FailedConsole Output

Started by user Stian Soiland-Reyes (stain)
Building remotely on jenkins-slave in workspace /var/lib/jenkins/workspace/ops-chembl-rdf
 > /usr/bin/git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
 > /usr/bin/git config remote.origin.url https://github.com/stain/ops-chembl-rdf.git # timeout=10
Fetching upstream changes from https://github.com/stain/ops-chembl-rdf.git
 > /usr/bin/git --version # timeout=10
 > /usr/bin/git -c core.askpass=true fetch --tags --progress https://github.com/stain/ops-chembl-rdf.git +refs/heads/*:refs/remotes/origin/*
 > /usr/bin/git rev-parse origin/master^{commit} # timeout=10
Checking out Revision 272609a58389d0c7d6edfbaa5cbcbf095572a776 (origin/master)
 > /usr/bin/git config core.sparsecheckout # timeout=10
 > /usr/bin/git checkout -f 272609a58389d0c7d6edfbaa5cbcbf095572a776
 > /usr/bin/git rev-list 923008fdc56a5a58b36b39b3e59706bceefc3b3e # timeout=10
Parsing POMs
maven32-agent.jar already up to date
maven32-interceptor.jar already up to date
maven3-interceptor-commons.jar already up to date
[ops-chembl-rdf] $ /var/lib/jenkins/tools/hudson.model.JDK/jdk7/bin/java -Xmx1024m -XX:MaxPermSize=1024m -cp /var/lib/jenkins/maven32-agent.jar:/var/lib/jenkins/tools/hudson.tasks.Maven_MavenInstallation/maven_3.2.1/boot/plexus-classworlds-2.5.1.jar:/var/lib/jenkins/tools/hudson.tasks.Maven_MavenInstallation/maven_3.2.1/conf/logging jenkins.maven3.agent.Maven32Main /var/lib/jenkins/tools/hudson.tasks.Maven_MavenInstallation/maven_3.2.1 /run/jenkins/slave.jar /var/lib/jenkins/maven32-interceptor.jar /var/lib/jenkins/maven3-interceptor-commons.jar 40015
<===[JENKINS REMOTING CAPACITY]===>channel started
Executing Maven:  -B -f /var/lib/jenkins/workspace/ops-chembl-rdf/pom.xml -Dmaven.repo.local=/var/lib/jenkins/workspace/ops-chembl-rdf/.repository clean install
[INFO] Scanning for projects...
[INFO] [buildinfo] Properties file found at '/tmp/buildInfo3218529108139835824.properties'
[INFO] Initializing Artifactory Build-Info Recording
[INFO] 
[INFO] Using the builder org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder with a thread count of 1
[HUDSON] Collecting dependencies info
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ChEMBL-RDF data 20.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] [buildinfo] Properties file found at '/tmp/buildInfo3218529108139835824.properties'
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ chembl-rdf ---
[INFO] Deleting /var/lib/jenkins/workspace/ops-chembl-rdf/target
[INFO] 
[INFO] --- wagon-maven-plugin:1.0:download (download-rdf) @ chembl-rdf ---
[INFO] Scanning remote file system: http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0 ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/cco.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/cco.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_activity.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_activity.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_assay.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_assay.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_bindingsite.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_bindingsite.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_biocmpt.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_biocmpt.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_cellline.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_cellline.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_document.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_document.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_journal.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_journal.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_moa.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_moa.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_molecule.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_molecule.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_molecule_chebi_ls.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_molecule_chebi_ls.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_molhierarchy.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_molhierarchy.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_protclass.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_protclass.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_source.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_source.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_target.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_target.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_target_targetcmpt_ls.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_target_targetcmpt_ls.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_targetcmpt.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_targetcmpt.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_targetcmpt_uniprot_ls.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_targetcmpt_uniprot_ls.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_targetrel.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_targetrel.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/chembl_20.0_unichem.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/chembl_20.0_unichem.ttl.gz ...
[INFO] Downloading http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0/void.ttl.gz to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/chembl/void.ttl.gz ...
[INFO] 
[INFO] --- wagon-maven-plugin:1.0:download-single (download-license) @ chembl-rdf ---
[INFO] Downloading: http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0//LICENSE to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/META-INF/LICENSE
[INFO] 
[INFO] --- wagon-maven-plugin:1.0:download-single (download-notice) @ chembl-rdf ---
[INFO] Downloading: http://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBL-RDF/20.0//REQUIRED.ATTRIBUTION to /var/lib/jenkins/workspace/ops-chembl-rdf/target/classes/META-INF/NOTICE
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ chembl-rdf ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/ops-chembl-rdf/src/main/resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:compile (default-compile) @ chembl-rdf ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ chembl-rdf ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /var/lib/jenkins/workspace/ops-chembl-rdf/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:testCompile (default-testCompile) @ chembl-rdf ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.12.4:test (default-test) @ chembl-rdf ---
[INFO] No tests to run.
