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From Apache Jenkins Server <jenk...@builds.apache.org>
Subject Build failed in Jenkins: ctakes-trunk-compiletest #199
Date Fri, 08 Mar 2013 21:39:59 GMT
See <https://builds.apache.org/job/ctakes-trunk-compiletest/199/changes>

Changes:

[chenpei] CTAKES-84 - During the XMLDiff in XMLUnit, need to handle that the xcas's elements
and attributes could be in different order, but they should be treated as similar.  Use ElementNameAndAttributeQualifier()
per doc: http://xmlunit.sourceforge.net/userguide/html/ar01s03.html#ElementQualifier

[chenpei] CTAKES-84 - Enabling the ctakes-regression-test module in the root pom.

[chenpei] CTAKES-84 - Adding Coreference pipeline to the regression test.

[chenpei] CTAKES-84 - The new regression test also tests the xml descriptor files.  Fixing
the errors it detected:
- Updating the chunker classname to org.apache instead of edu.mayo.
- Updating the Consituency Parser Path (still had the old name).

------------------------------------------
[...truncated 5789 lines...]
Skin: No rashes or other changes
Head: See present illness.
Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision
Ears: Hearing good. No tinnitus, vertigo, infections
Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble
Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore
Neck: No lumps, goiter, pain
Breasts: No lumps, pain, discharge.
Respiratory: No cough, wheezing, shortness of breath, pneumonia, tuberculosis.
Cardiac: No known heart disease. No orthopnea, chest pain, palpitations.
Gastrointestinal: Appetite good; no reflux. Bowel movement about once daily though
sometimes has hard stools for 2-3 d when especially tense; no diarrhea or
bleeding. No pain, jaundice, gallbladder or liver trouble
Urinary: No frequency, dysuria, hematuria or flank pain
Genitoreproductive: Regular menstrual periods. No vaginal discharge or itch
Musculoskeletal: Mild aching low back pain often after a long day?s work; no radiation
down legs; used to do back exercises, but not now. No other joint pain
Patient Centered Medicine 2
Peripheral Vascular: Varicose veins appeared in both legs during first pregnancy. Has had
swollen ankles after prolonged standing for 10 yr; no history of
phlebitis or leg pain
Neurological: No fainting, seizures, tremors, weakness, or tingling. Memory good
Psychiatric: No anxiety or nervousness or depression
Endocrine: No known thyroid trouble, temperature intolerance. Sweating average. No
symptoms or history of diabetes
Hematologic: No easy bleeding. No anemia
Adapted from Bates? Guide to Physical Examination and History Taking, Chapter 21, The Patient?s
Record, pp. 722-
726"...> at /CAS[1]/uima.cas.Sofa[1]/@sofaString to <uima.cas.Sofa sofaString="Patient
Centered Medicine 2
Revised: 7/27/99
DATA BASE: SAMPLE HISTORY
IDENTIFYING DATA 
CM is a 45-year-old, widowed, white saleswoman, born in the U.S.
CHIEF COMPLAINT
?Bad headaches?
HISTORY OF PRESENT ILLNESS 
Patient Perspective
She thinks her headaches may be like those in the past. However, she now has high blood
pressure and is concerned because her mother had high blood pressure and died of a
stroke. She is also concerned that they make her irritable with her family.
PAST MEDICAL HISTORY
Significant Childhood Illnesses
Only measles and chickenpox
Immunizations
Last tetanus 1998
Flu vaccine last November
Adult Illnesses/Hospitalizations
- Kidney infection 1982 treated with ampicillin and developed a generalized rash.
- Hypertension x 7 years, well controlled with home BPs normally 120-130/low 80s
Patient Centered Medicine 2
2 Revised: 7/27/99
Psychiatric Illnesses/Hospitalizations
None
Operations
Tonsillectomy, age 6,
Appendectomy, age 13
Injuries/Accidents
1998 foot laceration, 4 stitches
Obstetric History
