Hi
This could be because of the conflict between native java preinstalled
on Ubuntu and Sun java.
cheers
Ketan
David Withers wrote:
> Hi Marco,
>
> Do you get this error every time you start Taverna?
>
> David.
>
> On 16 Jul 2010, at 10:38, Marco Roos wrote:
>
>> Hello,
>>
>> FYI: I received the following error when starting Taverna 2.2.0 after
>> installing it on my Ubuntu 9.10 laptop:
>> 'An unexpected internal error occured in
>> Thread[BioMOBY GetOntologyThread,1,Service description providers]:
>> java.lang.InternalError
>>
>> I haven't tested this exensively, but everything seems to work ok
>> despite this. In case it matters: I see I need to reset my path to
>> GraphViz. I have previous versions of Taverna on my machine (1.7.2, 2.1).
>>
>> The stack trace:
>> WARN 2010-07-16 11:23:34,298
>> (net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to
>> find a version for the dependency log4j:log4j - skipping
>> WARN 2010-07-16 11:23:34,306
>> (net.sf.taverna.raven.repository.impl.ArtifactImpl:85) - Unable to
>> find a version for the dependency junit:junit - skipping
>> WARN 2010-07-16 11:23:37,673
>> (net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader:85) -
>> Using already found class org.apache.axis.AxisFault
>> ACL=loader{axis:axis:1.4} from 18474371
>> java.lang.LinkageError: loader (instance of
>> net/sf/taverna/raven/repository/impl/LocalArtifactClassLoader):
>> attempted duplicate class definition for name:
>> "org/apache/axis/AxisFault"
>> at java.lang.ClassLoader.defineClass1(Native Method)
>> at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
>> at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
>> at
>> java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
>> at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>> at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
>> at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>> at
>> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:312)
>> at
>> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.loadClass(LocalArtifactClassLoader.java:229)
>> at
>> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:318)
>> at
>> net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader.findClass(LocalArtifactClassLoader.java:276)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>> at
>> net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper.<init>(BiomobyQueryHelper.java:79)
>> at
>> net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider.findServiceDescriptionsAsync(BiomobyServiceProvider.java:57)
>> at
>> net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
>> ERROR 2010-07-16 11:23:38,672 (System.err:139) - Central class is
>> org.biomoby.client.CentralDigestCachedImpl
>> ERROR 2010-07-16 11:23:56,618
>> (net.sf.taverna.t2.workbench.ui.impl.Workbench:117) - Uncaught
>> exception in Thread[BioMOBY GetOntologyThread,1,Service description
>> providers]
>> java.lang.InternalError
>> at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:755)
>> at sun.misc.URLClassPath.getResource(URLClassPath.java:169)
>> at java.net.URLClassLoader$1.run(URLClassLoader.java:194)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>> at sun.misc.Launcher$ExtClassLoader.findClass(Launcher.java:229)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:296)
>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:296)
>> at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>> at
>> java.util.ResourceBundle$RBClassLoader.loadClass(ResourceBundle.java:435)
>> at
>> java.util.ResourceBundle$Control.newBundle(ResourceBundle.java:2289)
>> at java.util.ResourceBundle.loadBundle(ResourceBundle.java:1364)
>> at java.util.ResourceBundle.findBundle(ResourceBundle.java:1328)
>> at java.util.ResourceBundle.findBundle(ResourceBundle.java:1282)
>> at java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1224)
>> at java.util.ResourceBundle.getBundle(ResourceBundle.java:705)
>> at java.util.logging.Level.getLocalizedName(Level.java:223)
>> at java.util.logging.SimpleFormatter.format(SimpleFormatter.java:64)
>> at java.util.logging.StreamHandler.publish(StreamHandler.java:179)
>> at java.util.logging.ConsoleHandler.publish(ConsoleHandler.java:88)
>> at java.util.logging.Logger.log(Logger.java:458)
>> at java.util.logging.Logger.doLog(Logger.java:480)
>> at java.util.logging.Logger.log(Logger.java:503)
>> at org.biomoby.shared.MobyDataType.getDataType(MobyDataType.java:122)
>> at
>> net.sf.taverna.t2.activities.biomoby.BiomobyCache.cacheForRegistry(BiomobyCache.java:51)
>> at
>> net.sf.taverna.t2.activities.biomoby.BiomobyCache.cacheForRegistryEndpoint(BiomobyCache.java:75)
>> at
>> net.sf.taverna.t2.activities.biomoby.GetOntologyThread.run(GetOntologyThread.java:57)
>> Caused by: java.util.zip.ZipException: error in opening zip file
>> at java.util.zip.ZipFile.open(Native Method)
>> at java.util.zip.ZipFile.<init>(ZipFile.java:114)
>> at java.util.jar.JarFile.<init>(JarFile.java:135)
>> at java.util.jar.JarFile.<init>(JarFile.java:72)
>> at sun.misc.URLClassPath$JarLoader.getJarFile(URLClassPath.java:646)
>> at sun.misc.URLClassPath$JarLoader.access$600(URLClassPath.java:540)
>> at sun.misc.URLClassPath$JarLoader$1.run(URLClassPath.java:607)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at sun.misc.URLClassPath$JarLoader.ensureOpen(URLClassPath.java:599)
>> at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:753)
>> ... 28 more
>>
>> --
>> Marco Roos (PhD) <http://home.medewerker.uva.nl/m.roos1>
>> *BioSemantics group* <http://www.biosemantics.nl/>, Human Genetics
>> department <http://www.humgen.nl/>, Leiden University Medical Centre
>> <http://www.lumc.nl/>
>> Albinusdreef 2 (Building 2, room S3-46)
>> 2333 ZA Leiden
>> Tel. +31 (0) 71 526 8642
>> *Adaptive Information Disclosure group*
>> <http://adaptivedisclosure.org/>, Informatics Institute
>> <http://www.science.uva.nl/ii>, University of Amsterdam
>> <http://www.uva.nl/>
>> Kruislaan 403 ( room N2.30
>> <http://remote.science.uva.nl/%7Eroos/Kruislaan403_N230.png>) 1098 SJ
>> Amsterdam
>> Tel. +31 (0) 20 525 7522
>> *Communities:*
>> Professional: LinkedIn <http://www.linkedin.com/in/marcoroos>,
>> myExperiment <http://www.myexperiment.org/users/18> Personal: Hyves
>> <http://mroos62.hyves.nl/>
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>> Web site: http://www.taverna.org.uk
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>
> --
> David Withers
> School of Computer Science, University of Manchester,
> Oxford Road, Manchester, M13 9PL, UK.
> +44 (0)161 275 0683
>
>
>
>
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