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)
> BioSemantics group, Human Genetics department, Leiden University Medical
> Centre
> Albinusdreef 2 (Building 2, room S3-46)
> 2333 ZA Leiden
> Tel. +31 (0) 71 526 8642
> Adaptive Information Disclosure group, Informatics Institute, University of
> Amsterdam
> Kruislaan 403 ( room N2.30) 1098 SJ Amsterdam
> Tel. +31 (0) 20 525 7522
> Communities:
> Professional: LinkedIn, myExperiment Personal: Hyves
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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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