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/>
------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
taverna-users mailing list
[email protected]
[email protected]
Web site: http://www.taverna.org.uk
Mailing lists: http://www.taverna.org.uk/about/contact-us/
