SuccessConsole Output

Started by upstream project "qc-metrics-prb" build number 1
originally caused by:
 GitHub pull request #1 of commit f000f476dbdfc73b7617fead65279a6a4c443a05 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-08 (centos) in workspace /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/qc-metrics.git
 > git init /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/qc-metrics.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/bigdatagenomics/qc-metrics.git +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url https://github.com/bigdatagenomics/qc-metrics.git # timeout=10
 > git config remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/bigdatagenomics/qc-metrics.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/qc-metrics.git
 > git fetch --tags --progress https://github.com/bigdatagenomics/qc-metrics.git +refs/pull/*:refs/remotes/origin/pr/*
Checking out Revision 8d7be32a944cfbea78604324d75542edbbce9388 (detached)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 8d7be32a944cfbea78604324d75542edbbce9388
First time build. Skipping changelog.
[centos] $ /home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/mvn -DghprbTriggerAuthorEmail= -DghprbTargetBranch=master -DghprbSourceBranch=initial-setup -Dhadoop.version=2.2.0 "-DghprbActualCommitAuthor=Timothy Danford" -Dlabel=centos -Dsha1=origin/pr/1/merge -DghprbPullLink=https://github.com/bigdatagenomics/qc-metrics/pull/1 -DghprbActualCommit=f000f476dbdfc73b7617fead65279a6a4c443a05 -DGIT_BRANCH=initial-setup -DghprbPullAuthorEmail= -DghprbActualCommitAuthorEmail=tdanford@gmail.com -DghprbTriggerAuthor= -DghprbPullId=1 "-DghprbPullTitle=Initial setup" "-DghprbPullDescription=GitHub pull request #1 of commit f000f476dbdfc73b7617fead65279a6a4c443a05 automatically merged." clean package
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.qc-metrics:qc-metrics-core:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.qc-metrics:qc-metrics-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/pom.xml, line 353, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.qc-metrics:qc-metrics-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/pom.xml, line 357, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.qc-metrics:qc-metrics-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/pom.xml, line 353, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.qc-metrics:qc-metrics-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/pom.xml, line 357, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.qc-metrics:qc-metrics-cli:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.qc-metrics:qc-metrics-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/pom.xml, line 353, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.qc-metrics:qc-metrics-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/pom.xml, line 357, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.qc-metrics:qc-metrics-parent:pom:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 353, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 357, column 25
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] qc-metrics
[INFO] QC Metrics: Core
[INFO] QC Metrics: CLI
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building qc-metrics 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ qc-metrics-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ qc-metrics-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ qc-metrics-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ qc-metrics-parent ---
[INFO] Modified 0 of 17 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ qc-metrics-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ qc-metrics-parent ---
[INFO] No sources to compile
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building QC Metrics: Core 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core/0.16.0/adam-core-0.16.0.pom
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Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core/0.16.0/adam-core-0.16.0.jar
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core/0.16.0/adam-core-0.16.0-tests.jar
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Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core/0.16.0/adam-core-0.16.0-tests.jar (1603 KB at 3197.9 KB/sec)
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Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core/0.16.0/adam-core-0.16.0.jar (1915 KB at 3245.3 KB/sec)
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ qc-metrics-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ qc-metrics-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ qc-metrics-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.7:add-source (add-source) @ qc-metrics-core ---
[INFO] Source directory: /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ qc-metrics-core ---
[INFO] Modified 0 of 12 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ qc-metrics-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ qc-metrics-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.0 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.bdg-utils:bdg-utils-misc:0.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.bdg-utils:bdg-utils-metrics:0.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.bdg-utils:bdg-utils-parquet:0.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core:0.16.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core:0.16.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.bdg-utils:bdg-utils-misc:0.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.qc-metrics:qc-metrics-core:0.0.1-SNAPSHOT requires scala version: 2.10.4
[WARNING]  org.fusesource.scalate:scalate-util_2.10:1.6.1 requires scala version: 2.10.4
[WARNING]  org.fusesource.scalate:scalate-core_2.10:1.6.1 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 7 Scala sources to /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-core/target/scala-2.10.4/classes...
