SuccessConsole Output

Started by upstream project "bdg-services-prb" build number 20
originally caused by:
 GitHub pull request #5 of commit f66136384eeecef2f8c839da8c3c467acd6a5d1b automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on test02.amplab (CentOS 6.5) (test02 centos) in workspace /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos
 > git rev-parse --is-inside-work-tree # timeout=10
Fetching changes from the remote Git repository
 > git config remote.origin.url https://github.com/bigdatagenomics/bdg-services.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/bdg-services.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/bigdatagenomics/bdg-services.git +refs/pull/*:refs/remotes/origin/pr/*
Checking out Revision 2ecd6c599440f82e07d3ee85527bade6d732d851 (detached)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 2ecd6c599440f82e07d3ee85527bade6d732d851
 > git rev-list 8f5e31e5e167b3f8362504d4dea4ed32ab487c55 # timeout=10
First time build. Skipping changelog.
[centos] $ /home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/mvn -DghprbTriggerAuthorEmail=carl@yeksigian.com -DghprbTargetBranch=master -DghprbSourceBranch=reads -Dhadoop.version=1.0.4 "-DghprbActualCommitAuthor=Carl Yeksigian" -Dlabel=centos -Dsha1=origin/pr/5/merge -DghprbPullLink=https://github.com/bigdatagenomics/bdg-services/pull/5 -DghprbActualCommit=f66136384eeecef2f8c839da8c3c467acd6a5d1b -DghprbPullAuthorEmail=carl@yeksigian.com -DghprbActualCommitAuthorEmail=carl@yeksigian.com "-DghprbTriggerAuthor=Carl Yeksigian" -DghprbPullId=5 "-DghprbPullTitle=A simple read store" "-DghprbPullDescription=GitHub pull request #5 of commit f66136384eeecef2f8c839da8c3c467acd6a5d1b automatically merged." clean package
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-reads:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:build-helper-maven-plugin is missing. @ line 76, column 21
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 130, column 21
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-cli:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:build-helper-maven-plugin is missing. @ line 115, column 21
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 166, column 21
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-service-manager:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:build-helper-maven-plugin is missing. @ line 121, column 21
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 174, column 21
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-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 220, column 37
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 224, column 37
[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] BDG Services: Service setup and management for BDG Projects
[INFO] BDGS: Core
[INFO] BDGS: Service Manager
[INFO] BDGS: Read API Module
[INFO] BDGS: CLI Module
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building BDG Services: Service setup and management for BDG Projects 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ bdgs-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ bdgs-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ bdgs-parent ---
[INFO] Modified 0 of 19 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ bdgs-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ bdgs-parent ---
[INFO] No sources to compile
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building BDGS: Core 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core/0.12.2-SNAPSHOT/adam-core-0.12.2-20140820.163354-179.jar
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Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core/0.12.2-SNAPSHOT/adam-core-0.12.2-20140820.163354-179.jar (2036 KB at 939.1 KB/sec)
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ bdgs-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ bdgs-core ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ bdgs-core ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ bdgs-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ bdgs-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[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 6 Scala sources to /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/target/scala-2.10.3/classes...
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ bdgs-core ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ bdgs-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) @ bdgs-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[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 2 Scala sources to /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/target/scala-2.10.3/test-classes...
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ bdgs-core ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ bdgs-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ bdgs-core ---
Discovery starting.
Discovery completed in 147 milliseconds.
Run starting. Expected test count is: 5
DiscoverySuite:
YamlConfigurationSuite:
- Can read YAML configuration
TypedLocationTestSuite:
- can parse a straightforward path alright
- can parse a classpath:// URI correctly
- can parse a file:// URI correctly
- can parse an s3:// URI correctly
Run completed in 337 milliseconds.
Total number of tests run: 5
Suites: completed 3, aborted 0
Tests: succeeded 5, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ bdgs-core ---
[INFO] Building jar: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/target/bdgs-core-0.0.1-SNAPSHOT.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building BDGS: Service Manager 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ bdgs-service-manager ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ bdgs-service-manager ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9:add-source (default) @ bdgs-service-manager ---
[INFO] Source directory: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-service-manager/src/main/java/../gen-java added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ bdgs-service-manager ---
[INFO] Modified 0 of 2 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ bdgs-service-manager ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-service-manager/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ bdgs-service-manager ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-service-manager:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-service-manager:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-compiler:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-reflect:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scalatest:scalatest_2.10:2.0 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 2 Scala sources to /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-service-manager/target/scala-2.10.3/classes...
