Console Output

Started by upstream project "cannoli-prb" build number 256
originally caused by:
 GitHub pull request #203 of commit 734ed70a5caf8190091341886a69147ddfdbffa9, no merge conflicts.
Running as SYSTEM
[EnvInject] - Loading node environment variables.
Building remotely on research-jenkins-worker-03 (ubuntu) in workspace /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu
The recommended git tool is: NONE
No credentials specified
Wiping out workspace first.
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/cannoli.git
 > git init /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu # timeout=10
Using reference repository: /home/jenkins/gitcaches/adam.reference
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=15
 > 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
 > git config remote.origin.url https://github.com/bigdatagenomics/cannoli.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git
 > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/cannoli.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=15
Checking out Revision 734ed70a5caf8190091341886a69147ddfdbffa9 (detached)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 734ed70a5caf8190091341886a69147ddfdbffa9 # timeout=10
Commit message: "bump container image"
First time build. Skipping changelog.
[ubuntu] $ /bin/bash /tmp/jenkins456339525454921492.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-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/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/cannoliTestMvn9S4sRon

# 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/cannoliTestMvn9S4sRon: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 ${BASH_SOURCE[0]} ) && pwd )
+++ dirname /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/cannoli-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/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-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/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 2.4.7 ]]

# 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 2.4.7 Scala 2.12 and Hadoop 2.7.5'
Testing Cannoli version 0.11.0-SNAPSHOT on Spark 2.4.7 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
+ '[' 2.4.7 == 2.4.7 ']'
+ set +e
+ ./scripts/move_to_spark_2.sh
+ set -e

# 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
+ '[' 2.4.7 == 3.0.1 ']'

# 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
[Set GitHub commit status (universal)] ERROR on repos [GHRepository@2b9c7918[nodeId=MDEwOlJlcG9zaXRvcnk3ODQ3MzA5OA==,description=Distributed execution of bioinformatics tools on Apache Spark. Apache 2 licensed.,homepage=,name=cannoli,fork=false,archived=false,size=493,milestones={},language=Scala,commits={},source=<null>,parent=<null>,isTemplate=<null>,url=https://api.github.com/repos/bigdatagenomics/cannoli,id=78473098,nodeId=<null>,createdAt=2017-01-09T22:02:42Z,updatedAt=2020-10-27T02:58:52Z]] (sha:734ed70) with context:cannoli-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=2.4.7,label=ubuntu
Setting commit status on GitHub for https://github.com/bigdatagenomics/cannoli/commit/734ed70a5caf8190091341886a69147ddfdbffa9
Finished: FAILURE