FailedConsole Output

Started by upstream project "deca" build number 120
originally caused by:
 Started by an SCM change
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-04 (centos spark-test) in workspace /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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/deca.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/deca.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/bigdatagenomics/deca.git +refs/heads/*:refs/remotes/origin/*
Checking out Revision 45be0249b893e18bff15869d0d78f3c7367c6c7d (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 45be0249b893e18bff15869d0d78f3c7367c6c7d
 > git rev-list 5a399df4215cc96e92491aec37d80c58dd923b59 # timeout=10
[centos] $ /bin/bash /tmp/hudson5240785641265544847.sh
+ set -e
+ export JAVA_HOME=/usr/java/jdk1.8.0_60
+ JAVA_HOME=/usr/java/jdk1.8.0_60
+ export CONDA_BIN=/home/anaconda/bin/
+ CONDA_BIN=/home/anaconda/bin/
+ export MVN_BIN=/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/
+ MVN_BIN=/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/
+ export PATH=/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/bin/:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
+ PATH=/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/bin/:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
+ set +x
+ /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/jenkins-test

# make a tempdir for writing maven cruft to
DECA_MVN_TMP_DIR=$(mktemp -d -t decaTestMvnXXXXXXX)
++ mktemp -d -t decaTestMvnXXXXXXX
+ DECA_MVN_TMP_DIR=/tmp/decaTestMvnwmQYIr0

# add this tempdir to the poms...
find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${DECA_MVN_TMP_DIR}:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/decaTestMvnwmQYIr0:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/java/jdk1.8.0_60/bin/:/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/bin/:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
+ PATH=/usr/java/jdk1.8.0_60/bin/:/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/bin/:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8"
+ export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
+ MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )
+++ dirname /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/jenkins-test
++ cd /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts
++ pwd
+ DIR=/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/..
VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
++ grep '<version>' /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.1.1-SNAPSHOT

# is the hadoop version set?
if ! [[ ${HADOOP_VERSION} ]];
then
    echo "HADOOP_VERSION environment variable is not set."
    echo "Please set this variable before running."
    
    exit 1
fi
+ [[ -n 2.3.0 ]]

# is the spark version set?
if ! [[ ${SPARK_VERSION} ]];
then
    echo "SPARK_VERSION environment variable is not set."
    echo "Please set this variable before running."
    
    exit 1
fi
+ [[ -n 2.0.0 ]]

# print versions
echo "Testing DECA version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing DECA version 0.1.1-SNAPSHOT on Spark 2.0.0 and Hadoop 2.3.0'
Testing DECA version 0.1.1-SNAPSHOT on Spark 2.0.0 and Hadoop 2.3.0

# first, build the sources, run the unit tests, and generate a coverage report
mvn clean \
    -Dhadoop.version=${HADOOP_VERSION} \
    -Dspark.version=${SPARK_VERSION} 
+ mvn clean -Dhadoop.version=2.3.0 -Dspark.version=2.0.0
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, column 23
[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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 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. @ line 361, 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 365, 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] deca: Distributed Exome CNV Analyzer
[INFO] deca-core: Core variant calling algorithms
[INFO] deca-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: Distributed Exome CNV Analyzer 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-parent_2.11 ---
[INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-core_2.11 ---
[INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-cli_2.11 ---
[INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [0.124s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.039s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [0.051s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.342s
[INFO] Finished at: Mon Jan 08 00:27:16 PST 2018
[INFO] Final Memory: 19M/1472M
[INFO] ------------------------------------------------------------------------
    