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ bdgs-service-manager ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ bdgs-service-manager ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-service-manager/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ bdgs-service-manager ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-service-manager:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-service-manager:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-compiler:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-reflect:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scalatest:scalatest_2.10:2.0 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) @ bdgs-service-manager ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ bdgs-service-manager ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ bdgs-service-manager ---
Discovery starting.
Discovery completed in 91 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 160 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ bdgs-service-manager ---
[INFO] Building jar: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-service-manager/target/service-manager.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.1:shade (default) @ bdgs-service-manager ---
[INFO] Including org.scala-lang:scala-library:jar:2.10.3 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.10.3 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.10.3 in the shaded jar.
[INFO] Including org.bdgenomics.services:bdgs-core:jar:0.0.1-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core:jar:0.12.2-SNAPSHOT in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.21 in the shaded jar.
[INFO] Including com.esotericsoftware.reflectasm:reflectasm:jar:shaded:1.07 in the shaded jar.
[INFO] Including org.ow2.asm:asm:jar:4.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:1.2 in the shaded jar.
[INFO] Including org.scoverage:scalac-scoverage-plugin_2.10:jar:0.99.2 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.2.0 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:1.3.2 in the shaded jar.
[INFO] Including org.apache.spark:spark-core_2.10:jar:1.0.0 in the shaded jar.
[INFO] Including net.java.dev.jets3t:jets3t:jar:0.7.1 in the shaded jar.
[INFO] Including commons-httpclient:commons-httpclient:jar:3.1 in the shaded jar.
[INFO] Including org.apache.curator:curator-recipes:jar:2.4.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-framework:jar:2.4.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-client:jar:2.4.0 in the shaded jar.
[INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.5 in the shaded jar.
[INFO] Including jline:jline:jar:0.9.94 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-plus:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty.orbit:javax.transaction:jar:1.1.1.v201105210645 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-jndi:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty.orbit:javax.mail.glassfish:jar:1.4.1.v201005082020 in the shaded jar.
[INFO] Including org.eclipse.jetty.orbit:javax.activation:jar:1.1.0.v201105071233 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty.orbit:javax.servlet:jar:3.0.0.v201112011016 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-continuation:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:14.0.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.5 in the shaded jar.
[INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.5 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including com.ning:compress-lzf:jar:1.0.0 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including com.twitter:chill_2.10:jar:0.3.6 in the shaded jar.
[INFO] Including com.twitter:chill-java:jar:0.3.6 in the shaded jar.
[INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar.
[INFO] Including org.spark-project.akka:akka-remote_2.10:jar:2.2.3-shaded-protobuf in the shaded jar.
[INFO] Including org.spark-project.akka:akka-actor_2.10:jar:2.2.3-shaded-protobuf in the shaded jar.
[INFO] Including com.typesafe:config:jar:1.0.2 in the shaded jar.
[INFO] Including io.netty:netty:jar:3.6.6.Final in the shaded jar.
[INFO] Including org.spark-project.protobuf:protobuf-java:jar:2.4.1-shaded in the shaded jar.
[INFO] Including org.uncommons.maths:uncommons-maths:jar:1.2.2a in the shaded jar.
[INFO] Including org.spark-project.akka:akka-slf4j_2.10:jar:2.2.3-shaded-protobuf in the shaded jar.
[INFO] Including org.json4s:json4s-jackson_2.10:jar:3.2.6 in the shaded jar.
[INFO] Including org.json4s:json4s-core_2.10:jar:3.2.6 in the shaded jar.
[INFO] Including org.json4s:json4s-ast_2.10:jar:3.2.6 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.10.0 in the shaded jar.
[INFO] Including colt:colt:jar:1.2.0 in the shaded jar.
[INFO] Including concurrent:concurrent:jar:1.3.4 in the shaded jar.
[INFO] Including org.apache.mesos:mesos:jar:shaded-protobuf:0.18.1 in the shaded jar.
[INFO] Including io.netty:netty-all:jar:4.0.17.Final in the shaded jar.
[INFO] Including com.clearspring.analytics:stream:jar:2.5.1 in the shaded jar.
[INFO] Including com.codahale.metrics:metrics-core:jar:3.0.0 in the shaded jar.
