Egon,
CDK gets compiled ok (at least that's what I think). I talked to Uli and it seems like he gets the same error message ... maybe it's a system problem? What system are you working on?
With respect to taverna, I deletd the cdk.jar and now get the following error (which is still quite similar):
__________________
uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException
at org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerTask.execute(APIConsumerTask.java:192)
at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:462)
at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:407)
at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:329)
at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:521)
at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:261)
at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:199)
at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67)
Caused by: 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:585)
at org.embl.ebi.escience.scuflworkers.apiconsumer.APIConsumerTask.execute(APIConsumerTask.java:189)
... 7 more
Caused by: java.lang.NoSuchMethodError: org.openscience.cdk.graph.ConnectivityChecker.partitionIntoMolecules(Lorg/openscience/cdk/AtomContainer;)Lorg/openscience/cdk/SetOfMolecules;
at org.openscience.cdk.tools.HydrogenAdder.addImplicitHydrogensToSatisfyValency(HydrogenAdder.java:280)
at org.openscience.cdk.smiles.SmilesParser.parseSmiles(SmilesParser.java:326)
at org.openscience.cdk.applications.taverna.smiles.SmilesTools.parseSMILES(SmilesTools.java:46)
... 12 more
ERROR 2005-11-24 08:58:37,587 (uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask:222) - uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException
Getting results...
____________________
The protocol is just a constant string value (CCC) and the processor is 'parseSmiles'.
Any ideas?
Cheers
Nik
| Egon Willighagen <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED] 23.11.2005 22:08
|
To: [email protected] cc: (bcc: Nikolaus Stiefl/PH/Novartis) Subject: Re: [Cdk-user] Problems running CDK 'ant run' & running CDK-taverna Category:
|
On Wednesday 23 November 2005 16:56, [EMAIL PROTECTED] wrote:
> I am new to CDK as well as java. After installing Java 1.5, ant 1.6.5,
> taverna, CDK (release 20050826), cdk-taverna (release 20051018) on my
> RedHat box (Enterprise 3.0), I have the following problems:
>
> 1. When running 'ant run' I get the follwing error message:
>
> ______________
>
> dist.init:
>
> compile-needed-test:
>
> compile-module:
>
> run:
> [java] Exception in thread "main"
> java.lang.NoClassDefFoundError:
> org/openscience/cdk/applications/FileConvertor
> ______________
>
> I don't know if this is something serious but I woudl have expected this
> script to work ...
Does CDK get compiled? (it seems to work for me)
> 2. After installing taverna (no proxys enabled) and copying the
> cdk-taverna.jar and cdk.jar to the lib directory I am not able to start a
> simple 'parse smile' workflow. I get the following error
Only copy cdk-taverna.jar; not the cdk.jar too. The former should contain all
required CDK classes itself.
> __________________________
>
> ERROR 2005-11-23 16:50:31,433
> (org.embl.ebi.escience.baclava.AssigningServiceClient:123) - No mapping
> found for namespace type wfDefinition
<snip>
These were really Taverna errors...
> Caused by: java.lang.NoSuchMethodError:
> org.openscience.cdk.AtomContainer.addAtom(Lorg/openscience/cdk/interfaces/A
>tom;)V at
> ___________________________
This really is a version conflict, I think. Remove the cdk.jar and let me know
what that gives...
Egon
--
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