See <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/536/display/redirect>
------------------------------------------ [...truncated 39.27 KB...] <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[628,10] [deprecation] show() in Dialog has been deprecated [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[724,16] [unchecked] unchecked call to add(E) as a member of the raw type ArrayList [WARNING] where E is a type-variable: E extends Object declared in class ArrayList <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[779,24] [unchecked] unchecked call to add(E) as a member of the raw type ArrayList [WARNING] where E is a type-variable: E extends Object declared in class ArrayList <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[782,19] [unchecked] unchecked call to add(E) as a member of the raw type List [WARNING] where E is a type-variable: E extends Object declared in interface List <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[783,18] [unchecked] unchecked call to add(E) as a member of the raw type ArrayList [WARNING] where E is a type-variable: E extends Object declared in class ArrayList <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[785,20] [unchecked] unchecked call to add(E) as a member of the raw type ArrayList [WARNING] where E is a type-variable: E extends Object declared in class ArrayList <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[797,30] [unchecked] unchecked method invocation: method assignColorsFromList in class CasAnnotationViewer is applied to given types [WARNING] required: List<Color>,List<String> found: List,ArrayList <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[797,31] [unchecked] unchecked conversion [WARNING] required: List<Color> found: List <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[797,42] [unchecked] unchecked conversion [WARNING] required: List<String> found: ArrayList <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[798,31] [unchecked] unchecked method invocation: method assignCheckedFromList in class CasAnnotationViewer is applied to given types [WARNING] required: List<String> found: ArrayList <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[798,32] [unchecked] unchecked conversion [WARNING] required: List<String> found: ArrayList <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[800,21] [unchecked] unchecked call to <T>toArray(T[]) as a member of the raw type ArrayList [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[871,38] [unchecked] unchecked method invocation: method createCas in class CasCreationUtils is applied to given types [WARNING] required: Collection<? extends MetaDataObject>,TypeSystem,Properties found: List,TypeSystem,Properties <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java>:[871,50] [unchecked] unchecked conversion [INFO] [INFO] --- maven-resources-plugin:2.5:testResources (default-testResources) @ ctakes-ytex-uima --- [debug] execute contextualize [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] Copying 3 resources [INFO] [INFO] --- maven-compiler-plugin:2.4:testCompile (default-testCompile) @ ctakes-ytex-uima --- [INFO] Compiling 11 source files to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes> [WARNING] <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java>:[87,31] [unchecked] unchecked method invocation: method createConceptGraph in interface ConceptDao is applied to given types [WARNING] required: String,String,String,boolean,Set<String> found: <null>,String,String,boolean,Set <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java>:[89,15] [unchecked] unchecked conversion [INFO] [INFO] --- maven-surefire-plugin:2.12.1:test (default-test) @ ctakes-ytex-uima --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ ctakes-ytex-uima --- [INFO] Building jar: <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/ctakes-ytex-uima-3.2.3-SNAPSHOT.jar> [INFO] [INFO] --- maven-site-plugin:3.1:attach-descriptor (attach-descriptor) @ ctakes-ytex-uima --- [INFO] [INFO] --- maven-dependency-plugin:2.8:copy-dependencies (copy-dependencies) @ ctakes-ytex-uima --- [INFO] Copying uimaj-tools-2.9.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/uimaj-tools-2.9.0.jar> [INFO] Copying spring-asm-3.1.2.RELEASE.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/spring-asm-3.1.2.RELEASE.jar> [INFO] Copying spring-jdbc-3.1.2.RELEASE.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/spring-jdbc-3.1.2.RELEASE.jar> [INFO] Copying ctakes-core-res-3.2.3-SNAPSHOT.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/ctakes-core-res-3.2.3-SNAPSHOT.jar> [INFO] Copying log4j-1.2.17.