[WARNING] there were 1 feature warning(s); re-run with -feature for details
[WARNING] one warning found
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ qc-metrics-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.7:add-test-source (add-test-source) @ qc-metrics-core ---
[INFO] Test Source directory: /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ qc-metrics-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ qc-metrics-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.0 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.bdg-utils:bdg-utils-misc:0.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.bdg-utils:bdg-utils-metrics:0.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.bdg-utils:bdg-utils-parquet:0.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core:0.16.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core:0.16.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.bdg-utils:bdg-utils-misc:0.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.qc-metrics:qc-metrics-core:0.0.1-SNAPSHOT requires scala version: 2.10.4
[WARNING]  org.fusesource.scalate:scalate-util_2.10:1.6.1 requires scala version: 2.10.4
[WARNING]  org.fusesource.scalate:scalate-core_2.10:1.6.1 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 5 Scala sources to /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-core/target/scala-2.10.4/test-classes...
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ qc-metrics-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ qc-metrics-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ qc-metrics-core ---
Discovery starting.
Discovery completed in 172 milliseconds.
Run starting. Expected test count is: 11
GenotypesSummarySuite:
2015-03-01 19:32:48 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- simple genotypes summary
- empty genotypes summary
ComparisonTraversalEngineSuite:
- generate works on a simple RDD
- combine works on a simple RDD
GenotypeConcordanceRDDFunctionsSuite:
- concordance of identical and non-identical genotypes
- concordance of identical VCFs should be 1.0
GeneratorFilterSuite:
- CombinedFilter combines two independent filters
ComparisonsSuite:
- Dupe mismatches found
- Mismatched mapped positions histogram generated
- Test map quality scores
- Test base quality scores
Run completed in 23 seconds, 891 milliseconds.
Total number of tests run: 11
Suites: completed 6, aborted 0
Tests: succeeded 11, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ qc-metrics-core ---
[INFO] Building jar: /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-core/target/qc-metrics-core-0.0.1-SNAPSHOT.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building QC Metrics: CLI 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-cli/0.16.0/adam-cli-0.16.0.pom
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Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-cli/0.16.0/adam-cli-0.16.0.jar
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[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ qc-metrics-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ qc-metrics-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ qc-metrics-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.7:add-source (add-source) @ qc-metrics-cli ---
[INFO] Source directory: /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ qc-metrics-cli ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ qc-metrics-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ qc-metrics-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core:0.16.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.qc-metrics:qc-metrics-core:0.0.1-SNAPSHOT requires scala version: 2.10.4
[WARNING]  org.fusesource.scalate:scalate-util_2.10:1.6.1 requires scala version: 2.10.4
[WARNING]  org.fusesource.scalate:scalate-core_2.10:1.6.1 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 5 Scala sources to /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-cli/target/scala-2.10.4/classes...
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ qc-metrics-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.7:add-test-source (add-test-source) @ qc-metrics-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ qc-metrics-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ qc-metrics-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core:0.16.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.qc-metrics:qc-metrics-core:0.0.1-SNAPSHOT requires scala version: 2.10.4
[WARNING]  org.fusesource.scalate:scalate-util_2.10:1.6.1 requires scala version: 2.10.4
[WARNING]  org.fusesource.scalate:scalate-core_2.10:1.6.1 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ qc-metrics-cli ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ qc-metrics-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ qc-metrics-cli ---
Discovery starting.
Discovery completed in 83 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 150 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ qc-metrics-cli ---
[INFO] Building jar: /home/jenkins/workspace/qc-metrics-prb/hadoop.version/2.2.0/label/centos/qc-metrics-cli/target/qc-metrics-cli-0.0.1-SNAPSHOT.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] qc-metrics ........................................ SUCCESS [2.880s]
[INFO] QC Metrics: Core .................................. SUCCESS [50.053s]
[INFO] QC Metrics: CLI ................................... SUCCESS [9.873s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:02.968s
[INFO] Finished at: Sun Mar 01 19:33:21 PST 2015
[INFO] Final Memory: 68M/3595M
[INFO] ------------------------------------------------------------------------
Recording test results
Finished: SUCCESS