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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-package #475
Date Sat, 15 Oct 2016 11:43:22 GMT
See <https://builds.apache.org/job/ctakes-trunk-package/475/changes>

Changes:

[seanfinan] Adding ProcessDir.piper
Refactoring

[seanfinan] Adding ctakes-examples-res with sample notes
Copy notes to resources/ directory for binary build

[seanfinan] FilesInDirectoryCollectionReader now uses FileLocator to access resources in source
Adding Example that reads files from a directory using PipelineBuilder
moved ctakes-examples/data/ to a ctakes-examples-res module
Added all other sample notes in ctakes project to the ctakes-examples-res module
   TODO refactor all test and sample code in ctakes to use ctakes-examples-res sample notes

[seanfinan] Add AttributesCleartkSubPipe.piper
refactor other .piper files to use it

[seanfinan] Added extraction/copy of TypeSystem.xml to the resources/ directory for binary
packages.  Necessary to use the CVD.
Added * extensions to copy for README* etc.

[dligach] added region-based data printer

------------------------------------------
Started by an SCM change
[EnvInject] - Loading node environment variables.
Building remotely on ubuntu-eu2 (Ubuntu ubuntu ubuntu-eu docker) in workspace <https://builds.apache.org/job/ctakes-trunk-package/ws/>
Cleaning up <https://builds.apache.org/job/ctakes-trunk-package/ws/.>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/resources>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-context-tokenizer/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dependency-parser/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-side-effect-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-web/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup-fast/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-coreference/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dependency-parser-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-relation-extractor-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-chunker/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup-fast-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-drug-ner-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-drug-ner/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-smoking-status/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ne-contexts/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-pos-tagger/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-temporal-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-coreference-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion-zoner/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-clinical-pipeline/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-type-system/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-core-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-lvg/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-pos-tagger-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-relation-extractor/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-chunker-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-core/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-smoking-status-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-regression-test/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-dictionary-lookup/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-uima/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-lvg-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-distribution/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ytex-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-assertion-zoner-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-template-filler/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-utils/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-ne-contexts-res/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-constituency-parser/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-side-effect/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-preprocessor/target>
Deleting <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-constituency-parser-res/target>
Updating http://svn.apache.org/repos/asf/ctakes/trunk at revision '2016-10-15T11:42:46.475
+0000'
U         ctakes-clinical-pipeline-res/src/main/resources/org/apache/ctakes/clinical/pipeline/DefaultFastPipeline.piper
U         ctakes-distribution/src/main/assembly/bin.xml
U         pom.xml
A         ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline
A         ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/pipeline/AttributesCleartkSubPipe.piper
A         ctakes-examples-res
A         ctakes-examples-res/src
A         ctakes-examples-res/src/main
A         ctakes-examples-res/src/main/resources
A         ctakes-examples-res/src/main/resources/org
A         ctakes-examples-res/src/main/resources/org/apache
A         ctakes-examples-res/src/main/resources/org/apache/ctakes
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_2.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/shark_bite.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/README
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/mother_goose/OneMistyMoistyMorning.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_AAA_Leak_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_FebrileSez_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_PVD_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_LaborProgressNote_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-DVT.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_PROMCheck_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_Gen_Abscess_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_RO-AAA_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_MVAPrego_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_IUD_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/GenSurg_UmbilicalHernia_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_RoutBirthNote_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/OBGYN_HysterectomyAndBSO_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/Peds_Dysphagia_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/rtf/VascSurg_FollowUp_1.rtf
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/right_knee_arthroscopy
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/claudication
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_past_smoker.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_past_smoker.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_unknown.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc1_07543210_sample_current.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/smoker/doc2_07543210_sample_current.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/SampleInputRadiologyNotes.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/pain_no_swelling.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_1.xml
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/cda/testpatient_cn_2.xml
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/dr_nutritious_1.txt
A         ctakes-examples-res/src/main/resources/org/apache/ctakes/examples/notes/edge_cases_plaintext_1.txt
D         ctakes-examples/data
D         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPipeline.piper
D         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCuiPipeline.piper
D         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkPropsPipeline.piper
D         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldPropsPipeline.piper
D         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertPropsPipeline.piper
A         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldTkProps.piper
A         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldProps.piper
A         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldAssertProps.piper
A         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorld.piper
A         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/HelloWorldCui.piper
A         ctakes-examples/src/main/resources/org/apache/ctakes/examples/pipeline/ProcessDir.piper
U         ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPropsPiperRunner.java
A         ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirBuilderRunner.java
U         ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldPiperRunner.java
U         ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/HelloWorldCuiPiperRunner.java
A         ctakes-examples/src/main/java/org/apache/ctakes/examples/pipeline/ProcessDirPiperRunner.java
U         ctakes-examples/pom.xml
U         ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPrinter.java
U         ctakes-core/src/main/java/org/apache/ctakes/core/cr/FilesInDirectoryCollectionReader.java
At revision 1765036

Parsing POMs
ERROR: Failed to parse POMs
java.io.IOException: remote file operation failed: <https://builds.apache.org/job/ctakes-trunk-package/ws/>
at hudson.remoting.Channel@1b735c02:ubuntu-eu2: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException:
org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing
the POMs:
[ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples-res/pom.xml>
of <https://builds.apache.org/job/ctakes-trunk-package/ws/pom.xml> does not exist @


	at hudson.FilePath.act(FilePath.java:1014)
	at hudson.FilePath.act(FilePath.java:996)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.parsePoms(MavenModuleSetBuild.java:960)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:679)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
	at hudson.model.Run.execute(Run.java:1741)
	at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:531)
	at hudson.model.ResourceController.execute(ResourceController.java:98)
	at hudson.model.Executor.run(Executor.java:410)
Caused by: hudson.remoting.ProxyException: hudson.maven.MavenModuleSetBuild$MavenExecutionException:
org.apache.maven.project.ProjectBuildingException: Some problems were encountered while processing
the POMs:
[ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples-res/pom.xml>
of <https://builds.apache.org/job/ctakes-trunk-package/ws/pom.xml> does not exist @


	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1364)
	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1098)
	at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2772)
	at hudson.remoting.UserRequest.perform(UserRequest.java:153)
	at hudson.remoting.UserRequest.perform(UserRequest.java:50)
	at hudson.remoting.Request$2.run(Request.java:332)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:745)
	at ......remote call to ubuntu-eu2(Native Method)
	at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1416)
	at hudson.remoting.UserResponse.retrieve(UserRequest.java:253)
	at hudson.remoting.Channel.call(Channel.java:781)
	at hudson.FilePath.act(FilePath.java:1007)
	... 8 more
Caused by: hudson.remoting.ProxyException: org.apache.maven.project.ProjectBuildingException:
Some problems were encountered while processing the POMs:
[ERROR] Child module <https://builds.apache.org/job/ctakes-trunk-package/ws/ctakes-examples-res/pom.xml>
of <https://builds.apache.org/job/ctakes-trunk-package/ws/pom.xml> does not exist @


	at org.apache.maven.project.DefaultProjectBuilder.build(DefaultProjectBuilder.java:364)
	at hudson.maven.MavenEmbedder.buildProjects(MavenEmbedder.java:361)
	at hudson.maven.MavenEmbedder.readProjects(MavenEmbedder.java:331)
	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1301)
	at hudson.maven.MavenModuleSetBuild$PomParser.invoke(MavenModuleSetBuild.java:1098)
	at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2772)
	at hudson.remoting.UserRequest.perform(UserRequest.java:153)
	at hudson.remoting.UserRequest.perform(UserRequest.java:50)
	at hudson.remoting.Request$2.run(Request.java:332)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:745)

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