Console Output

Started by upstream project "mango-prb" build number 980
originally caused by:
 GitHub pull request #559 of commit 60132b7b46fbeba2aad65f1e89d226369db4df68 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-staging-worker-02 (ubuntu ubuntu-gpu ubuntu-avx2 staging-02 staging) in workspace /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu
 > 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/mango.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/mango.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/bigdatagenomics/mango.git +refs/pull/*:refs/remotes/origin/pr/*
Checking out Revision 1bae3680bdee3e62285fe7b567f1f2fbf734928a (origin/pr/559/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 1bae3680bdee3e62285fe7b567f1f2fbf734928a
 > git rev-list 107de5fc646f062dad6fcec985c76e854fd43c5a # timeout=10
First time build. Skipping changelog.
[ubuntu] $ /bin/bash /tmp/hudson2529118613807894787.sh
+ set -e
+ set +x
+ docker run --rm -v /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu:/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu -e COVERALLS_REPO_TOKEN=D8pVcSLX2bfAMpSDM0urS9ESDJ2zMAQom -e WORKSPACE=/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu -e SPARK_VERSION=2.4.6 -e HADOOP_VERSION=2.7.5 -e SCALAVER=2.11 --user jenkins:jenkins --entrypoint=/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test bigdatagenomics/mango-jenkins:0.0.1--fa4bec2a923815ede5c05a36cdb8a046a3029461
Unable to find image 'bigdatagenomics/mango-jenkins:0.0.1--fa4bec2a923815ede5c05a36cdb8a046a3029461' locally
0.0.1--fa4bec2a923815ede5c05a36cdb8a046a3029461: Pulling from bigdatagenomics/mango-jenkins
22dbe790f715: Already exists
0250231711a0: Already exists
6fba9447437b: Already exists
c2b4d327b352: Already exists
cddb9bb0d37c: Already exists
b535486c968f: Already exists
f3e976e6210c: Already exists
b2c11b10291d: Already exists
72758226cb91: Already exists
6f3c2ec4884a: Already exists
a5b68b7a1de5: Already exists
40a6a8034266: Pulling fs layer
dc1cf84a223a: Pulling fs layer
f85f015a92dc: Pulling fs layer
e2e1e146d9ec: Pulling fs layer
3c1102c33697: Pulling fs layer
fe6e9ca9a3a1: Pulling fs layer
fe6e9ca9a3a1: Waiting
dc1cf84a223a: Verifying Checksum
dc1cf84a223a: Download complete
40a6a8034266: Verifying Checksum
40a6a8034266: Download complete
40a6a8034266: Pull complete
dc1cf84a223a: Pull complete
fe6e9ca9a3a1: Verifying Checksum
fe6e9ca9a3a1: Download complete
3c1102c33697: Verifying Checksum
3c1102c33697: Download complete
e2e1e146d9ec: Verifying Checksum
e2e1e146d9ec: Download complete
f85f015a92dc: Verifying Checksum
f85f015a92dc: Download complete
f85f015a92dc: Pull complete
e2e1e146d9ec: Pull complete
3c1102c33697: Pull complete
fe6e9ca9a3a1: Pull complete
Digest: sha256:a2ff80933e79bbe1de108a9b9a0fb38fd947912523fe20ddc428bdc76dfe8378
Status: Downloaded newer image for bigdatagenomics/mango-jenkins:0.0.1--fa4bec2a923815ede5c05a36cdb8a046a3029461

# navigate to mango parent directory, set in Jenkins
if [ -z "$WORKSPACE" ]
then
	echo "WORKSPACE variable is not set. Defaulting to current directory.."
	WORKSPACE="$(echo $PWD)"
fi
+ '[' -z /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu ']'

# make a tempdir for writing maven cruft to
MANGO_MVN_TMP_DIR=$(mktemp -d -t mangoTestMvnXXXXXXX)
++ mktemp -d -t mangoTestMvnXXXXXXX
+ MANGO_MVN_TMP_DIR=/tmp/mangoTestMvn4yX3mjM

# make a temp directory for installing/downloading jars to
MANGO_TMP_DIR=$(mktemp -d -t mangoTestXXXXXXX)
++ mktemp -d -t mangoTestXXXXXXX
+ MANGO_TMP_DIR=/tmp/mangoTestbvvonDN

MANGO_TMP_DIR=$MANGO_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
+ MANGO_TMP_DIR=/tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded
mkdir $MANGO_TMP_DIR
+ mkdir /tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded

# run integration tests
# set the TMPDIR envar, which is used by python to choose where to make temp directories
export TMPDIR=${MANGO_TMP_DIR}
+ export TMPDIR=/tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded

# Copy workspace into our temp space for testing
cp -r $WORKSPACE $MANGO_TMP_DIR
+ cp -r /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.6/label/ubuntu /tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded

# new project root is tmp dir, where everything was copied
PROJECT_ROOT=$MANGO_TMP_DIR
+ PROJECT_ROOT=/tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded

pushd $PROJECT_ROOT
+ pushd /tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded
/tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded /home

# 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=${MANGO_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/mangoTestMvn4yX3mjM:g' '{}' ';'
find . -name "*.bak" -exec rm {} \;
+ find . -name '*.bak' -exec rm '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ PATH=/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/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'
VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
++ grep '<version>' /tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded/pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
grep: /tmp/mangoTestbvvonDN/deleteMePleaseThisIsNoLongerNeeded/pom.xml: No such file or directory
+ VERSION=

exit 1
+ exit 1
Build step 'Execute shell' marked build as failure
Finished: FAILURE