Started by upstream project "bdg-utils" build number 2161 originally caused by: Started by timer Running as SYSTEM [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-05 (ubuntu20 ubuntu worker-05) in workspace /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu The recommended git tool is: NONE No credentials specified Cloning the remote Git repository Cloning repository https://github.com/bigdatagenomics/utils.git > git init /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/utils.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/utils.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/utils.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch Checking out Revision ca8592e2f43113d33e8b1245cf579df2a15c0a76 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f ca8592e2f43113d33e8b1245cf579df2a15c0a76 # timeout=10 Commit message: "Modifying pom.xml files for new development after 0.3.0 release." > git rev-list --no-walk ca8592e2f43113d33e8b1245cf579df2a15c0a76 # timeout=10 [EnvInject] - Executing scripts and injecting environment variables after the SCM step. [EnvInject] - Injecting as environment variables the properties content JAVA_HOME=/usr/lib/jvm/java-8-oracle [EnvInject] - Variables injected successfully. [ubuntu] $ /bin/bash /tmp/jenkins6124940551031432781.sh + set -e + export JAVA_HOME=/usr/lib/jvm/java-8-oracle + JAVA_HOME=/usr/lib/jvm/java-8-oracle + export PATH=/usr/lib/jvm/java-8-oracle/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:/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:/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:/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:/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/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:/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:/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:/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:/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 + /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to UTILS_MVN_TMP_DIR=$(mktemp -d -t utilsTestMvnXXXXXXX) ++ mktemp -d -t utilsTestMvnXXXXXXX + UTILS_MVN_TMP_DIR=/tmp/utilsTestMvnXcGMpIh # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${UTILS_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/utilsTestMvnXcGMpIh:g' '{}' ';' find . -name "*.bak" -exec rm {} \; + find . -name '*.bak' -exec rm '{}' ';' # 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/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:/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:/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:/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:/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/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:/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:/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:/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:/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 ${BASH_SOURCE[0]} ) && pwd ) +++ dirname /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/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/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.4.0-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 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 2.4.6 ]] if [ ${SPARK_VERSION} == 3.0.0 ]; then ./scripts/move_to_spark_3.sh fi + '[' 2.4.6 == 3.0.0 ']' # 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 2.11 ]] if [ ${SCALA_VERSION} == 2.11 ]; then # 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 ']' + 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 if [ ${SCALA_VERSION} == 2.12 ]; then ./scripts/move_to_scala_2.12.sh fi + '[' 2.11 == 2.12 ']' # print versions echo "Testing bdg-utils version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION} and Scala ${SCALA_VERSION}" + echo 'Testing bdg-utils version 0.4.0-SNAPSHOT on Spark 2.4.6 and Hadoop 2.7.5 and Scala 2.11' Testing bdg-utils version 0.4.0-SNAPSHOT on Spark 2.4.6 and Hadoop 2.7.5 and Scala 2.11 # clean before building mvn clean + mvn clean 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? Sending e-mails to: 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