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From Javier Blasco <jabla...@unizar.es>
Subject Problems with cTAKES 3.1 installation (in Mac OS X 10.9 and Windows 8)
Date Tue, 14 Oct 2014 15:12:41 GMT
I have started working on NLP very recently.
I am trying to install cTAKES (following this guide
<https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide>)
but I am stumbling across many problems.

I do manage to lauch the java application but I get several errors when I
try to load the AE suggested in the CVD example
(AggregatePlaintextUMLSProcessor.xml).

Below are the errors.
Thanks a lot in advance!

Regards,

----

*Mac OS X 10.9*
Currently I have java version "1.7.0_67"

Exception in thread "AWT-EventQueue-0"
java.lang.UnsupportedClassVersionError:
org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE :
Unsupported major.minor version 51.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
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$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:171)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:204)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
at
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
at java.awt.Component.processMouseEvent(Component.java:6414)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
at java.awt.Component.processEvent(Component.java:6179)
at java.awt.Container.processEvent(Container.java:2084)
at java.awt.Component.dispatchEventImpl(Component.java:4776)
at java.awt.Container.dispatchEventImpl(Container.java:2142)
at java.awt.Component.dispatchEvent(Component.java:4604)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4209)
at java.awt.Container.dispatchEventImpl(Container.java:2128)
at java.awt.Window.dispatchEventImpl(Window.java:2492)
at java.awt.Component.dispatchEvent(Component.java:4604)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
at java.awt.EventQueue.access$400(EventQueue.java:82)
at java.awt.EventQueue$2.run(EventQueue.java:676)
at java.awt.EventQueue$2.run(EventQueue.java:674)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:690)
at java.awt.EventQueue$3.run(EventQueue.java:688)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)


*Windows 7 - **Log file*
14/10/14 17:06:11 - 14:
org.apache.uima.tools.cvd.MainFrame.handleException(527): Grave: Error
initializing "org.apache.uima.resource.impl.DataResource_impl" from
descriptor
file:/C:/Users/USUARIO/Documents/apache-ctakes-3.2.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml.
org.apache.uima.resource.ResourceInitializationException: Error
initializing "org.apache.uima.resource.impl.DataResource_impl" from
descriptor
file:/C:/Users/USUARIO/Documents/apache-ctakes-3.2.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml.
at
org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:144)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:243)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:565)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
at
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: org.apache.uima.resource.ResourceInitializationException: Could
not access the resource data at
file:org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml.
at
org.apache.uima.resource.impl.DataResource_impl.initialize(DataResource_impl.java:127)
at
org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:123)
... 61 more

*Windows 7 - output to stdin*

C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>set
CURRENT_DIR=C:\Users\USUARIO\Documents\apache-ctakes-3.2.0

C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>if not
"C:\Users\USUARIO\Documents\apache-ctakes-3.2.0" == "" goto gotHome

C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>if exist
"C:\Users\USUARIO\Documents\apache-ctakes-3.2.0\bin\runctakesCVD.bat" goto
okHome

C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>cd
C:\Users\USUARIO\Documents\apache-ctakes-3.2.0

C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>java -Dctakes.umlsuser=***
-Dctakes.umlspw=**** -cp
"C:\Users\USUARIO\Documents\apache-ctakes-3.2.0/lib/*;C:\Users\USUARIO\Documents\apache-ctakes-3.2.0/desc/;C:\Users\USUARIO\Documents\apache-ctakes-3.2.0/resources/"
-Dlog4j.configuration=file:/C:\Users\USUARIO\Documents\apache-ctakes-3.2.0/config/log4j.xml
-Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
14 oct 2014 17:06:01  INFO ClearNLPDependencyParserAE - using Morphy
analysis? true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
14 oct 2014 17:06:09  INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
14 oct 2014 17:06:09  INFO ContextDependentTokenizerAnnotator - Finite
state machines loaded.
14 oct 2014 17:06:09  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
14 oct 2014 17:06:09  INFO NegationContextAnalyzer - initBoundaryData()
called for ContextInitializer
14 oct 2014 17:06:09  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
14 oct 2014 17:06:09  INFO StatusContextAnalyzer - initBoundaryData()
called for ContextInitializer
14 oct 2014 17:06:09  INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
14 oct 2014 17:06:09  INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
14 oct 2014 17:06:10  INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip

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