Hi all
I downloaded taverna 2.1 on my fedora 64bit and now when I run it I see
this on the terminal :
./taverna
Central class is org.biomoby.client.CentralDigestCachedImpl
Central class is org.biomoby.client.CentralDigestCachedImpl
Exception in thread "BioMOBY GetOntologyThread" java.lang.InternalError
at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:769)
at sun.misc.URLClassPath.getResource(URLClassPath.java:185)
at java.net.URLClassLoader$1.run(URLClassLoader.java:209)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:316)
at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
at
java.util.ResourceBundle$RBClassLoader.loadClass(ResourceBundle.java:463)
at
java.util.ResourceBundle$Control.newBundle(ResourceBundle.java:2401)
at java.util.ResourceBundle.loadBundle(ResourceBundle.java:1424)
at java.util.ResourceBundle.findBundle(ResourceBundle.java:1383)
at java.util.ResourceBundle.findBundle(ResourceBundle.java:1310)
at java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1252)
at java.util.ResourceBundle.getBundle(ResourceBundle.java:733)
at java.util.logging.Level.getLocalizedName(Level.java:240)
at java.util.logging.SimpleFormatter.format(SimpleFormatter.java:86)
at java.util.logging.StreamHandler.publish(StreamHandler.java:196)
at java.util.logging.ConsoleHandler.publish(ConsoleHandler.java:105)
at java.util.logging.Logger.log(Logger.java:476)
at java.util.logging.Logger.doLog(Logger.java:498)
at java.util.logging.Logger.log(Logger.java:521)
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:131)
at java.util.jar.JarFile.<init>(JarFile.java:150)
at java.util.jar.JarFile.<init>(JarFile.java:87)
at sun.misc.URLClassPath$JarLoader.getJarFile(URLClassPath.java:660)
at sun.misc.URLClassPath$JarLoader.access$600(URLClassPath.java:555)
at sun.misc.URLClassPath$JarLoader$1.run(URLClassPath.java:622)
at java.security.AccessController.doPrivileged(Native Method)
at sun.misc.URLClassPath$JarLoader.ensureOpen(URLClassPath.java:614)
at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:767)
... 27 more
ERROR 2009-07-20 16:53:53,074 (org.biomoby.shared.MobyException:86) - ;
nested exception is:
java.net.SocketException: Too many open files
ERROR 2009-07-20 16:53:53,075 (org.biomoby.shared.MobyException:86) -
===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Too many open files
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
ERROR 2009-07-20 16:53:53,076
(net.sf.taverna.t2.activities.biomoby.BiomobyCache:59) - Error whilst
caching for Biomoby registry
org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Too many open files
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
at
org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:257)
at
org.biomoby.client.CentralDigestCachedSimpleImpl.updateCache(CentralDigestCachedSimpleImpl.java:190)
at
net.sf.taverna.t2.activities.biomoby.BiomobyCache.cacheForRegistry(BiomobyCache.java:49)
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: org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: java.net.SocketException: Too many open files
Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
Fault actor: null
When calling:
http://moby.ucalgary.ca/moby/MOBY-Central.pl
===========
at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
at
org.biomoby.client.CentralImpl.getResourceRefs(CentralImpl.java:1807)
at
org.biomoby.client.CentralDigestCachedImpl.getResourceURL(CentralDigestCachedImpl.java:438)
at
org.biomoby.client.CentralDigestCachedImpl.fillDataTypesCache(CentralDigestCachedImpl.java:140)
... 4 more
Caused by: java.net.SocketException: Too many open files
at org.apache.axis.AxisFault.makeFault(AxisFault.java:101)
at
org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:154)
at
org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)
at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)
at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:2443)
at org.apache.axis.client.Call.invoke(Call.java:2366)
at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:247)
... 7 more
Caused by: java.net.SocketException: Too many open files
at java.net.Socket.createImpl(Socket.java:406)
at java.net.Socket.<init>(Socket.java:380)
at java.net.Socket.<init>(Socket.java:198)
at
org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:149)
at
org.apache.axis.components.net.DefaultSocketFactory.create(DefaultSocketFactory.java:120)
at
org.apache.axis.transport.http.HTTPSender.getSocket(HTTPSender.java:191)
at
org.apache.axis.transport.http.HTTPSender.writeToSocket(HTTPSender.java:404)
at
org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:138)
... 16 more
Jul 20, 2009 4:54:08 PM java.util.prefs.FileSystemPreferences
checkLockFile0ErrorCode
WARNING: Could not lock User prefs. Unix error code 24.
Jul 20, 2009 4:54:08 PM java.util.prefs.FileSystemPreferences syncWorld
WARNING: Couldn't flush user prefs: java.util.prefs.BackingStoreException:
Couldn't get file lock.
Do you have any advices for me?
It seems to be some little problems also with the renderer window and java
heap space memory lack!
thanks
cheers
--
Achille Zappa
-Bioinformatics
National Cancer Research Institute (IST)
Largo Benzi 10
16132 Genova - ITALY
Tel. 010 5737288
-IEIIT - Sezione di Genova
National Research Council (CNR)
via De Marini, 6
16149 Genova - ITALY
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