[INFO] Including com.codahale.metrics:metrics-jvm:jar:3.0.0 in the shaded jar.
[INFO] Including com.codahale.metrics:metrics-json:jar:3.0.0 in the shaded jar.
[INFO] Including com.codahale.metrics:metrics-graphite:jar:3.0.0 in the shaded jar.
[INFO] Including org.tachyonproject:tachyon:jar:0.4.1-thrift in the shaded jar.
[INFO] Including org.apache.ant:ant:jar:1.9.0 in the shaded jar.
[INFO] Including org.apache.ant:ant-launcher:jar:1.9.0 in the shaded jar.
[INFO] Including org.spark-project:pyrolite:jar:2.0.1 in the shaded jar.
[INFO] Including net.sf.py4j:py4j:jar:0.8.1 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.4.4 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.7.6 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.0 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.5 in the shaded jar.
[INFO] Including com.twitter:parquet-avro:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-column:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-common:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-encoding:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-generator:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-hadoop:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-jackson:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-format:jar:2.0.0 in the shaded jar.
[INFO] Including fi.tkk.ics.hadoop.bam:hadoop-bam:jar:6.2 in the shaded jar.
[INFO] Including picard:picard:jar:1.107 in the shaded jar.
[INFO] Including cofoja:cofoja:jar:1.0 in the shaded jar.
[INFO] Including tribble:tribble:jar:1.107 in the shaded jar.
[INFO] Including variant:variant:jar:1.107 in the shaded jar.
[INFO] Including samtools:samtools:jar:1.107 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.5.5 in the shaded jar.
[INFO] Including com.google.code.findbugs:annotations:jar:2.0.0 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-client:jar:1.0.4 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-core:jar:1.0.4 in the shaded jar.
[INFO] Including xmlenc:xmlenc:jar:0.52 in the shaded jar.
[INFO] Including org.apache.commons:commons-math:jar:2.1 in the shaded jar.
[INFO] Including commons-configuration:commons-configuration:jar:1.6 in the shaded jar.
[INFO] Including commons-collections:commons-collections:jar:3.2.1 in the shaded jar.
[INFO] Including commons-lang:commons-lang:jar:2.4 in the shaded jar.
[INFO] Including commons-digester:commons-digester:jar:1.8 in the shaded jar.
[INFO] Including commons-beanutils:commons-beanutils:jar:1.7.0 in the shaded jar.
[INFO] Including commons-beanutils:commons-beanutils-core:jar:1.8.0 in the shaded jar.
[INFO] Including commons-el:commons-el:jar:1.0 in the shaded jar.
[INFO] Including hsqldb:hsqldb:jar:1.8.0.10 in the shaded jar.
[INFO] Including oro:oro:jar:2.0.8 in the shaded jar.
[INFO] Including com.amazonaws:aws-java-sdk:jar:1.7.13 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.3 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.1.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.1.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.1.1 in the shaded jar.
[INFO] Including joda-time:joda-time:jar:2.4 in the shaded jar.
[INFO] Including org.yaml:snakeyaml:jar:1.14-SNAPSHOT in the shaded jar.
[INFO] Including org.apache.thrift:libthrift:jar:0.9.1 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.1 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.2.5 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.2.4 in the shaded jar.
[WARNING] commons-logging-1.1.1.jar, jcl-over-slf4j-1.7.5.jar define 6 overlappping classes: 
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING]   - org.apache.commons.logging.Log
[WARNING] kryo-2.21.jar, objenesis-1.2.jar define 32 overlappping classes: 
[WARNING]   - org.objenesis.Objenesis
[WARNING]   - org.objenesis.strategy.StdInstantiatorStrategy
[WARNING]   - org.objenesis.instantiator.basic.ObjectStreamClassInstantiator
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactorySerializationInstantiator
[WARNING]   - org.objenesis.instantiator.perc.PercSerializationInstantiator
[WARNING]   - org.objenesis.instantiator.NullInstantiator
[WARNING]   - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator
[WARNING]   - org.objenesis.instantiator.gcj.GCJInstantiatorBase
[WARNING]   - org.objenesis.ObjenesisException
[WARNING]   - org.objenesis.instantiator.basic.ObjectInputStreamInstantiator$MockStream
[WARNING]   - 22 more...