[JENKINS] Recording test results
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ chembl-rdf ---
[INFO] Building jar: /var/lib/jenkins/workspace/ops-chembl-rdf/target/chembl-rdf-20.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ chembl-rdf ---
[INFO] Installing /var/lib/jenkins/workspace/ops-chembl-rdf/target/chembl-rdf-20.0-SNAPSHOT.jar to /var/lib/jenkins/workspace/ops-chembl-rdf/.repository/org/openphacts/data/chembl-rdf/20.0-SNAPSHOT/chembl-rdf-20.0-SNAPSHOT.jar
[INFO] Installing /var/lib/jenkins/workspace/ops-chembl-rdf/pom.xml to /var/lib/jenkins/workspace/ops-chembl-rdf/.repository/org/openphacts/data/chembl-rdf/20.0-SNAPSHOT/chembl-rdf-20.0-SNAPSHOT.pom
[INFO] Artifactory Build Info Recorder: Saving Build Info to '/var/lib/jenkins/workspace/ops-chembl-rdf/target/build-info.json'
[INFO] Deploying artifact: http://repository.mygrid.org.uk/artifactory/ops/org/openphacts/data/chembl-rdf/20.0-SNAPSHOT/chembl-rdf-20.0-SNAPSHOT.jar
[INFO] Deploying artifact: http://repository.mygrid.org.uk/artifactory/ops/org/openphacts/data/chembl-rdf/20.0-SNAPSHOT/chembl-rdf-20.0-SNAPSHOT.pom
[INFO] Artifactory Build Info Recorder: Deploying build info ...
[INFO] Deploying build info to: http://repository.mygrid.org.uk/artifactory/api/build
[INFO] Build successfully deployed. Browse it in Artifactory under http://repository.mygrid.org.uk/artifactory/webapp/builds/ops-chembl-rdf/6/2015-04-30T14:40:28.319+0100/
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 27:26 min
[INFO] Finished at: 2015-04-30T15:07:54+00:00
[INFO] Final Memory: 17M/64M
[INFO] ------------------------------------------------------------------------
[JENKINS] Archiving /var/lib/jenkins/workspace/ops-chembl-rdf/pom.xml to org.openphacts.data/chembl-rdf/20.0-SNAPSHOT/chembl-rdf-20.0-SNAPSHOT.pom
[JENKINS] Archiving /var/lib/jenkins/workspace/ops-chembl-rdf/target/chembl-rdf-20.0-SNAPSHOT.jar to org.openphacts.data/chembl-rdf/20.0-SNAPSHOT/chembl-rdf-20.0-SNAPSHOT.jar
ERROR: Failed to parse POMs
java.io.IOException: java.io.IOException: Failed to extract /var/lib/jenkins/workspace/ops-chembl-rdf/transfer of 2 files
	at hudson.FilePath.readFromTar(FilePath.java:2297)
	at hudson.FilePath.copyRecursiveTo(FilePath.java:2208)
	at jenkins.model.StandardArtifactManager.archive(StandardArtifactManager.java:61)
	at hudson.maven.MavenBuild$ProxyImpl.performArchiving(MavenBuild.java:483)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:851)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:536)
	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:374)
Caused by: java.io.IOException: java.lang.InterruptedException
	at hudson.remoting.FastPipedInputStream.read(FastPipedInputStream.java:177)
	at hudson.util.HeadBufferingStream.read(HeadBufferingStream.java:61)
	at com.jcraft.jzlib.InflaterInputStream.fill(InflaterInputStream.java:175)
	at com.jcraft.jzlib.InflaterInputStream.read(InflaterInputStream.java:106)
	at org.apache.tools.tar.TarBuffer.readBlock(TarBuffer.java:257)
	at org.apache.tools.tar.TarBuffer.readRecord(TarBuffer.java:223)
	at hudson.org.apache.tools.tar.TarInputStream.read(TarInputStream.java:345)
	at java.io.FilterInputStream.read(FilterInputStream.java:107)
	at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:1792)
	at org.apache.commons.io.IOUtils.copyLarge(IOUtils.java:1769)
	at org.apache.commons.io.IOUtils.copy(IOUtils.java:1744)
	at hudson.util.IOUtils.copy(IOUtils.java:40)
	at hudson.FilePath.readFromTar(FilePath.java:2287)
	... 9 more
Caused by: java.lang.InterruptedException
	at java.lang.Object.wait(Native Method)
	at hudson.remoting.FastPipedInputStream.read(FastPipedInputStream.java:175)
	... 21 more

	at hudson.FilePath.copyRecursiveTo(FilePath.java:2215)
	at jenkins.model.StandardArtifactManager.archive(StandardArtifactManager.java:61)
	at hudson.maven.MavenBuild$ProxyImpl.performArchiving(MavenBuild.java:483)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:851)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:536)