G3, P3, 3 living children. Menarche age 12. Last menses 2 weeks ago.
Transfusions
None
CURRENT HEALTH STATUS
Medications
Aspirin for headaches
Multivitamin 1 per day
Hydrochlorothiazide 25 mg per day (x 7 years)
No herbs or supplements
Allergies/Drug Reactions
Ampicillin causes rash
Health Screening
- Last pap smear 2000, normal.
- Normal mammogram in 2000.
- Does breast self-exams monthly
- Cholesterol = 220 (in 2000)
Diet, Sleep, Exercise
- Diet ? Low in calcium with little milk or cheese. She frequently eats mid-morning and
evening snacks that are high in fat. She does follow a low salt diet.
- Sleep ? Generally good, average 7 hr
- Exercise ? ?No time?
Habits
- Alcohol ? Rare drink (wine) only, no history of abuse
- Drugs ? Never tried illegal drugs
Alternative Therapies
None
Patient Centered Medicine 2
PSYCHOSOCIAL HISTORY
- 4 yr ago her husband died suddenly of heart attack, leaving little savings and no
insurance.
- Lives alone, recently moved to a small apartment to be near daughter
- Cosmetic saleswoman for 15 years at Sears. Likes her job but feels stressed by demands
from the new manager
- Not sexually active since the death of her husband who was her only partner
- Denies depression
- Feels safe at work and home
FAMILY HISTORY
- Mother died, 67, stroke; had varicose veins, headaches, hypertension
- Father died, 43, train accident
- One brother, 56, has high blood pressure, otherwise well
- One brother, 51, apparently well except for mild arthritis
- Daughter, 23, ?migraine headaches,? otherwise well
- Son, 21, well
- Son, 20, well
REVIEW OF SYSTEMS:
General: Has gained about 10 lb in the past 4 yr, no fatigue
Skin: No rashes or other changes
Head: See present illness.
Eyes: Reading glasses for 5 yr, last checked 1 yr ago. No double or blurry vision
Ears: Hearing good. No tinnitus, vertigo, infections
Nose, Sinuses: occasional mild cold. No hay fever, sinus trouble
Mouth and Throat: Last to dentist 2 yr ago. Occasional canker sore
Neck: No lumps, goiter, pain
Breasts: No lumps, pain, discharge.
Respiratory: No cough, wheezing, shortness of breath, pneumonia, tuberculosis.
Cardiac: No known heart disease. No orthopnea, chest pain, palpitations.
Gastrointestinal: Appetite good; no reflux. Bowel movement about once daily though
sometimes has hard stools for 2-3 d when especially tense; no diarrhea or
bleeding. No pain, jaundice, gallbladder or liver trouble
Urinary: No frequency, dysuria, hematuria or flank pain
Genitoreproductive: Regular menstrual periods. No vaginal discharge or itch
Musculoskeletal: Mild aching low back pain often after a long day?s work; no radiation
down legs; used to do back exercises, but not now. No other joint pain
Patient Centered Medicine 2
Peripheral Vascular: Varicose veins appeared in both legs during first pregnancy. Has had
swollen ankles after prolonged standing for 10 yr; no history of
phlebitis or leg pain
Neurological: No fainting, seizures, tremors, weakness, or tingling. Memory good
Psychiatric: No anxiety or nervousness or depression
Endocrine: No known thyroid trouble, temperature intolerance. Sweating average. No
symptoms or history of diabetes
Hematologic: No easy bleeding. No anemia
Adapted from Bates? Guide to Physical Examination and History Taking, Chapter 21, The Patient?s
Record, pp. 722-
726"...> at /CAS[1]/uima.cas.Sofa[1]/@sofaString

	at junit.framework.Assert.fail(Assert.java:50)
	at junit.framework.Assert.assertTrue(Assert.java:20)
	at org.apache.ctakes.regression.test.RegressionPipelineTest.compareXMLOutput(RegressionPipelineTest.java:136)
	at org.apache.ctakes.regression.test.RegressionPipelineTest$StatusCallbackListenerImpl.collectionProcessComplete(RegressionPipelineTest.java:187)
	at org.apache.uima.collection.impl.cpm.BaseCPMImpl.run(BaseCPMImpl.java:538)
	at java.lang.Thread.run(Thread.java:662)

Results :