[WARNING] cofoja-1.0.jar, asm-4.0.jar define 21 overlappping classes: 
[WARNING]   - org.objectweb.asm.Item
[WARNING]   - org.objectweb.asm.signature.SignatureWriter
[WARNING]   - org.objectweb.asm.MethodWriter
[WARNING]   - org.objectweb.asm.Type
[WARNING]   - org.objectweb.asm.Opcodes
[WARNING]   - org.objectweb.asm.Handler
[WARNING]   - org.objectweb.asm.MethodVisitor
[WARNING]   - org.objectweb.asm.Label
[WARNING]   - org.objectweb.asm.FieldWriter
[WARNING]   - org.objectweb.asm.signature.SignatureVisitor
[WARNING]   - 11 more...
[WARNING] jsr305-1.3.9.jar, annotations-2.0.0.jar define 34 overlappping classes: 
[WARNING]   - javax.annotation.Nonnegative
[WARNING]   - javax.annotation.CheckForSigned
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Tainted
[WARNING]   - javax.annotation.meta.TypeQualifierValidator
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.Detainted
[WARNING]   - javax.annotation.Nonnull$Checker
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - 24 more...
[WARNING] commons-beanutils-core-1.8.0.jar, commons-collections-3.2.1.jar, commons-beanutils-1.7.0.jar define 10 overlappping classes: 
[WARNING]   - org.apache.commons.collections.FastHashMap$EntrySet
[WARNING]   - org.apache.commons.collections.ArrayStack
[WARNING]   - org.apache.commons.collections.FastHashMap$1
[WARNING]   - org.apache.commons.collections.FastHashMap$KeySet
[WARNING]   - org.apache.commons.collections.FastHashMap$CollectionView
[WARNING]   - org.apache.commons.collections.BufferUnderflowException
[WARNING]   - org.apache.commons.collections.Buffer
[WARNING]   - org.apache.commons.collections.FastHashMap$CollectionView$CollectionViewIterator
[WARNING]   - org.apache.commons.collections.FastHashMap$Values
[WARNING]   - org.apache.commons.collections.FastHashMap
[WARNING] commons-beanutils-core-1.8.0.jar, commons-beanutils-1.7.0.jar define 82 overlappping classes: 
[WARNING]   - org.apache.commons.beanutils.WrapDynaBean
[WARNING]   - org.apache.commons.beanutils.Converter
[WARNING]   - org.apache.commons.beanutils.converters.IntegerConverter
[WARNING]   - org.apache.commons.beanutils.locale.LocaleBeanUtilsBean
[WARNING]   - org.apache.commons.beanutils.locale.converters.DecimalLocaleConverter
[WARNING]   - org.apache.commons.beanutils.locale.converters.DoubleLocaleConverter
[WARNING]   - org.apache.commons.beanutils.converters.ShortConverter
[WARNING]   - org.apache.commons.beanutils.converters.StringArrayConverter
[WARNING]   - org.apache.commons.beanutils.locale.LocaleConvertUtilsBean
[WARNING]   - org.apache.commons.beanutils.LazyDynaClass
[WARNING]   - 72 more...
[WARNING] picard-1.107.jar, ant-1.9.0.jar define 6 overlappping classes: 
[WARNING]   - org.apache.tools.bzip2.CBZip2OutputStream$Data
[WARNING]   - org.apache.tools.bzip2.CBZip2InputStream$Data
[WARNING]   - org.apache.tools.bzip2.CBZip2OutputStream
[WARNING]   - org.apache.tools.bzip2.CBZip2InputStream
[WARNING]   - org.apache.tools.bzip2.CRC
[WARNING]   - org.apache.tools.bzip2.BZip2Constants
[WARNING] kryo-2.21.jar, minlog-1.2.jar define 2 overlappping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING] kryo-2.21.jar, reflectasm-1.07-shaded.jar define 23 overlappping classes: 
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Opcodes
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Frame
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Label
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldWriter
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.AnnotationVisitor
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Item
[WARNING]   - com.esotericsoftware.reflectasm.AccessClassLoader
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Edge
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ClassVisitor
[WARNING]   - 13 more...
[WARNING] maven-shade-plugin has detected that some .class files
[WARNING] are present in two or more JARs. When this happens, only
[WARNING] one single version of the class is copied in the uberjar.
