SuccessConsole Output

Started by upstream project "deca-prb" build number 7
originally caused by:
 GitHub pull request #2 of commit 77981d8e6e849f6419e082ce8150e50e04677844 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-07 (centos spark-test) in workspace /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos
Cloning the remote Git repository
Cloning repository https://github.com/fnothaft/deca.git
 > git init /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos # timeout=10
Fetching upstream changes from https://github.com/fnothaft/deca.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/fnothaft/deca.git +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url https://github.com/fnothaft/deca.git # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/fnothaft/deca.git # timeout=10
Fetching upstream changes from https://github.com/fnothaft/deca.git
 > git fetch --tags --progress https://github.com/fnothaft/deca.git +refs/pull/*:refs/remotes/origin/pr/*
Checking out Revision 91903450d9b8fa3c69248715df697b77a7f00391 (origin/pr/2/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 91903450d9b8fa3c69248715df697b77a7f00391
First time build. Skipping changelog.
[centos] $ /bin/bash /tmp/hudson8369281239287908893.sh
+ set -e
+ export JAVA_HOME=/usr/java/jdk1.8.0_60
+ JAVA_HOME=/usr/java/jdk1.8.0_60
+ export PATH=/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.model.JDK/JDK_7u60/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.model.JDK/JDK_7u60/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
+ java -version
java version "1.8.0_60"
Java(TM) SE Runtime Environment (build 1.8.0_60-b27)
Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)
+ javac -version
javac 1.8.0_60
+ /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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/decaTestMvn7cBbHic

# 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/decaTestMvn7cBbHic: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.model.JDK/JDK_7u60/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.model.JDK/JDK_7u60/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 ${BASH_SOURCE[0]} ) && pwd )
+++ dirname /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/scripts/jenkins-test
++ cd /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/scripts
++ pwd
+ DIR=/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.0.1-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 1.4.1 ]]

# this next line is supposed to fail
set +e
+ set +e

echo "Rewriting POM.xml files to Scala 2.10 and Spark 1 should error..."
+ echo 'Rewriting POM.xml files to Scala 2.10 and Spark 1 should error...'
Rewriting POM.xml files to Scala 2.10 and Spark 1 should error...
./scripts/move_to_spark_1.sh
+ ./scripts/move_to_spark_1.sh
POM is already set up for Spark 1 (Spark 1/2 artifacts are missing -spark2 suffix in artifact names).
Cowardly refusing to move to Spark 1 a second time...
if [[ $? == 0 ]];
then
    echo "Running move_to_spark_1.sh when POMs are set up for Spark 1 should fail, but error code was 0 (success)."
    exit 1
fi
+ [[ 1 == 0 ]]

./scripts/move_to_scala_2.10.sh
+ ./scripts/move_to_scala_2.10.sh
Scala version is already set to 2.10 (Scala artifacts have _2.10 version suffix in artifact name).
Cowardly refusing to move to Scala 2.10 a second time...
if [[ $? == 0 ]];
then
    echo "Running move_to_scala_2.10.sh when POMs are set up for Scala 2.10 should fail, but error code was 0 (success)."
    exit 1
fi
+ [[ 1 == 0 ]]

set -e
+ set -e

# are we testing for spark 2.0.0? if so, we need to rewrite our poms first
if [ ${SPARK_VERSION} == 2.0.0 ];
then
    
    echo "Rewriting POM.xml files for Spark 2."
    ./scripts/move_to_spark_2.sh

    # shouldn't be able to move to spark 2 twice
    set +e
    ./scripts/move_to_spark_2.sh
    if [[ $? == 0 ]];
    then
        echo "We have already moved to Spark 2, so running move_to_spark_2.sh a second time should fail, but error code was 0 (success)."
        exit 1
    fi
    set -e
fi
+ '[' 1.4.1 == 2.0.0 ']'

# are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first
if [ ${SCALAVER} == 2.11 ];
then
    echo "Rewriting POM.xml files for Scala 2.11."
    ./scripts/move_to_scala_2.11.sh

    # shouldn't be able to move to scala 2.11 twice
    set +e
    ./scripts/move_to_scala_2.11.sh
    if [[ $? == 0 ]];
    then
        echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)."
        exit 1
    fi
    set -e
fi
+ '[' 2.11 == 2.11 ']'
+ echo 'Rewriting POM.xml files for Scala 2.11.'
Rewriting POM.xml files for Scala 2.11.
+ ./scripts/move_to_scala_2.11.sh
+ set +e
+ ./scripts/move_to_scala_2.11.sh
Scala version is already set to 2.11 (Scala artifacts have _2.11 version suffix in artifact name).
Cowardly refusing to move to Scala 2.11 a second time...
+ [[ 1 == 0 ]]
+ set -e