# make sure we can build the native code
mvn -U \
    -P native-lgpl \
    package \
    -DskipTests \
    -Dhadoop.version=${HADOOP_VERSION} \
    -Dspark.version=${SPARK_VERSION} \
    -DargLine=${DECA_MVN_TMP_DIR}
+ mvn -U -P native-lgpl package -DskipTests -Dhadoop.version=2.3.0 -Dspark.version=2.0.0 -DargLine=/tmp/decaTestMvnwmQYIr0
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, column 23
[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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 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. @ line 361, 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 365, 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] deca: Distributed Exome CNV Analyzer
[INFO] deca-core: Core variant calling algorithms
[INFO] deca-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: Distributed Exome CNV Analyzer 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 20 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala:-1: info: compiling
[INFO] Compiling 15 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/classes at 1515400041987
[WARNING] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure
[WARNING]       case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector)
[WARNING]               ^
[WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala:-1: info: compiling
[INFO] Compiling 5 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/test-classes at 1515400050609
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes at 1515400058471
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/test-classes at 1515400063782
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-cli_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.4.3:shade (default) @ deca-cli_2.11 ---
[INFO] Including net.fnothaft:jsr203-s3a:jar:0.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.3.0-incubating in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.8 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-serialization-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-SNAPSHOT in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.4 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.23.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.hammerlab:genomic-loci_2.11:jar:1.4.4 in the shaded jar.
[INFO] Including org.hammerlab:args4s_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including org.hammerlab:iterator_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including org.hammerlab:string-utils_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.11.3 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.0 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:2.7 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.2 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.1 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.11.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:1.2.4 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:16.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.23.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.23.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.23.0 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.1.0 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.1.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-multibindings:jar:4.1.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.16 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.2.4 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar.
[INFO] Including org.scalanlp:breeze_2.11:jar:0.12 in the shaded jar.
[INFO] Including org.scalanlp:breeze-macros_2.11:jar:0.12 in the shaded jar.
[INFO] Including com.github.fommil.netlib:core:jar:1.1.2 in the shaded jar.
[INFO] Including net.sourceforge.f2j:arpack_combined_all:jar:0.1 in the shaded jar.
[INFO] Including net.sf.opencsv:opencsv:jar:2.3 in the shaded jar.
[INFO] Including com.github.rwl:jtransforms:jar:2.4.0 in the shaded jar.
[INFO] Including junit:junit:jar:4.8.2 in the shaded jar.
[INFO] Including org.spire-math:spire_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including org.spire-math:spire-macros_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including com.chuusai:shapeless_2.11:jar:2.0.0 in the shaded jar.
[INFO] Including org.scalanlp:breeze-natives_2.11:jar:0.12 in the shaded jar.
[INFO] Skipping pom dependency com.github.fommil.netlib:all:pom:1.1.2 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-osx-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:native_ref-java:jar:1.1 in the shaded jar.
[INFO] Including com.github.fommil:jniloader:jar:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-i686:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-win-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-win-i686:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-armhf:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-osx-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:native_system-java:jar:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-linux-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-linux-i686:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-linux-armhf:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-win-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-win-i686:jar:natives:1.1 in the shaded jar.
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar with /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-shaded.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.086s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [17.237s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [27.611s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 47.057s
[INFO] Finished at: Mon Jan 08 00:28:05 PST 2018
[INFO] Final Memory: 96M/1365M
[INFO] ------------------------------------------------------------------------