[WARNING] Usually this is not harmful and you can skeep these
[WARNING] warnings, otherwise try to manually exclude artifacts
[WARNING] based on mvn dependency:tree -Ddetail=true and the above
[WARNING] output
[WARNING] See http://docs.codehaus.org/display/MAVENUSER/Shade+Plugin
[INFO] Replacing /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-service-manager/target/bdgs-cli-0.0.1-SNAPSHOT.jar with /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-service-manager/target/bdgs-service-manager-0.0.1-SNAPSHOT-shaded.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ bdgs-service-manager ---
[INFO] Building jar: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-service-manager/target/service-manager-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building BDGS: Read API Module 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ bdgs-reads ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ bdgs-reads ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9:add-source (default) @ bdgs-reads ---
[INFO] Source directory: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-reads/src/main/java/../gen-java added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ bdgs-reads ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ bdgs-reads ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 6 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ bdgs-reads ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-reads:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-reads:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-compiler:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-reflect:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scalatest:scalatest_2.10:2.0 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 6 Scala sources and 11 Java sources to /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-reads/target/scala-2.10.3/classes...
[WARNING] there were 1 feature warning(s); re-run with -feature for details
[WARNING] one warning found
[WARNING] warning: [options] bootstrap class path not set in conjunction with -source 1.6
[WARNING] Note: Some input files use unchecked or unsafe operations.
[WARNING] Note: Recompile with -Xlint:unchecked for details.
[WARNING] 1 warning
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ bdgs-reads ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ bdgs-reads ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 3 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ bdgs-reads ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-reads:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-reads:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-compiler:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-reflect:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scalatest:scalatest_2.10:2.0 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 2 Scala sources to /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-reads/target/scala-2.10.3/test-classes...
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ bdgs-reads ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ bdgs-reads ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ bdgs-reads ---
Discovery starting.
Discovery completed in 204 milliseconds.
Run starting. Expected test count is: 2
DiscoverySuite:
ReadServiceSuite:
Starting query
Sent retrieve_samples
Returning bytes from /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-reads/target/scala-2.10.3/test-classes/reads-0-2-0
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Returning bytes from /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-reads/target/scala-2.10.3/test-classes/reads-0-2-0
- Can communicate over Thrift
ADAMReadStoreSuite:
Returning bytes from /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-reads/target/scala-2.10.3/test-classes/reads-0-2-0
Returning bytes from /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-reads/target/scala-2.10.3/test-classes/reads-0-2-0
- Returns calls from test bam
Run completed in 5 seconds, 742 milliseconds.
Total number of tests run: 2
Suites: completed 3, aborted 0
Tests: succeeded 2, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ bdgs-reads ---
[INFO] Building jar: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-reads/target/bdgs-reads-0.0.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ bdgs-reads ---
[INFO] Building jar: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-reads/target/bdgs-reads-0.0.1-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building BDGS: CLI Module 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ bdgs-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ bdgs-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.9:add-source (default) @ bdgs-cli ---
[INFO] Source directory: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-cli/src/main/java/../gen-java added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ bdgs-cli ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ bdgs-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ bdgs-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-cli:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-cli:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-compiler:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-reflect:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scalatest:scalatest_2.10:2.0 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 1 Scala source to /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-cli/target/scala-2.10.3/classes...
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ bdgs-cli ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ bdgs-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ bdgs-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-cli:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.bdgenomics.services:bdgs-cli:0.0.1-SNAPSHOT requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-compiler:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scala-lang:scala-reflect:2.10.3 requires scala version: 2.10.3
[WARNING]  org.scalatest:scalatest_2.10:2.0 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) @ bdgs-cli ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ bdgs-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ bdgs-cli ---
Discovery starting.
Discovery completed in 101 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 170 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ bdgs-cli ---
[INFO] Building jar: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-cli/target/cli.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.1:shade (default) @ bdgs-cli ---
[INFO] Including org.scala-lang:scala-library:jar:2.10.3 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.10.3 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.10.3 in the shaded jar.
[INFO] Including org.bdgenomics.services:bdgs-reads:jar:0.0.1-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.services:bdgs-core:jar:0.0.1-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core:jar:0.12.2-SNAPSHOT in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.21 in the shaded jar.
[INFO] Including com.esotericsoftware.reflectasm:reflectasm:jar:shaded:1.07 in the shaded jar.
[INFO] Including org.ow2.asm:asm:jar:4.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:1.2 in the shaded jar.
[INFO] Including org.scoverage:scalac-scoverage-plugin_2.10:jar:0.99.2 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.2.0 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:1.3.2 in the shaded jar.