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/log4j-1.2.17.jar> [INFO] Copying aopalliance-1.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/aopalliance-1.0.jar> [INFO] Copying ant-contrib-1.0b3.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/ant-contrib-1.0b3.jar> [INFO] Copying spring-beans-3.1.2.RELEASE.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/spring-beans-3.1.2.RELEASE.jar> [INFO] Copying jaxb-impl-2.2.5.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/jaxb-impl-2.2.5.jar> [INFO] Copying commons-collections-3.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/commons-collections-3.0.jar> [INFO] Copying commons-lang-2.4.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/commons-lang-2.4.jar> [INFO] Copying cglib-2.2.2.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/cglib-2.2.2.jar> [INFO] Copying cleartk-ml-2.0.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/cleartk-ml-2.0.0.jar> [INFO] Copying xml-apis-1.0.b2.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/xml-apis-1.0.b2.jar> [INFO] Copying hibernate-ehcache-4.2.6.Final.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/hibernate-ehcache-4.2.6.Final.jar> [INFO] Copying findstructapi-0.0.1.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/findstructapi-0.0.1.jar> [INFO] Copying sqlwrapper-0.0.1.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/sqlwrapper-0.0.1.jar> [INFO] Copying antlr-2.7.7.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/antlr-2.7.7.jar> [INFO] Copying commons-pool-1.5.4.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/commons-pool-1.5.4.jar> [INFO] Copying weka-stable-3.6.10.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/weka-stable-3.6.10.jar> [INFO] Copying ctakes-resources-orangebook-hsqldb-3.1.3.jar to 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<https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/slf4j-api-1.6.1.jar> [INFO] Copying lvgdist-2016.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/lvgdist-2016.0.jar> [INFO] Copying asm-3.3.1.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/asm-3.3.1.jar> [INFO] Copying commons-logging-1.1.1.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/commons-logging-1.1.1.jar> [INFO] Copying slf4j-log4j12-1.6.1.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/slf4j-log4j12-1.6.1.jar> [INFO] Copying commons-dbcp-1.4.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/commons-dbcp-1.4.jar> [INFO] Copying ctakes-resources-rxnorm-hsqldb-2011ab-3.1.3.jar to 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Copying commons-beanutils-1.8.3.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/commons-beanutils-1.8.3.jar> [INFO] Copying openaifsm-0.0.1.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/openaifsm-0.0.1.jar> [INFO] Copying mysql-connector-java-5.1.26.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/mysql-connector-java-5.1.26.jar> [INFO] Copying jchronic-0.2.6.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/jchronic-0.2.6.jar> [INFO] Copying jakarta-regexp-1.4.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/jakarta-regexp-1.4.jar> [INFO] Copying med-facts-i2b2-1.2-SNAPSHOT.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/medfacts-i2b2-1.2.jar> [INFO] Copying jcarafe-core_2.9.1-0.9.8.3.RC4.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/jcarafe.core-2.9.1.jar> [INFO] Copying commons-logging-api-1.1.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/commons-logging-api-1.1.jar> [INFO] Copying cleartk-util-2.0.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/cleartk-util-2.0.0.jar> [INFO] Copying uimaj-adapter-vinci-2.9.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/uimaj-adapter-vinci-2.9.0.jar> [INFO] Copying ctakes-ytex-res-3.2.3-SNAPSHOT.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/ctakes-ytex-res-3.2.3-SNAPSHOT.jar> [INFO] Copying aspectjweaver-1.7.3.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/aspectjweaver-1.7.3.jar> [INFO] Copying spring-expression-3.1.2.RELEASE.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/spring-expression-3.1.2.RELEASE.jar> [INFO] Copying jboss-logging-3.1.0.GA.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/jboss-logging-3.1.0.GA.jar> [INFO] Copying ctakes-dictionary-lookup-res-3.2.3-SNAPSHOT.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/ctakes-dictionary-lookup-res-3.2.3-SNAPSHOT.jar> [INFO] Copying lucene-queryparser-4.0.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/lucene-queryparser-4.0.0.jar> [INFO] Copying java-cup-0.11a.