apis.jar"/>
		
		<extension name="others" href="../others.jsp"/>
		
		<j2se version="1.5.0+"
     		max-heap-size="512M"
      	href="http://java.sun.com/products/autodl/j2se"
      />
	</resources>
	
	<application-desc main-class="org.tigr.microarray.mev.TMEV">
		<argument>-fileType</argument>
		<argument>tdms</argument>
		<argument>-fileUrl</argument>
		<argument>http://base.onk.lu.se:80/onk/extensions/mev-launcher.jar/MevExport/0a9280a6b4aaa7bb/1755.servlet</argument>
	</application-desc>
</jnlp>

[Nicklas Nordborg]

goose.jar and mail.jar are included in the jnlp file generated by the others.jsp page. I can't reproduce the error, neither on Linux or on Windows.

[Jari Häkkinen]

Replying to nicklas:

goose.jar and mail.jar are included in the jnlp file generated by the others.jsp page. I can't reproduce the error, neither on Linux or on Windows.

I'll do some more investigations on my mac.

[Nicklas Nordborg]

It doesn't work on the music Mac here either, but I get a different error:

An error occurred while launching/running the application.

Title: MeV: MultiExperiment Viewer
Vendor: http://www.tm4.org
Category: Launch File Error

JAR resources in JNLP file are not signed by same certificate

The JNLP file in question is the file that is generated by others.jsp, which contains mail.jar and goose.jar. I guess each JAR file that is pre-signed needs to go into a separate JNLP file.

[Nicklas Nordborg]

Seems like this problem was fixed by #193.