# print versions
echo "Testing DECA version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing DECA version 0.0.1-SNAPSHOT on Spark 1.4.1 and Hadoop 2.3.0'
Testing DECA version 0.0.1-SNAPSHOT on Spark 1.4.1 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=1.4.1
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:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 67, 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 135, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 352, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 352, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 352, 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 356, 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 360, 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 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-parent_2.11 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-core_2.11 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-cli_2.11 ---
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [0.125s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.017s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [0.015s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.292s
[INFO] Finished at: Mon Jan 30 13:56:05 PST 2017
[INFO] Final Memory: 19M/1472M
[INFO] ------------------------------------------------------------------------
    
# if those pass, build the distribution package and the integration tests
mvn -U \
    test \
    -P coverage scoverage:report
+ mvn -U 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:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 67, 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 135, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 352, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 352, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 352, 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 356, 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 360, 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 0.0.1-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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 4 .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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 4 .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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 0.0.1-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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 2 .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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 1 Scala source to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scala-2.11.4/classes...
[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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/src/test/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 1 Scala source to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scala-2.11.4/test-classes...
[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 62 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 120 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] >>> 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 2 .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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 1 Scala source to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scala-2.11.4/scoverage-classes...
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [1 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scoverage-data]
[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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/src/test/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] 
[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 64 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 130 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] <<< 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 0.0.1-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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 2 .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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.11.4/classes at 1485813383570
[INFO] prepare-compile in 0 s
[INFO] compile in 3 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.11.4/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.11.4/test-classes at 1485813387461
[INFO] prepare-compile in 0 s
[INFO] compile in 3 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 111 milliseconds.
Run starting. Expected test count is: 0
DecaMainSuite:
- no op to test setup !!! IGNORED !!!
Run completed in 184 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 2 .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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/annotations:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.11.4/scoverage-classes at 1485813392271
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [49 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 3 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.11.4/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[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 120 milliseconds.
Run starting. Expected test count is: 0
DecaMainSuite:
- no op to test setup !!! IGNORED !!!
Run completed in 194 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 [1.527s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [14.466s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [14.900s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 31.128s
[INFO] Finished at: Mon Jan 30 13:56:37 PST 2017
[INFO] Final Memory: 58M/1317M
[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=1.4.1 -DargLine=/tmp/decaTestMvn7cBbHic
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:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 67, 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 135, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 352, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 352, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-distribution_2.11:pom:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 352, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 352, 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 356, 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 360, 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 0.0.1-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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 4 .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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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:2.2.1:jar-no-fork (attach-sources) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1: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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 0.0.1-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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 2 .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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] 
[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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/src/test/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] 
[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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/deca-core_2.11-0.0.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/deca-core_2.11-0.0.1-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1: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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/deca-core_2.11-0.0.1-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.0.1-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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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 2 .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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.11.4/classes at 1485813404801
[INFO] prepare-compile in 0 s
[INFO] compile in 3 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.11.4/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.adam:adam-core_2.11:0.21.0 requires scala version: 2.11.8
[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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.11-0.0.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ deca-cli_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.11-0.0.1-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ deca-cli_2.11 ---
[INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:2.9.1:javadoc' has not been previously called for the module: 'org.bdgenomics.deca:deca-core_2.11:jar:0.0.1-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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-core/target/apidocs
[ERROR] Error fetching link: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/About.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-frame.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-summary.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-tree.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/constant-values.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/class-use/About.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/overview-tree.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/index-all.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/allclasses-frame.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/allclasses-noframe.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/index.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.11-0.0.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.4.3:shade (default) @ deca-cli_2.11 ---
[INFO] Including org.bdgenomics.utils:utils-cli_2.11:jar:0.2.11 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_2.11:jar:0.2.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics_2.11:jar:0.2.11 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.4 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.23 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-serialization_2.11:jar:0.2.11 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.0.0 in the shaded jar.
[INFO] Including commons-cli:commons-cli:jar:1.2 in the shaded jar.
[INFO] Including commons-httpclient:commons-httpclient:jar:3.1 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.5.0 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:1.2.4 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.deca:deca-core_2.11:jar:0.0.1-SNAPSHOT in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:1.3.2 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core_2.11:jar:0.21.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io_2.11:jar:0.2.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd_2.11:jar:0.2.11 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 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.slf4j:slf4j-log4j12:jar:1.7.21 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.1 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.netflix.servo:servo-core:jar:0.10.0 in the shaded jar.
[INFO] Including com.google.code.findbugs:annotations:jar:2.0.0 in the shaded jar.
[INFO] Including com.netflix.servo:servo-internal:jar:0.10.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:16.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli_2.11:jar:0.21.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis_2.11:jar:0.21.0 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.0.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.0 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:4.0 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:1.7.10 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.7 in the shaded jar.
[WARNING] annotations-2.0.0.jar, jsr305-1.3.9.jar define 34 overlapping classes: 
[WARNING]   - javax.annotation.RegEx
[WARNING]   - javax.annotation.concurrent.Immutable
[WARNING]   - javax.annotation.meta.TypeQualifierDefault
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Nonnull
[WARNING]   - javax.annotation.CheckReturnValue
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - javax.annotation.MatchesPattern
[WARNING]   - 24 more...
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.11-0.0.1-SNAPSHOT.jar with /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.11-0.0.1-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: distribution 0.0.1-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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-distribution/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.3.2:exec (Generate Documentation) @ deca-distribution_2.11 ---
! LaTeX Error: File `ifxetex.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Enter file name: 
! Emergency stop.
<read *> 
         