[INFO] Including org.apache.spark:spark-core_2.10:jar:1.0.0 in the shaded jar.
[INFO] Including net.java.dev.jets3t:jets3t:jar:0.7.1 in the shaded jar.
[INFO] Including commons-httpclient:commons-httpclient:jar:3.1 in the shaded jar.
[INFO] Including org.apache.curator:curator-recipes:jar:2.4.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-framework:jar:2.4.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-client:jar:2.4.0 in the shaded jar.
[INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.5 in the shaded jar.
[INFO] Including jline:jline:jar:0.9.94 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-plus:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty.orbit:javax.transaction:jar:1.1.1.v201105210645 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-jndi:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty.orbit:javax.mail.glassfish:jar:1.4.1.v201005082020 in the shaded jar.
[INFO] Including org.eclipse.jetty.orbit:javax.activation:jar:1.1.0.v201105071233 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty.orbit:javax.servlet:jar:3.0.0.v201112011016 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-continuation:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:8.1.14.v20131031 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:14.0.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.5 in the shaded jar.
[INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.5 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including com.ning:compress-lzf:jar:1.0.0 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including com.twitter:chill_2.10:jar:0.3.6 in the shaded jar.
[INFO] Including com.twitter:chill-java:jar:0.3.6 in the shaded jar.
[INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar.
[INFO] Including org.spark-project.akka:akka-remote_2.10:jar:2.2.3-shaded-protobuf in the shaded jar.
[INFO] Including org.spark-project.akka:akka-actor_2.10:jar:2.2.3-shaded-protobuf in the shaded jar.
[INFO] Including com.typesafe:config:jar:1.0.2 in the shaded jar.
[INFO] Including io.netty:netty:jar:3.6.6.Final in the shaded jar.
[INFO] Including org.spark-project.protobuf:protobuf-java:jar:2.4.1-shaded in the shaded jar.
[INFO] Including org.uncommons.maths:uncommons-maths:jar:1.2.2a in the shaded jar.
[INFO] Including org.spark-project.akka:akka-slf4j_2.10:jar:2.2.3-shaded-protobuf in the shaded jar.
[INFO] Including org.json4s:json4s-jackson_2.10:jar:3.2.6 in the shaded jar.
[INFO] Including org.json4s:json4s-core_2.10:jar:3.2.6 in the shaded jar.
[INFO] Including org.json4s:json4s-ast_2.10:jar:3.2.6 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.10.0 in the shaded jar.
[INFO] Including colt:colt:jar:1.2.0 in the shaded jar.
[INFO] Including concurrent:concurrent:jar:1.3.4 in the shaded jar.
[INFO] Including org.apache.mesos:mesos:jar:shaded-protobuf:0.18.1 in the shaded jar.
[INFO] Including io.netty:netty-all:jar:4.0.17.Final in the shaded jar.
[INFO] Including com.clearspring.analytics:stream:jar:2.5.1 in the shaded jar.
[INFO] Including com.codahale.metrics:metrics-core:jar:3.0.0 in the shaded jar.
[INFO] Including com.codahale.metrics:metrics-jvm:jar:3.0.0 in the shaded jar.
[INFO] Including com.codahale.metrics:metrics-json:jar:3.0.0 in the shaded jar.
[INFO] Including com.codahale.metrics:metrics-graphite:jar:3.0.0 in the shaded jar.
[INFO] Including org.tachyonproject:tachyon:jar:0.4.1-thrift in the shaded jar.
[INFO] Including org.apache.ant:ant:jar:1.9.0 in the shaded jar.
[INFO] Including org.apache.ant:ant-launcher:jar:1.9.0 in the shaded jar.
[INFO] Including org.spark-project:pyrolite:jar:2.0.1 in the shaded jar.
[INFO] Including net.sf.py4j:py4j:jar:0.8.1 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.4.4 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.7.6 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.0 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.5 in the shaded jar.
[INFO] Including com.twitter:parquet-avro:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-column:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-common:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-encoding:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-generator:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-hadoop:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-jackson:jar:1.4.3 in the shaded jar.
[INFO] Including com.twitter:parquet-format:jar:2.0.0 in the shaded jar.
[INFO] Including fi.tkk.ics.hadoop.bam:hadoop-bam:jar:6.2 in the shaded jar.