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/java-cup-0.11a.jar> [INFO] Copying spring-aop-3.1.2.RELEASE.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/spring-aop-3.1.2.RELEASE.jar> [INFO] Copying lucene-queries-4.0.0.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/lucene-queries-4.0.0.jar> [INFO] Copying ehcache-core-2.4.6.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/ehcache-core-2.4.6.jar> [INFO] Copying ctakes-core-3.2.3-SNAPSHOT.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/ctakes-core-3.2.3-SNAPSHOT.jar> [INFO] Copying jaxb-api-2.2.5.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/jaxb-api-2.2.5.jar> [INFO] Copying opennlp-tools-1.7.2.jar to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/lib/opennlp-tools-1.7.2.jar> [INFO] [INFO] --- maven-antrun-plugin:1.6:run (generate-test-config) @ ctakes-ytex-uima --- [INFO] Executing tasks main: generateTestYtexProperties: [echo] <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex/ytex.properties> does not exist, generating ytex.properties for hsqldb in /tmp/ctakes-test-hsqldb/ctakes/ctakes [copy] Copying 1 file to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes/org/apache/ctakes/ytex> templateToConfig.init: templateToConfig.extractTemplates: templateToConfig.updateConfig: [echo] config.source.dir = <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/../ctakes-ytex-res/src/main/resources> [echo] config.generated.dir = <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes> [copy] Copying 6 files to <https://builds.apache.org/job/ctakes-trunk-package/org.apache.ctakes$ctakes-ytex-uima/ws/target/test-classes> templateToConfig: deleteTestDb: [delete] Deleting directory /tmp/ctakes-test-hsqldb/ctakes test.setup: init: umls.check.mrconso: [echo] umls.schema ${db.schema} [echo] umls.catalog [sql] Executing commands [sql] 1 of 1 SQL statements executed successfully [echo] mrconso.out = 0 [echo] [delete] Deleting: /tmp/mrconso-check.txt [echo] mrconso.exists = ${mrconso.exists} umls.all: [echo] mrconso.exists = ${mrconso.exists} init: umls.drop.view: [echo] drop v_snomed_fword_lookup table jdbc.sqlcmd: [echo] db.schemaPUBLIC [echo] umls.schema ${db.schema} [echo] umls.catalog [echo] execute ./hsql/./umls/drop_view.sql [copy] Copying 1 file to /tmp [echo] executing /tmp/ytex2029570364.sql [sql] Executing resource: /tmp/ytex2029570364.sql [sql] 3 of 3 SQL statements executed successfully [delete] Deleting: /tmp/ytex2029570364.sql [delete] Deleting: /tmp/ytex1120717829use.sql init.conn: [copy] Copying 1 file to /tmp umls.create.view: [echo] create the v_snomed_fword_lookup table jdbc.sqlcmd: [echo] db.schemaPUBLIC [echo] umls.schema ${db.schema} [echo] umls.catalog [echo] execute ./hsql/./umls/create_view.sql [copy] Copying 1 file to /tmp [echo] executing /tmp/ytex1973651204.sql [sql] Executing resource: /tmp/ytex1973651204.sql [sql] 2 of 2 SQL statements executed successfully [delete] Deleting: /tmp/ytex1973651204.sql [delete] Deleting: /tmp/ytex1466786827use.sql umls.import.view: [echo] import v_snomed_fword_lookup from /home/jenkins/jenkins-slave/workspace/ctakes-trunk-package/ctakes-ytex/scripts/data/umls/v_snomed_fword_lookup.txt. Be patient, this can take a while. jdl: [echo] jdl.format /home/jenkins/jenkins-slave/workspace/ctakes-trunk-package/ctakes-ytex/scripts/data/umls/v_snomed_fword_lookup.xml [echo] jdl.data /home/jenkins/jenkins-slave/workspace/ctakes-trunk-package/ctakes-ytex/scripts/data/umls/v_snomed_fword_lookup.txt [echo] umls.prefix [copy] Copying 1 file to /tmp [java] 2017-03-30 11:59:46,385 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - delimiter 9 encapsulator 65534 [java] 2017-03-30 11:59:46,397 INFO org.apache.ctakes.jdl.data.loader.CsvLoader - insert into PUBLIC.v_snomed_fword_lookup (cui,tui,fword,fstem,tok_str,sException in thread "main" java.lang.NoSuchMethodError: org.hsqldb.DatabaseURL.parseURL(Ljava/lang/String;ZZ)Lorg/hsqldb/persisttem_str) values (?,?,?,?,?,?) [java] /HsqlProperties; [java] at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) [java] at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) [java] at java.sql.DriverManager.getConnection(DriverManager.java:664) [java] at java.sql.DriverManager.getConnection(DriverManager.java:247) [java] at org.apache.ctakes.jdl.data.base.JdlConnection.openConnection(JdlConnection.java:77) [java] at org.apache.ctakes.jdl.data.base.JdlConnection.getOpenConnection(JdlConnection.java:93) [java] at org.apache.ctakes.jdl.data.loader.CsvLoader.dataInsert(CsvLoader.java:133) [java] at org.apache.ctakes.jdl.AppJdl.execute(AppJdl.java:90) [java] at org.apache.ctakes.jdl.AppMain.main(AppMain.java:88)