l.10 \usepackage

pandoc: Error producing PDF
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-distribution_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-distribution_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-distribution_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-distribution/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-distribution_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ deca-distribution_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ deca-distribution_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-distribution_2.11 >>>
[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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-distribution/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.3.2:exec (Generate Documentation) @ deca-distribution_2.11 ---
! LaTeX Error: File `ifxetex.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Enter file name: 
! Emergency stop.
<read *> 
         
l.10 \usepackage

pandoc: Error producing PDF
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.11 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.4.1:single (default) @ deca-distribution_2.11 ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-distribution/target/deca-distribution_2.11-0.0.1-SNAPSHOT-bin.tar.gz
[INFO] Building tar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-distribution/target/deca-distribution_2.11-0.0.1-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/deca-distribution/target/deca-distribution_2.11-0.0.1-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [1.844s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [2.903s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [13.406s]
[INFO] deca: distribution ................................ SUCCESS [1.694s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 19.981s
[INFO] Finished at: Mon Jan 30 13:56:58 PST 2017
[INFO] Final Memory: 94M/1410M
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${DECA_MVN_TMP_DIR}
+ find /tmp/decaTestMvn7cBbHic
/tmp/decaTestMvn7cBbHic
rm -rf ${DECA_MVN_TMP_DIR}
+ rm -rf /tmp/decaTestMvn7cBbHic

# and move our poms back to their original values
# this will allow us to pass our porcelain test at the end
if [ ${SPARK_VERSION} == 2.0.0 ];
then
    
    echo "Rewriting POM.xml files back to Spark 1."
    ./scripts/move_to_spark_1.sh
fi
+ '[' 1.4.1 == 2.0.0 ']'
if [ ${SCALAVER} == 2.11 ];
then
    echo "Rewriting POM.xml files back to Scala 2.10."
    ./scripts/move_to_scala_2.10.sh
fi
+ '[' 2.11 == 2.11 ']'
+ echo 'Rewriting POM.xml files back to Scala 2.10.'
Rewriting POM.xml files back to Scala 2.10.
+ ./scripts/move_to_scala_2.10.sh

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${DECA_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/decaTestMvn7cBbHic:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

if test -n "$(git status --porcelain | grep -v -e html -e pdf)"
then
    echo "Applying move_to_xyz script marred a pom.xml file."
    echo "Exiting..."
    exit 1
fi
++ git status --porcelain
++ grep -v -e html -e pdf
+ test -n ''

./scripts/format-source
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/scripts
+ pushd /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/scripts/..
~/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos ~/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos
+ mvn org.scalariform:scalariform-maven-plugin:format license:format
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_2.10:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 67, 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 135, 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_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 352, 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_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.10:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, 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_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 352, 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_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.10:pom:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 352, 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 356, 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 360, 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 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.10 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-parent_2.10 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.10 ---
[INFO] Modified 0 of 2 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-core_2.10 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.10 ---
[INFO] Modified 0 of 2 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-cli_2.10 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [0.825s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.062s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [0.050s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.252s
[INFO] Finished at: Mon Jan 30 13:57:01 PST 2017
[INFO] Final Memory: 16M/1119M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.4.1/label/centos
if test -n "$(git status --porcelain | grep -v -e html -e pdf)"
then
    echo "Please run './scripts/format-source'"
    exit 1
fi
++ git status --porcelain
++ grep -v -e html -e pdf
+ test -n ''

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

Recording test results
Publishing Scoverage XML and HTML report...
Finished: SUCCESS