# if those pass, build the distribution package and the integration tests
mvn -U \
    clean \
    test \
    -P coverage scoverage:report
+ mvn -U clean test -P coverage scoverage:report
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, column 23
[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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 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. @ line 361, 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 365, 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] deca: Distributed Exome CNV Analyzer
[INFO] deca-core: Core variant calling algorithms
[INFO] deca-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: Distributed Exome CNV Analyzer 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-parent_2.11 ---
[INFO] Skipping SCoverage execution for project with packaging type 'pom'
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-core_2.11 ---
[INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 20 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala:-1: info: compiling
[INFO] Compiling 15 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/classes at 1515400090844
[WARNING] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure
[WARNING]       case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector)
[WARNING]               ^
[WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 9 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala:-1: info: compiling
[INFO] Compiling 5 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/test-classes at 1515400100390
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 ---
Discovery starting.
Discovery completed in 471 milliseconds.
Run starting. Expected test count is: 16
NormalizationSuite:
2018-01-08 00:28:28 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2018-01-08 00:28:31 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_0_3]
2018-01-08 00:28:31 WARN  Executor:66 - 1 block locks were not released by TID = 5:
[rdd_0_1]
- mean centers data by columns
- zScores data by rows
2018-01-08 00:28:32 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_3_1]
2018-01-08 00:28:32 WARN  Executor:66 - 1 block locks were not released by TID = 11:
[rdd_3_3]
2018-01-08 00:28:32 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2018-01-08 00:28:32 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2018-01-08 00:28:32 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
2018-01-08 00:28:32 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
2018-01-08 00:28:32 WARN  Executor:66 - 1 block locks were not released by TID = 21:
[rdd_3_1]
2018-01-08 00:28:32 WARN  Executor:66 - 1 block locks were not released by TID = 23:
[rdd_3_3]
- removes top k components of data
2018-01-08 00:28:33 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:28:33 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2018-01-08 00:28:33 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:28:33 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
2018-01-08 00:28:33 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
2018-01-08 00:28:33 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:28:34 WARN  Executor:66 - 1 block locks were not released by TID = 35:
[rdd_23_0]
2018-01-08 00:28:34 WARN  Executor:66 - 1 block locks were not released by TID = 41:
[rdd_23_0]
2018-01-08 00:28:34 WARN  Executor:66 - 1 block locks were not released by TID = 44:
[rdd_4_0]
- produces same results with fixed k
2018-01-08 00:28:34 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:28:34 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2018-01-08 00:28:34 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_7_0]
2018-01-08 00:28:34 WARN  Executor:66 - 1 block locks were not released by TID = 13:
[rdd_7_0]
2018-01-08 00:28:34 WARN  Executor:66 - 1 block locks were not released by TID = 18:
[rdd_4_0]
- filters and centers SVD results
2018-01-08 00:28:35 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:28:35 WARN  Executor:66 - 1 block locks were not released by TID = 8:
[rdd_1_0]
2018-01-08 00:28:35 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_10_0]
2018-01-08 00:28:35 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_10_0]
2018-01-08 00:28:35 WARN  Executor:66 - 1 block locks were not released by TID = 24:
[rdd_21_0]
2018-01-08 00:28:35 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:28:36 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:28:36 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:28:36 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:28:37 WARN  Executor:66 - 1 block locks were not released by TID = 99:
[rdd_64_0]
- filters and normalizes read depth data
HMMSuite:
2018-01-08 00:28:37 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:28:37 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Generates transition matrix for array of distances
- Handles contig boundaries in computing transition matrix
2018-01-08 00:28:37 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:28:37 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Discovers CNVs
DecaSuite:
2018-01-08 00:28:39 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:28:39 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- read XHMM matrix
2018-01-08 00:28:39 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:28:39 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2018-01-08 00:28:40 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_9_0]
2018-01-08 00:28:40 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_9_0]
- write XHMM matrix
CoverageSuite:
- Finds correct first target
- computes coverage for targets
- counts fragments not just reads
- counts imperfectly paired fragments
- incorporates CIGAR into fragment analysis
Run completed in 15 seconds, 57 milliseconds.
Total number of tests run: 16
Suites: completed 5, aborted 0
Tests: succeeded 16, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 20 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-core_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala:-1: info: compiling
[INFO] Compiling 15 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/scoverage-classes at 1515400124011
[WARNING] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure
[WARNING]       case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector)
[WARNING]               ^
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [1316 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scoverage-data]
[WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 9 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 ---
Discovery starting.
Discovery completed in 494 milliseconds.
Run starting. Expected test count is: 16
NormalizationSuite:
2018-01-08 00:28:55 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2018-01-08 00:28:58 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_0_3]
2018-01-08 00:28:58 WARN  Executor:66 - 1 block locks were not released by TID = 5:
[rdd_0_1]
- mean centers data by columns
- zScores data by rows
2018-01-08 00:28:59 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_3_1]
2018-01-08 00:28:59 WARN  Executor:66 - 1 block locks were not released by TID = 11:
[rdd_3_3]
2018-01-08 00:28:59 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2018-01-08 00:28:59 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2018-01-08 00:28:59 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
2018-01-08 00:28:59 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
2018-01-08 00:28:59 WARN  Executor:66 - 1 block locks were not released by TID = 21:
[rdd_3_1]
2018-01-08 00:28:59 WARN  Executor:66 - 1 block locks were not released by TID = 23:
[rdd_3_3]
- removes top k components of data
2018-01-08 00:29:00 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:29:00 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2018-01-08 00:29:00 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:29:00 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
2018-01-08 00:29:00 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
2018-01-08 00:29:01 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:29:01 WARN  Executor:66 - 1 block locks were not released by TID = 35:
[rdd_23_0]
2018-01-08 00:29:01 WARN  Executor:66 - 1 block locks were not released by TID = 41:
[rdd_23_0]
2018-01-08 00:29:01 WARN  Executor:66 - 1 block locks were not released by TID = 44:
[rdd_4_0]
- produces same results with fixed k
2018-01-08 00:29:01 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:29:01 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2018-01-08 00:29:01 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_7_0]
2018-01-08 00:29:02 WARN  Executor:66 - 1 block locks were not released by TID = 13:
[rdd_7_0]
2018-01-08 00:29:02 WARN  Executor:66 - 1 block locks were not released by TID = 18:
[rdd_4_0]
- filters and centers SVD results
2018-01-08 00:29:02 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:29:02 WARN  Executor:66 - 1 block locks were not released by TID = 8:
[rdd_1_0]
2018-01-08 00:29:02 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_10_0]
2018-01-08 00:29:02 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_10_0]
2018-01-08 00:29:03 WARN  Executor:66 - 1 block locks were not released by TID = 24:
[rdd_21_0]
2018-01-08 00:29:03 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:29:03 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:29:03 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:29:04 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2018-01-08 00:29:04 WARN  Executor:66 - 1 block locks were not released by TID = 99:
[rdd_64_0]
- filters and normalizes read depth data
HMMSuite:
2018-01-08 00:29:04 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:29:04 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Generates transition matrix for array of distances
- Handles contig boundaries in computing transition matrix
2018-01-08 00:29:04 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:29:05 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Discovers CNVs
DecaSuite:
2018-01-08 00:29:06 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:29:07 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- read XHMM matrix
2018-01-08 00:29:07 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2018-01-08 00:29:07 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2018-01-08 00:29:07 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_9_0]
2018-01-08 00:29:07 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_9_0]
- write XHMM matrix
CoverageSuite:
- Finds correct first target
- computes coverage for targets
- counts fragments not just reads
- counts imperfectly paired fragments
- incorporates CIGAR into fragment analysis
Run completed in 15 seconds, 804 milliseconds.
Total number of tests run: 16
Suites: completed 5, aborted 0
Tests: succeeded 16, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-cli_2.11 ---
[INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes at 1515400153436
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/test-classes at 1515400159230
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 ---
Discovery starting.
Discovery completed in 127 milliseconds.
Run starting. Expected test count is: 0
DecaMainSuite:
- no op to test setup !!! IGNORED !!!
Run completed in 196 milliseconds.
Total number of tests run: 0
Suites: completed 2, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 1, pending 0
No tests were executed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/annotations:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/scoverage-classes at 1515400165029
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [316 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/scoverage-classes
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 ---
Discovery starting.
Discovery completed in 119 milliseconds.
Run starting. Expected test count is: 0
DecaMainSuite:
- no op to test setup !!! IGNORED !!!
Run completed in 189 milliseconds.
Total number of tests run: 0
Suites: completed 2, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 1, pending 0
No tests were executed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.480s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [1:03.221s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [21.115s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:27.017s
[INFO] Finished at: Mon Jan 08 00:29:33 PST 2018
[INFO] Final Memory: 66M/1346M
[INFO] ------------------------------------------------------------------------