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

[JENKINS] Recording test results
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] Apache cTAKES ..................................... SUCCESS [3.584s]
[INFO] Apache cTAKES common type system .................. SUCCESS [6.920s]
[INFO] Apache cTAKES utils ............................... SUCCESS [2.001s]
[INFO] Apache cTAKES core ................................ SUCCESS [6.523s]
[INFO] Apache cTAKES part-of-speech tagger ............... SUCCESS [3.444s]
[INFO] Apache cTAKES chunker ............................. SUCCESS [1.590s]
[INFO] Apache cTAKES document preprocessor ............... SUCCESS [1.645s]
[INFO] Apache cTAKES dictionary lookup ................... SUCCESS [9.623s]
[INFO] Apache cTAKES context dependent tokenizer ......... SUCCESS [0.866s]
[INFO] Apache cTAKES LVG lexical tools ................... SUCCESS [1.764s]
[INFO] Apache cTAKES named entity contexts ............... SUCCESS [2.111s]
[INFO] Apache cTAKES Constituency Parser ................. SUCCESS [1.163s]
[INFO] Apache cTAKES Dependency Parser ................... SUCCESS [4.734s]
[INFO] Apache cTAKES Relation Extractor .................. SUCCESS [6.205s]
[INFO] Apache cTAKES CoReference Resolver ................ SUCCESS [3.782s]
[INFO] Apache cTAKES Drug NER ............................ SUCCESS [3.507s]
[INFO] Apache cTAKES Side Effects ........................ SUCCESS [3.682s]
[INFO] Apache cTAKES Smoking Status ...................... SUCCESS [3.483s]
[INFO] Apache cTAKES Pad Term Spotter .................... SUCCESS [4.193s]
[INFO] Apache cTAKES Assertion's zoner ................... SUCCESS [1.178s]
[INFO] Apache cTAKES Assertion ........................... SUCCESS [5.460s]
[INFO] Apache cTAKES Temporal Information Extraction ..... SUCCESS [7.930s]
[INFO] Apache cTAKES ctakes-clinical-pipeline ............ SUCCESS [2.911s]
[INFO] Apache cTAKES Distribution ........................ SUCCESS [0.600s]
[INFO] Apache cTAKES Regression-test ..................... FAILURE [15:03.098s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 16:34.494s
[INFO] Finished at: Fri Mar 08 21:30:33 UTC 2013
[INFO] Final Memory: 33M/198M
[INFO] ------------------------------------------------------------------------
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Waiting for Jenkins to finish collecting data
mavenExecutionResult exceptions not empty
message : Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12:test
(default-test) on project ctakes-regression-test: Failure or timeout
cause : Failure or timeout
Stack trace : 
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.12:test
(default-test) on project ctakes-regression-test: Failure or timeout
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:217)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:84)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:59)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.singleThreadedBuild(LifecycleStarter.java:183)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:161)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:320)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:156)
	at org.jvnet.hudson.maven3.launcher.Maven3Launcher.main(Maven3Launcher.java:79)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchStandard(Launcher.java:329)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:239)
	at org.jvnet.hudson.maven3.agent.Maven3Main.launch(Maven3Main.java:158)
	at hudson.maven.Maven3Builder.call(Maven3Builder.java:100)
	at hudson.maven.Maven3Builder.call(Maven3Builder.java:66)
	at hudson.remoting.UserRequest.perform(UserRequest.java:118)
	at hudson.remoting.UserRequest.perform(UserRequest.java:48)
	at hudson.remoting.Request$2.run(Request.java:326)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
	at java.lang.Thread.run(Thread.java:662)
Caused by: org.apache.maven.plugin.MojoExecutionException: Failure or timeout
	at org.apache.maven.plugin.surefire.SurefirePlugin.assertNoFailureOrTimeout(SurefirePlugin.java:665)
	at org.apache.maven.plugin.surefire.SurefirePlugin.handleSummary(SurefirePlugin.java:646)
	at org.apache.maven.plugin.surefire.AbstractSurefireMojo.executeAfterPreconditionsChecked(AbstractSurefireMojo.java:137)
	at org.apache.maven.plugin.surefire.AbstractSurefireMojo.execute(AbstractSurefireMojo.java:98)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:101)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:209)
	... 27 more
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