FailedConsole Output

Started by upstream project "cannoli" build number 2148
originally caused by:
 Started by timer
Running as SYSTEM
[EnvInject] - Loading node environment variables.
Building remotely on research-jenkins-worker-01 (ubuntu) in workspace /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu
The recommended git tool is: NONE
No credentials specified
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/cannoli.git
 > git init /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git
 > git --version # timeout=10
 > git --version # 'git version 2.25.1'
 > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/cannoli.git +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/bigdatagenomics/cannoli.git # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
Checking out Revision 111c645ff0fb9b021a0efec16078d46596481be0 (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 111c645ff0fb9b021a0efec16078d46596481be0 # timeout=10
Commit message: "Add additional command line arguments, header lines for freebayes."
 > git rev-list --no-walk 111c645ff0fb9b021a0efec16078d46596481be0 # timeout=10
Cleaning workspace
 > git rev-parse --verify HEAD # timeout=10
Resetting working tree
 > git reset --hard # timeout=10
 > git clean -fdx # timeout=10
[ubuntu] $ /bin/bash /tmp/jenkins3556107033039062267.sh
+ set -e
+ export JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ export CONDA_BIN=/home/anaconda/bin/
+ CONDA_BIN=/home/anaconda/bin/
+ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ set +x
+ /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test

# make a tempdir for writing maven cruft to
CANNOLI_MVN_TMP_DIR=$(mktemp -d -t cannoliTestMvnXXXXXXX)
++ mktemp -d -t cannoliTestMvnXXXXXXX
+ CANNOLI_MVN_TMP_DIR=/tmp/cannoliTestMvntECuMSe

# 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=${CANNOLI_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/cannoliTestMvntECuMSe:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
+ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/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 ${BASH_SOURCE[0]} ) && pwd )
+++ dirname /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/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/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.11.0-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 2.7.5 ]]

# is the scala version set?
if ! [[ ${SCALA_VERSION} ]];
then
    echo "SCALA_VERSION environment variable is not set."
    echo "Please set this variable before running."
    exit 1
fi
+ [[ -n 2.12 ]]

# 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 3.0.1 ]]

# print versions
echo "Testing Cannoli version ${VERSION} on Spark ${SPARK_VERSION} Scala ${SCALA_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing Cannoli version 0.11.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 2.7.5'
Testing Cannoli version 0.11.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 2.7.5

# move to Scala 2.11 if requested
if [ ${SCALA_VERSION} == 2.11 ];
then
    set +e
    ./scripts/move_to_scala_2.11.sh
    set -e
fi
+ '[' 2.12 == 2.11 ']'

# move to Scala 2.12 if requested
if [ ${SCALA_VERSION} == 2.12 ];
then
    set +e
    ./scripts/move_to_scala_2.12.sh
    set -e
fi
+ '[' 2.12 == 2.12 ']'
+ set +e
+ ./scripts/move_to_scala_2.12.sh
Scala version is already set to 2.12 (Scala artifacts have _2.12 version suffix in artifact name).
Cowardly refusing to move to Scala 2.12 a second time...
+ set -e

# move to Spark 2.x if requested
if [ ${SPARK_VERSION} == 2.4.7 ];
then
    set +e
    ./scripts/move_to_spark_2.sh
    set -e
fi
+ '[' 3.0.1 == 2.4.7 ']'

# move to Spark 3.x if requested
if [ ${SPARK_VERSION} == 3.0.1 ];
then
    set +e
    ./scripts/move_to_spark_3.sh
    set -e
fi
+ '[' 3.0.1 == 3.0.1 ']'
+ set +e
+ ./scripts/move_to_spark_3.sh
POM is already set up for Spark 3 (Spark 3 artifacts have -spark3 suffix in artifact names).
Cowardly refusing to move to Spark 3 a second time...
+ set -e

# first, build the sources, run the unit tests, and generate a coverage report
mvn clean \
    -Dhadoop.version=${HADOOP_VERSION}
+ mvn clean -Dhadoop.version=2.7.5
The JAVA_HOME environment variable is not defined correctly
This environment variable is needed to run this program
NB: JAVA_HOME should point to a JDK not a JRE
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...
ERROR: cannot find scoverage report
Sending e-mails to: heuermh@gmail.com fnothaft@berkeley.edu
ERROR: Couldn't connect to host, port: 127.0.0.1, 25; timeout 60000
com.sun.mail.util.MailConnectException: Couldn't connect to host, port: 127.0.0.1, 25; timeout 60000;
  nested exception is:
	java.net.ConnectException: Connection refused (Connection refused)
	at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2210)
	at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:722)
	at javax.mail.Service.connect(Service.java:342)
	at javax.mail.Service.connect(Service.java:222)
	at javax.mail.Service.connect(Service.java:171)
	at javax.mail.Transport.send0(Transport.java:230)
	at javax.mail.Transport.send(Transport.java:100)
	at hudson.tasks.MailSender.run(MailSender.java:130)
	at hudson.tasks.Mailer.perform(Mailer.java:176)
	at hudson.tasks.Mailer.perform(Mailer.java:139)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:741)
	at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:690)
	at hudson.model.Build$BuildExecution.post2(Build.java:186)
	at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:635)
	at hudson.model.Run.execute(Run.java:1919)
	at hudson.matrix.MatrixRun.run(MatrixRun.java:153)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:428)
Caused by: java.net.ConnectException: Connection refused (Connection refused)
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:607)
	at com.sun.mail.util.SocketFetcher.createSocket(SocketFetcher.java:333)
	at com.sun.mail.util.SocketFetcher.getSocket(SocketFetcher.java:214)
	at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2160)
	... 18 more
Finished: FAILURE