[INFO] Including picard:picard:jar:1.107 in the shaded jar.
[INFO] Including cofoja:cofoja:jar:1.0 in the shaded jar.
[INFO] Including tribble:tribble:jar:1.107 in the shaded jar.
[INFO] Including variant:variant:jar:1.107 in the shaded jar.
[INFO] Including samtools:samtools:jar:1.107 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.5.5 in the shaded jar.
[INFO] Including com.google.code.findbugs:annotations:jar:2.0.0 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-client:jar:1.0.4 in the shaded jar.
[INFO] Including org.apache.hadoop:hadoop-core:jar:1.0.4 in the shaded jar.
[INFO] Including xmlenc:xmlenc:jar:0.52 in the shaded jar.
[INFO] Including org.apache.commons:commons-math:jar:2.1 in the shaded jar.
[INFO] Including commons-configuration:commons-configuration:jar:1.6 in the shaded jar.
[INFO] Including commons-collections:commons-collections:jar:3.2.1 in the shaded jar.
[INFO] Including commons-lang:commons-lang:jar:2.4 in the shaded jar.
[INFO] Including commons-digester:commons-digester:jar:1.8 in the shaded jar.
[INFO] Including commons-beanutils:commons-beanutils:jar:1.7.0 in the shaded jar.
[INFO] Including commons-beanutils:commons-beanutils-core:jar:1.8.0 in the shaded jar.
[INFO] Including commons-el:commons-el:jar:1.0 in the shaded jar.
[INFO] Including hsqldb:hsqldb:jar:1.8.0.10 in the shaded jar.
[INFO] Including oro:oro:jar:2.0.8 in the shaded jar.
[INFO] Including com.amazonaws:aws-java-sdk:jar:1.7.13 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.1.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.1.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.1.1 in the shaded jar.
[INFO] Including joda-time:joda-time:jar:2.4 in the shaded jar.
[INFO] Including org.yaml:snakeyaml:jar:1.14-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.services:bdgs-service-manager:jar:0.0.1-SNAPSHOT in the shaded jar.
[INFO] Including org.apache.thrift:libthrift:jar:0.9.1 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.1 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.2.5 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.6 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.2.4 in the shaded jar.
[WARNING] commons-logging-1.1.1.jar, jcl-over-slf4j-1.7.5.jar define 6 overlappping classes: 
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING]   - org.apache.commons.logging.Log
[WARNING] kryo-2.21.jar, objenesis-1.2.jar define 32 overlappping classes: 
[WARNING]   - org.objenesis.Objenesis
[WARNING]   - org.objenesis.strategy.StdInstantiatorStrategy
[WARNING]   - org.objenesis.instantiator.basic.ObjectStreamClassInstantiator
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactorySerializationInstantiator
[WARNING]   - org.objenesis.instantiator.perc.PercSerializationInstantiator
[WARNING]   - org.objenesis.instantiator.NullInstantiator
[WARNING]   - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator
[WARNING]   - org.objenesis.instantiator.gcj.GCJInstantiatorBase
[WARNING]   - org.objenesis.ObjenesisException
[WARNING]   - org.objenesis.instantiator.basic.ObjectInputStreamInstantiator$MockStream
[WARNING]   - 22 more...
[WARNING] cofoja-1.0.jar, asm-4.0.jar define 21 overlappping classes: 
[WARNING]   - org.objectweb.asm.Item
[WARNING]   - org.objectweb.asm.signature.SignatureWriter
[WARNING]   - org.objectweb.asm.MethodWriter
[WARNING]   - org.objectweb.asm.Type
[WARNING]   - org.objectweb.asm.Opcodes
[WARNING]   - org.objectweb.asm.Handler
[WARNING]   - org.objectweb.asm.MethodVisitor
[WARNING]   - org.objectweb.asm.Label
[WARNING]   - org.objectweb.asm.FieldWriter
[WARNING]   - org.objectweb.asm.signature.SignatureVisitor
[WARNING]   - 11 more...
[WARNING] jsr305-1.3.9.jar, annotations-2.0.0.jar define 34 overlappping classes: 
[WARNING]   - javax.annotation.Nonnegative
[WARNING]   - javax.annotation.CheckForSigned
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Tainted
[WARNING]   - javax.annotation.meta.TypeQualifierValidator
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.Detainted
[WARNING]   - javax.annotation.Nonnull$Checker
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - 24 more...
