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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #445
Date Tue, 05 Nov 2013 01:58:35 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/445/changes>

Changes:

[chenpei] CTAKES-253 - Didn't need an additional .length()>0 in NumTokenAdapter check since
Strings.isNullOrEmpty() does it already

[chenpei] CTAKES-251 - Infinite recursion in DrugMentionAnnotator.java Thanks Bruce.
Adding the temp patch for the interim while there will be a new drug module(s) coming soon...

[chenpei] CTAKES-150 - Apostrophe parsing is not thread safe because of global variable. 
Thanks Kim.

[chenpei] CTAKES-253 - YTEX ctakes patches port. Thanks Vijay Garla.
* ctakes-context-tokenizer\src\main\java\org\apache\ctakes\contexttokenizer\ae\ContextDependentTokenizerAnnotator.java

add null check: changed to avoid NPE in case BaseToken is null. Also ignore newline tokens
(they should be treated as whitespace). 
* ctakes-core\src\main\java\org\apache\ctakes\core\fsm\adapters\NumberTokenAdapter.java 
add null check: ignore empty numbertokens 
* ctakes-core\src\main\java\org\apache\ctakes\core\fsm\machine\DateFSM.java 
Modified to include years in dates

[chenpei] CTAKES-254 - Add empty string check Apostrophe in contraction breaks TokenizerPTB
CTAKES-256 - Add a test doc that contains various edge cases for regression testing

------------------------------------------
[...truncated 3403 lines...]
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.syntax.WordToken_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.BodyLateralityModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.BodySideModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.BodySideModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ConditionalModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ConditionalModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ContextAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ContextAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.CourseModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.CourseModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.DateAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.DateAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.EntityMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.EntityMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.EventMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.EventMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.FractionAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.FractionAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.GenericModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.GenericModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.HistoryOfModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabDeltaFlagModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabEstimatedModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabInterpretationModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabReferenceRangeModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabValueModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.LabValueModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationAllergyModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationEventMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationEventMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.Modifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.Modifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.PolarityModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.PolarityModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.Predicate'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.Predicate_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureDeviceModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.ProcedureMethodModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.RangeAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.RangeAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SemanticArgument'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SemanticArgument_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SemanticRoleRelation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SeverityModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SeverityModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SignSymptomMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SignSymptomMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SubjectModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.SubjectModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.TimeAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.TimeAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.TimeMention'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.TimeMention_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textsem.UncertaintyModifier_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.List'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.List_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Paragraph'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Paragraph_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Segment'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Segment_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Sentence'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.textspan.Sentence_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.Pair'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.Pair_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.Pairs'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.Pairs_Type'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.ProbabilityDistribution'.
[INFO] JCasGen: Replacing: 'org.apache.ctakes.typesystem.type.util.ProbabilityDistribution_Type'.
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-type-system ---
[INFO] Compiling 284 source files to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-type-system/target/classes>
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-type-system
---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-type-system/src/test/resources>
[INFO] Copying 3 resources
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-type-system
---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-type-system ---
[INFO] Surefire report directory: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-type-system/target/surefire-reports>

-------------------------------------------------------
 T E S T S
-------------------------------------------------------

Results :

Tests run: 0, Failures: 0, Errors: 0, Skipped: 0

[JENKINS] Recording test results
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES utils 3.2.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-utils ---
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-utils ---
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-utils ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-utils/src/main/resources>
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-utils ---
[INFO] Compiling 26 source files to <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-utils/target/classes>
[WARNING] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java>:[74,28]
[deprecation] open(org.apache.lucene.store.Directory) in org.apache.lucene.index.IndexReader
has been deprecated
[WARNING] <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-utils/src/main/java/org/apache/ctakes/utils/wiki/WikiIndex.java>:[275,60]
[deprecation] LUCENE_30 in org.apache.lucene.util.Version has been deprecated
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-utils ---
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-utils ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-utils/src/main/resources>
[INFO] Copying 3 resources
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-utils ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-utils
---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-utils/src/test/resources>
[INFO] Copying 3 resources
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-utils ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-utils ---
[INFO] Surefire report directory: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-utils/target/surefire-reports>

-------------------------------------------------------
 T E S T S
-------------------------------------------------------

Results :

Tests run: 0, Failures: 0, Errors: 0, Skipped: 0

[JENKINS] Recording test results
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES Resources core 3.2.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-core-res ---
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-core-res ---
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-core-res ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 14 resources
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-core-res ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-remote-resources-plugin:1.4:process (default) @ ctakes-core-res ---
[INFO] 
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-core-res ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 14 resources
[INFO] Copying 3 resources
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-core-res ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-core-res
---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-core-res/src/test/resources>
[INFO] Copying 3 resources
[INFO] Copying 3 resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-core-res ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.12:test (default-test) @ ctakes-core-res ---
[INFO] Surefire report directory: <https://builds.apache.org/job/ctakes-trunk-compiletest/ws/ctakes-core-res/target/surefire-reports>

-------------------------------------------------------
 T E S T S
-------------------------------------------------------

Results :

Tests run: 0, Failures: 0, Errors: 0, Skipped: 0

[JENKINS] Recording test results
ERROR: Maven JVM terminated unexpectedly with exit code 143


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