# if those pass, build the distribution package
mvn -U \
    -P distribution \
    package \
    -DskipTests \
    -Dhadoop.version=${HADOOP_VERSION} \
    -Dspark.version=${SPARK_VERSION} \
    -DargLine=${DECA_MVN_TMP_DIR}
+ mvn -U -P distribution package -DskipTests -Dhadoop.version=2.3.0 -Dspark.version=2.0.0 -DargLine=/tmp/decaTestMvnwmQYIr0
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, column 23
[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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-distribution_2.11:pom:0.1.1-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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 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. @ line 361, 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 365, 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] deca: Distributed Exome CNV Analyzer
[INFO] deca-core: Core variant calling algorithms
[INFO] deca-cli: Command line interface for a distributed variant caller
[INFO] deca: distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: Distributed Exome CNV Analyzer 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ deca-parent_2.11 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.11 ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 20 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ deca-core_2.11 ---
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes at 1515400181811
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-cli_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-cli_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ deca-cli_2.11 ---
[INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:2.10.4:javadoc' has not been previously called for the module: 'org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-SNAPSHOT'. Trying to invoke it...
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/apidocs
[ERROR] Error fetching link: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/apidocs/package-list. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.deca.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_60
Building tree for all the packages and classes...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/About.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-frame.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-summary.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-tree.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/constant-values.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/class-use/About.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-use.html...
Building index for all the packages and classes...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/overview-tree.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/index-all.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/allclasses-frame.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/allclasses-noframe.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/index.html...
Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.4.3:shade (default) @ deca-cli_2.11 ---
[INFO] Including net.fnothaft:jsr203-s3a:jar:0.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.3.0-incubating in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.8 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-serialization-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-SNAPSHOT in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.4 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.23.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.hammerlab:genomic-loci_2.11:jar:1.4.4 in the shaded jar.
[INFO] Including org.hammerlab:args4s_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including org.hammerlab:iterator_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including org.hammerlab:string-utils_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.11.3 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.0 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:2.7 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.2 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.1 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.11.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:1.2.4 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:16.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.23.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.23.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.23.0 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.1.0 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.1.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-multibindings:jar:4.1.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.16 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.2.4 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar.
[INFO] Including org.scalanlp:breeze_2.11:jar:0.12 in the shaded jar.
[INFO] Including org.scalanlp:breeze-macros_2.11:jar:0.12 in the shaded jar.
[INFO] Including com.github.fommil.netlib:core:jar:1.1.2 in the shaded jar.
[INFO] Including net.sourceforge.f2j:arpack_combined_all:jar:0.1 in the shaded jar.
[INFO] Including net.sf.opencsv:opencsv:jar:2.3 in the shaded jar.
[INFO] Including com.github.rwl:jtransforms:jar:2.4.0 in the shaded jar.
[INFO] Including junit:junit:jar:4.8.2 in the shaded jar.
[INFO] Including org.spire-math:spire_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including org.spire-math:spire-macros_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including com.chuusai:shapeless_2.11:jar:2.0.0 in the shaded jar.
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar with /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: distribution 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-distribution_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-distribution_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.3.2:exec (Generate Documentation) @ deca-distribution_2.11 ---
pandoc: source/*.md: openFile: does not exist (No such file or directory)
pandoc: source/*.md: openFile: does not exist (No such file or directory)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.998s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [2.819s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [21.378s]
[INFO] deca: distribution ................................ FAILURE [0.197s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 27.528s
[INFO] Finished at: Mon Jan 08 00:30:01 PST 2018
[INFO] Final Memory: 94M/1119M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.3.2:exec (Generate Documentation) on project deca-distribution_2.11: Command execution failed. Process exited with an error: 1 (Exit value: 1) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :deca-distribution_2.11
Build step 'Execute shell' marked build as failure
Recording test results
Sending e-mails to: fnothaft@berkeley.edu
Finished: FAILURE