[WARNING] commons-beanutils-core-1.8.0.jar, commons-collections-3.2.1.jar, commons-beanutils-1.7.0.jar define 10 overlappping classes: 
[WARNING]   - org.apache.commons.collections.FastHashMap$EntrySet
[WARNING]   - org.apache.commons.collections.ArrayStack
[WARNING]   - org.apache.commons.collections.FastHashMap$1
[WARNING]   - org.apache.commons.collections.FastHashMap$KeySet
[WARNING]   - org.apache.commons.collections.FastHashMap$CollectionView
[WARNING]   - org.apache.commons.collections.BufferUnderflowException
[WARNING]   - org.apache.commons.collections.Buffer
[WARNING]   - org.apache.commons.collections.FastHashMap$CollectionView$CollectionViewIterator
[WARNING]   - org.apache.commons.collections.FastHashMap$Values
[WARNING]   - org.apache.commons.collections.FastHashMap
[WARNING] commons-beanutils-core-1.8.0.jar, commons-beanutils-1.7.0.jar define 82 overlappping classes: 
[WARNING]   - org.apache.commons.beanutils.WrapDynaBean
[WARNING]   - org.apache.commons.beanutils.Converter
[WARNING]   - org.apache.commons.beanutils.converters.IntegerConverter
[WARNING]   - org.apache.commons.beanutils.locale.LocaleBeanUtilsBean
[WARNING]   - org.apache.commons.beanutils.locale.converters.DecimalLocaleConverter
[WARNING]   - org.apache.commons.beanutils.locale.converters.DoubleLocaleConverter
[WARNING]   - org.apache.commons.beanutils.converters.ShortConverter
[WARNING]   - org.apache.commons.beanutils.converters.StringArrayConverter
[WARNING]   - org.apache.commons.beanutils.locale.LocaleConvertUtilsBean
[WARNING]   - org.apache.commons.beanutils.LazyDynaClass
[WARNING]   - 72 more...
[WARNING] picard-1.107.jar, ant-1.9.0.jar define 6 overlappping classes: 
[WARNING]   - org.apache.tools.bzip2.CBZip2OutputStream$Data
[WARNING]   - org.apache.tools.bzip2.CBZip2InputStream$Data
[WARNING]   - org.apache.tools.bzip2.CBZip2OutputStream
[WARNING]   - org.apache.tools.bzip2.CBZip2InputStream
[WARNING]   - org.apache.tools.bzip2.CRC
[WARNING]   - org.apache.tools.bzip2.BZip2Constants
[WARNING] kryo-2.21.jar, minlog-1.2.jar define 2 overlappping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING] kryo-2.21.jar, reflectasm-1.07-shaded.jar define 23 overlappping classes: 
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Opcodes
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Frame
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Label
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldWriter
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.AnnotationVisitor
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Item
[WARNING]   - com.esotericsoftware.reflectasm.AccessClassLoader
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Edge
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ClassVisitor
[WARNING]   - 13 more...
[WARNING] maven-shade-plugin has detected that some .class files
[WARNING] are present in two or more JARs. When this happens, only
[WARNING] one single version of the class is copied in the uberjar.
[WARNING] Usually this is not harmful and you can skeep these
[WARNING] warnings, otherwise try to manually exclude artifacts
[WARNING] based on mvn dependency:tree -Ddetail=true and the above
[WARNING] output
[WARNING] See http://docs.codehaus.org/display/MAVENUSER/Shade+Plugin
[INFO] Replacing /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-cli/target/bdgs-cli-0.0.1-SNAPSHOT.jar with /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-cli/target/bdgs-cli-0.0.1-SNAPSHOT-shaded.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ bdgs-cli ---
[INFO] Building jar: /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-cli/target/cli-tests.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] BDG Services: Service setup and management for BDG Projects  SUCCESS [2.457s]
[INFO] BDGS: Core ........................................ SUCCESS [19.131s]
[INFO] BDGS: Service Manager ............................. SUCCESS [18.113s]
[INFO] BDGS: Read API Module ............................. SUCCESS [22.814s]
[INFO] BDGS: CLI Module .................................. SUCCESS [17.875s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:20.582s
[INFO] Finished at: Thu Aug 28 12:51:39 PDT 2014
[INFO] Final Memory: 278M/2543M
[INFO] ------------------------------------------------------------------------
Finished: SUCCESS