java.lang.LinkageError: org/apache/commons/logging/Log

JIRA | Tony Squier | 5 years ago
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    Reported by Jerzy Orlowski to moby-dev and taverna-hackers on 2008-10-02: {quote} I am trying to execute an attached workflow with simple input (attached) using executeworkflow.sh What I get is: {code} $ ./executeworkflow.sh -inputdoc /tmp/workflows/1653746517794550_input.xmml /tmp/workflows/1653746517794550_workflow_scufl.xml Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/Objects ... done Fetching namespace ontology from http://biomoby.org/RESOURCES/MOBY-S/Namespaces Exception in thread "Thread-15" java.lang.LinkageError: loader constraint violation: loader (instance of net/sf/taverna/raven/repository/impl/LocalArtifactClassLoader) previously initiated loading for a different type with name "org/apache/commons/logging/Log" at org.biomoby.shared.MobyException.<init>(MobyException.java:55) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1525) at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:521) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280) at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67) {code} And the system hangs (executeworkflow.sh produce no result, no progress report and does not terminate) {quote} Reproducable on my machine with 1.7.1 on OS X and Java 10.5: {code} : stain@mira ~/Downloads/mobydevproblemswithbiomobypluginsintaverna;/Applications/Taverna.app/Contents/MacOS/executeworkflow.sh -inputdoc 1653746517794550_input.xmml 1653746517794550_workflow_scufl.xml .. Fetching data type ontology from http://biomoby.org/RESOURCES/MOBY-S/Objects ... done Fetching namespace ontology from http://biomoby.org/RESOURCES/MOBY-S/Namespaces Exception in thread "Thread-16" java.lang.LinkageError: Class org/apache/commons/logging/Log violates loader constraints at org.biomoby.shared.MobyException.<init>(MobyException.java:55) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:230) at org.biomoby.client.CentralImpl.call(CentralImpl.java:1525) at org.biomoby.client.taverna.plugin.BiomobyTask.execute(BiomobyTask.java:521) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.runAndGenerateTemplates(ProcessorTask.java:576) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.doInvocationWithRetryLogic(ProcessorTask.java:517) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeOnce(ProcessorTask.java:436) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invokeWithoutIteration(ProcessorTask.java:642) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.invoke(ProcessorTask.java:353) at uk.ac.soton.itinnovation.taverna.enactor.entities.ProcessorTask.handleRun(ProcessorTask.java:280) at uk.ac.soton.itinnovation.freefluo.core.task.NewState$1.run(NewState.java:67) {code}

    JIRA | 8 years ago | Stian Soiland-Reyes
    java.lang.LinkageError: Class org/apache/commons/logging/Log violates loader constraints

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    Root Cause Analysis

    1. java.lang.LinkageError

      org/apache/commons/logging/Log

      at com.javahollic.confluence.su.actions.ConfigureConfluenceSUAction.execute()
    2. com.javahollic.confluence
      ConfigureConfluenceSUAction.execute
      1. com.javahollic.confluence.su.actions.ConfigureConfluenceSUAction.execute(ConfigureConfluenceSUAction.java:117)
      1 frame