	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:374)
Caused by: java.util.concurrent.ExecutionException: java.io.IOException: Pipe is already closed
	at hudson.remoting.Channel$3.adapt(Channel.java:785)
	at hudson.remoting.Channel$3.adapt(Channel.java:780)
	at hudson.remoting.FutureAdapter.get(FutureAdapter.java:59)
	at hudson.FilePath.copyRecursiveTo(FilePath.java:2211)
	... 8 more
Caused by: java.io.IOException: Pipe is already closed
	at hudson.remoting.PipeWindow.checkDeath(PipeWindow.java:108)
	at hudson.remoting.PipeWindow$Real.get(PipeWindow.java:203)
	at hudson.remoting.ProxyOutputStream._write(ProxyOutputStream.java:141)
	at hudson.remoting.ProxyOutputStream.write(ProxyOutputStream.java:109)
	at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
	at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
	at com.jcraft.jzlib.DeflaterOutputStream.deflate(DeflaterOutputStream.java:144)
	at com.jcraft.jzlib.DeflaterOutputStream.write(DeflaterOutputStream.java:102)
	at java.io.BufferedOutputStream.write(BufferedOutputStream.java:122)
	at org.apache.tools.tar.TarBuffer.writeBlock(TarBuffer.java:410)
	at org.apache.tools.tar.TarBuffer.writeRecord(TarBuffer.java:351)
	at hudson.org.apache.tools.tar.TarOutputStream.writeEOFRecord(TarOutputStream.java:356)
	at hudson.org.apache.tools.tar.TarOutputStream.finish(TarOutputStream.java:137)
	at hudson.org.apache.tools.tar.TarOutputStream.close(TarOutputStream.java:149)
	at hudson.util.io.TarArchiver.close(TarArchiver.java:125)
	at hudson.FilePath.writeToTar(FilePath.java:2262)
	at hudson.FilePath.access$2100(FilePath.java:191)
	at hudson.FilePath$45.invoke(FilePath.java:2201)
	at hudson.FilePath$45.invoke(FilePath.java:2197)
	at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2688)
	at hudson.remoting.UserRequest.perform(UserRequest.java:118)
	at hudson.remoting.UserRequest.perform(UserRequest.java:48)
	at hudson.remoting.Request$2.run(Request.java:328)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at hudson.remoting.Engine$1$1.run(Engine.java:63)
	at java.lang.Thread.run(Thread.java:745)
	at ......remote call to jenkins-slave(Native Method)
	at hudson.remoting.Channel.attachCallSiteStackTrace(Channel.java:1360)
	at hudson.remoting.UserResponse.retrieve(UserRequest.java:221)
	at hudson.remoting.Channel$3.adapt(Channel.java:783)
	... 11 more
Caused by: java.io.IOException: Pipe is already closed
	at hudson.remoting.FastPipedOutputStream.write(FastPipedOutputStream.java:153)
	at hudson.remoting.FastPipedOutputStream.write(FastPipedOutputStream.java:137)
	at hudson.remoting.ProxyOutputStream$Chunk$1.run(ProxyOutputStream.java:245)
	at hudson.remoting.PipeWriter$1.run(PipeWriter.java:158)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at hudson.remoting.SingleLaneExecutorService$1.run(SingleLaneExecutorService.java:112)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:68)
	at jenkins.util.ContextResettingExecutorService$2.call(ContextResettingExecutorService.java:46)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:745)
Caused by: hudson.remoting.FastPipedInputStream$ClosedBy: The pipe was closed at...
	at hudson.remoting.FastPipedInputStream.close(FastPipedInputStream.java:112)
	at java.io.FilterInputStream.close(FilterInputStream.java:181)
	at com.jcraft.jzlib.InflaterInputStream.close(InflaterInputStream.java:168)
	at org.apache.tools.tar.TarBuffer.close(TarBuffer.java:456)
	at hudson.org.apache.tools.tar.TarInputStream.close(TarInputStream.java:110)
	at hudson.FilePath.readFromTar(FilePath.java:2304)
	at hudson.FilePath.copyRecursiveTo(FilePath.java:2208)
	at jenkins.model.StandardArtifactManager.archive(StandardArtifactManager.java:61)
	at hudson.maven.MavenBuild$ProxyImpl.performArchiving(MavenBuild.java:483)
	at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.doRun(MavenModuleSetBuild.java:851)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:536)
	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:374)
channel stopped
Finished: FAILURE