FailedConsole Output

Started by upstream project "deca-prb" build number 16
originally caused by:
 GitHub pull request #15 of commit 794d921aa38bc8ccaac871639d1833e74e120398 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-08 (centos spark-test) 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 76eeb32298aa1a584103496b1a999696d31ee1b8 (origin/pr/15/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 76eeb32298aa1a584103496b1a999696d31ee1b8
First time build. Skipping changelog.
[centos] $ /bin/bash /tmp/hudson3532982266487698706.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/decaTestMvneMcuUDJ

# 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/decaTestMvneMcuUDJ: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=0.0.1-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 2.0.0 ]]

# 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 2.0.0 and Hadoop 2.3.0'
Testing DECA version 0.0.1-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...
[ERROR] The build could not read 1 project -> [Help 1]
[ERROR]   
[ERROR]   The project org.bdgenomics.deca:deca-core_2.11:0.0.1-SNAPSHOT (/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/pom.xml) has 1 error
[ERROR]     'dependencies.dependency.version' for org.seqdoop:hadoop-bam:jar is missing. @ line 160, column 17
[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/ProjectBuildingException
Build step 'Execute shell' marked build as failure
Recording test results
ERROR: Step ?Publish JUnit test result report? failed: Test reports were found but none of them are new. Did tests run? 
For example, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scalatest-reports/TEST-org.bdgenomics.deca.CoverageSuite.xml is 20 days old

Publishing Scoverage XML and HTML report...
null
Finished: FAILURE