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/tmp/adamTestMvna19d7Vj/TempSuite2286153567415561966.adam/_header
rm -rf ${ADAM_MVN_TMP_DIR}
+ rm -rf /tmp/adamTestMvna19d7Vj

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${ADAM_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/adamTestMvna19d7Vj:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# run integration tests

# make a temp directory
ADAM_TMP_DIR=$(mktemp -d -t adamTestXXXXXXX)
mktemp -d -t adamTestXXXXXXX
++ mktemp -d -t adamTestXXXXXXX
+ ADAM_TMP_DIR=/tmp/adamTestkZRtPNK

# Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR
ADAM_TMP_DIR=$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
+ ADAM_TMP_DIR=/tmp/adamTestkZRtPNK/deleteMePleaseThisIsNoLongerNeeded
mkdir $ADAM_TMP_DIR
+ mkdir /tmp/adamTestkZRtPNK/deleteMePleaseThisIsNoLongerNeeded

# set the TMPDIR envar, which is used by python to choose where to make temp directories
export TMPDIR=${ADAM_TMP_DIR}
+ export TMPDIR=/tmp/adamTestkZRtPNK/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/adamTestkZRtPNK/deleteMePleaseThisIsNoLongerNeeded

pushd $PROJECT_ROOT
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/3.0.0/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/3.0.0/label/ubuntu

# Copy the jar into our temp space for testing
cp -r . $ADAM_TMP_DIR
+ cp -r . /tmp/adamTestkZRtPNK/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/3.0.0/label/ubuntu

pushd $ADAM_TMP_DIR
+ pushd /tmp/adamTestkZRtPNK/deleteMePleaseThisIsNoLongerNeeded
/tmp/adamTestkZRtPNK/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/3.0.0/label/ubuntu

# what hadoop version are we on? format string for downloading spark assembly
if [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
    HADOOP=hadoop2.7
else
    echo "Unknown Hadoop version."
    exit 1
fi
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7

# set spark artifact string for downloading assembly
SPARK=spark-${SPARK_VERSION}
+ SPARK=spark-3.0.0
    
# download prepackaged spark assembly

# Spark 2.4.3+ needs special case for Scala 2.12
if [ ${SCALAVER} == 2.12 ];
then
    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-without-hadoop-scala-2.12.tgz" \
        -o ${SPARK}-bin-without-hadoop-scala-2.12.tgz

    tar xzvf ${SPARK}-bin-without-hadoop-scala-2.12.tgz
    export SPARK_HOME=${ADAM_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12

    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=hadoop/core/hadoop-2.7.7/hadoop-2.7.7.tar.gz" \
        -o hadoop-2.7.7.tar.gz

    tar xzvf hadoop-2.7.7.tar.gz

    # remove references to avro 1.7.x
    find hadoop-2.7.7 -name *.jar | grep avro | xargs rm

    # download avro 1.8.x
    #curl \
    #    -L "https://repo1.maven.org/maven2/org/apache/avro/avro/1.8.2/avro-1.8.2.jar" \
    #    -o hadoop-2.7.7/share/hadoop/common/avro-1.8.2.jar

    export SPARK_DIST_CLASSPATH=$(hadoop-2.7.7/bin/hadoop classpath)
else
    curl \
        -v \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
        -o ${SPARK}-bin-${HADOOP}.tgz

    tar xzvf ${SPARK}-bin-${HADOOP}.tgz
    export SPARK_HOME=${ADAM_TMP_DIR}/${SPARK}-bin-${HADOOP}
fi
+ '[' 2.12 == 2.12 ']'
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-3.0.0/spark-3.0.0-bin-without-hadoop-scala-2.12.tgz' -o spark-3.0.0-bin-without-hadoop-scala-2.12.tgz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

100   153  100   153    0     0    227      0 --:--:-- --:--:-- --:--:--   227
+ tar xzvf spark-3.0.0-bin-without-hadoop-scala-2.12.tgz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/3aeb5f6ad39f838ee5c1b6d75957491c1cfd31f0
Finished: FAILURE