Re: [Taverna-users] Taverna 2.3 and R

Wed, 03 Aug 2011 07:32:40 -0700 

On 03/08/2011 15:08, Eleni Mina wrote:

Hello all,


Hello,


I was wondering if anyone else is experiencing problems running R under
Taverna 2.3 . The same workflow that runs perfectly in Taverna 2.2,
never stops running in 2.3 and when i cancel it i get the following
error:"(net.sf.taverna.t2.provenance.lineageservice.WorkflowDataProcessor:215) - No 
workflow port data for /o:probes " . It seems that it can't communicate with R at 
all.



The workflows should run the same. Can you try the attached (very 
simple) workflow?



Also, as it seems to be a provenance issue, can you try running your 
workflow with provenance switched off? You can do that under

(File or Taverna) -> Preferences -> Data and provenance


Thanks a lot.
Regards,
Eleni


Alan

<workflow xmlns="http://taverna.sf.net/2008/xml/t2flow"; version="1" 
producedBy="taverna-2.3.0"><dataflow id="dafa054f-5f79-41ee-b9cd-1402f9453a0f" 
role="top"><name>Workflow2</name><inputPorts 
/><outputPorts><port><name>Rshell_a</name><annotations 
/></port></outputPorts><processors><processor><name>Rshell</name><inputPorts 
/><outputPorts><port><name>a</name><depth>0</depth><granularDepth>0</granularDepth></port></outputPorts><annotations
 
/><activities><activity><raven><group>net.sf.taverna.t2.activities</group><artifact>rshell-activity</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.activities.rshell.RshellActivity</class><inputMap
 /><outputMap><map from="a" to="a" /></outputMap><configBean 
encoding="xstream"><net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean
 xmlns="">
  <inputs />
  <outputs>
    
<net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
      <name>a</name>
      <depth>0</depth>
      <mimeTypes />
      <granularDepth>0</granularDepth>
    
</net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean>
  </outputs>
  <rVersion>false</rVersion>
  <script>a &lt;- 8;</script>
  <connectionSettings>
    <host>localhost</host>
    <port>6311</port>
    <keepSessionAlive>false</keepSessionAlive>
    <newRVersion>false</newRVersion>
  </connectionSettings>
  <inputSymanticTypes />
  <outputSymanticTypes>
    <net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
      <name>a</name>
      <symanticType>STRING</symanticType>
    </net.sf.taverna.t2.activities.rshell.RShellPortSymanticTypeBean>
  </outputSymanticTypes>
</net.sf.taverna.t2.activities.rshell.RshellActivityConfigurationBean></configBean><annotations
 
/></activity></activities><dispatchStack><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize</class><configBean
 
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig
 xmlns="">
  <maxJobs>1</maxJobs>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ParallelizeConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry</class><configBean
 
encoding="xstream"><net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig
 xmlns="">
  <backoffFactor>1.0</backoffFactor>
  <initialDelay>1000</initialDelay>
  <maxDelay>5000</maxDelay>
  <maxRetries>0</maxRetries>
</net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.RetryConfig></configBean></dispatchLayer><dispatchLayer><raven><group>net.sf.taverna.t2.core</group><artifact>workflowmodel-impl</artifact><version>1.3</version></raven><class>net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke</class><configBean
 encoding="xstream"><null xmlns="" 
/></configBean></dispatchLayer></dispatchStack><iterationStrategyStack><iteration><strategy
 /></iteration></iterationStrategyStack></processor></processors><conditions 
/><datalinks><datalink><sink 
type="dataflow"><port>Rshell_a</port></sink><source 
type="processor"><processor>Rshell</processor><port>a</port></source></datalink></datalinks><annotations><annotation_chain_2_2
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
        <identification>6a92fb5f-4925-49d0-9cc3-3d691504e2b4</identification>
      </annotationBean>
      <date>2011-08-03 15:24:07.486 BST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
        <identification>f25e8f89-0f5a-468c-9503-70409b9db080</identification>
      </annotationBean>
      <date>2011-08-03 15:24:31.666 BST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
        <identification>a9c1317e-ac61-491f-aa71-8ff79e89ae5b</identification>
      </annotationBean>
      <date>2011-08-03 15:26:55.998 BST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
        <identification>7c263878-b84c-4b5a-a0c7-1ea3e1ba68de</identification>
      </annotationBean>
      <date>2011-08-03 15:28:45.894 BST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2><annotation_chain_2_2
 encoding="xstream"><net.sf.taverna.t2.annotation.AnnotationChainImpl xmlns="">
  <annotationAssertions>
    <net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
      <annotationBean 
class="net.sf.taverna.t2.annotation.annotationbeans.IdentificationAssertion">
        <identification>dafa054f-5f79-41ee-b9cd-1402f9453a0f</identification>
      </annotationBean>
      <date>2011-08-03 15:29:15.847 BST</date>
      <creators />
      <curationEventList />
    </net.sf.taverna.t2.annotation.AnnotationAssertionImpl>
  </annotationAssertions>
</net.sf.taverna.t2.annotation.AnnotationChainImpl></annotation_chain_2_2></annotations></dataflow></workflow>
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