FailedConsole Output

Started by upstream project "deca-prb" build number 19
originally caused by:
 GitHub pull request #18 of commit 440fccb725fb017b640d7f781218541de80fcd84 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-01 (spark-packaging spark-compile spark-experimental-docker spark-release spark-docs centos) in workspace /home/jenkins/workspace/deca-prb/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/pull/*:refs/remotes/origin/pr/*
Checking out Revision 866266bc884b21ca5bdb0eef03999925122222d8 (origin/pr/18/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 866266bc884b21ca5bdb0eef03999925122222d8
First time build. Skipping changelog.
[centos] $ /bin/bash /tmp/hudson8865986599097298624.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-prb/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/decaTestMvnvYvGpZz

# 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/decaTestMvnvYvGpZz: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 ${BASH_SOURCE[0]} ) && pwd )
+++ dirname /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/jenkins-test
++ cd /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts
++ pwd
+ DIR=/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/deca-prb/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-prb/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 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 359, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 363, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 367, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 359, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 363, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 367, 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 359, 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 363, 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 367, 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-prb/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-prb/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-prb/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 [0.123s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.044s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [0.050s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.339s
[INFO] Finished at: Sun Sep 17 23:09:15 PDT 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:0.1.1-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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 359, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 363, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 367, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 359, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 363, 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-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 367, 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 359, 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 363, 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 367, 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-prb/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-prb/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-prb/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-prb/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-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/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-prb/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_2.11:0.2.11 requires scala version: 2.11.4
[WARNING] Multiple versions of scala libraries detected!
[INFO] Using zinc server for incremental compilation
[error] Required file not found: sbt-interface.jar
[error] See zinc -help for information about locating necessary files
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.374s]
[INFO] deca-core: Core variant calling algorithms ........ FAILURE [2.313s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4.894s
[INFO] Finished at: Sun Sep 17 23:09:21 PDT 2017
[INFO] Final Memory: 32M/1088M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal net.alchim31.maven:scala-maven-plugin:3.2.2:compile (scala-compile-first) on project deca-core_2.11: Execution scala-compile-first of goal net.alchim31.maven:scala-maven-plugin:3.2.2:compile failed. CompileFailed -> [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/PluginExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :deca-core_2.11
Build step 'Execute shell' marked build as failure
Recording test results
ERROR: Step ?Publish JUnit test result report? failed: No test report files were found. Configuration error?
Publishing Scoverage XML and HTML report...
null
Finished: FAILURE