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/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/.part-r-00001.gz.parquet.crc
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/part-r-00001.gz.parquet
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/part-r-00002.gz.parquet
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/._SUCCESS.crc
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/._metadata.crc
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/._references.avro.crc
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/_SUCCESS
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/.part-r-00003.gz.parquet.crc
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/_metadata
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/.part-r-00002.gz.parquet.crc
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/_samples.avro
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/_common_metadata
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/._samples.avro.crc
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/_references.avro
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/part-r-00003.gz.parquet
/tmp/adamTestMvnclqxK6D/TempSuite8078909427780917876.adam/._common_metadata.crc
/tmp/adamTestMvnclqxK6D/sorted.sam5350256494908199197.sam
/tmp/adamTestMvnclqxK6D/ordered.sam8333813347724970791.sam
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/._SUCCESS.crc
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/part-00002-1f7caeb0-72b9-4e25-8966-6c270a4be78a-c000.snappy.parquet
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/._processingSteps.avro.crc
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/._references.avro.crc
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/_SUCCESS
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/.part-00002-1f7caeb0-72b9-4e25-8966-6c270a4be78a-c000.snappy.parquet.crc
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/._readGroups.avro.crc
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/part-00000-1f7caeb0-72b9-4e25-8966-6c270a4be78a-c000.snappy.parquet
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/part-00001-1f7caeb0-72b9-4e25-8966-6c270a4be78a-c000.snappy.parquet
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/_references.avro
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/_processingSteps.avro
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/_readGroups.avro
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/.part-00001-1f7caeb0-72b9-4e25-8966-6c270a4be78a-c000.snappy.parquet.crc
/tmp/adamTestMvnclqxK6D/TempSuite7083040563997790313.adam/.part-00000-1f7caeb0-72b9-4e25-8966-6c270a4be78a-c000.snappy.parquet.crc
/tmp/adamTestMvnclqxK6D/TempSuite2602399295201979804
/tmp/adamTestMvnclqxK6D/TempSuite4732730400867361678.bed
/tmp/adamTestMvnclqxK6D/TempSuite4732730400867361678.bed/._SUCCESS.crc
/tmp/adamTestMvnclqxK6D/TempSuite4732730400867361678.bed/.part-00000.crc
/tmp/adamTestMvnclqxK6D/TempSuite4732730400867361678.bed/part-00000
/tmp/adamTestMvnclqxK6D/TempSuite4732730400867361678.bed/_SUCCESS
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/._SUCCESS.crc
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/._metadata.crc
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/._processingSteps.avro.crc
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/._references.avro.crc
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/_SUCCESS
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/_metadata
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/._readGroups.avro.crc
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/_common_metadata
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/_references.avro
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/_processingSteps.avro
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/_readGroups.avro
/tmp/adamTestMvnclqxK6D/TempSuite5850275542414204743.adam/._common_metadata.crc
/tmp/adamTestMvnclqxK6D/TempSuite879427380540594416
/tmp/adamTestMvnclqxK6D/TempSuite1508981579484303580
/tmp/adamTestMvnclqxK6D/TempSuite5341582192208087247.bed
/tmp/adamTestMvnclqxK6D/TempSuite5341582192208087247.bed/._SUCCESS.crc
/tmp/adamTestMvnclqxK6D/TempSuite5341582192208087247.bed/.part-00000.crc
/tmp/adamTestMvnclqxK6D/TempSuite5341582192208087247.bed/part-00000
/tmp/adamTestMvnclqxK6D/TempSuite5341582192208087247.bed/_SUCCESS
rm -rf ${ADAM_MVN_TMP_DIR}
+ rm -rf /tmp/adamTestMvnclqxK6D

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/adamTestMvnclqxK6D: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/adamTestCLmUaRO

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

pushd $PROJECT_ROOT
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu

# Copy the jar into our temp space for testing
cp -r . $ADAM_TMP_DIR
+ cp -r . /tmp/adamTestCLmUaRO/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu

pushd $ADAM_TMP_DIR
+ pushd /tmp/adamTestCLmUaRO/deleteMePleaseThisIsNoLongerNeeded
/tmp/adamTestCLmUaRO/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu

# what hadoop version are we on? format string for downloading spark assembly
if [[ $HADOOP_VERSION =~ ^2\.6 ]]; then
    HADOOP=hadoop2.6
elif [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
    HADOOP=hadoop2.7
else
    echo "Unknown Hadoop version."
    exit 1
fi
+ [[ 2.7.5 =~ ^2\.6 ]]
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7

# set spark artifact string for downloading assembly
SPARK=spark-${SPARK_VERSION}
+ SPARK=spark-2.4.3
    
# 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 "http://www-us.apache.org/dist/hadoop/common/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 "http://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=$(hadoop-2.7.7/bin/hadoop classpath)
else
    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${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-2.4.3/spark-2.4.3-bin-without-hadoop-scala-2.12.tgz' -o spark-2.4.3-bin-without-hadoop-scala-2.12.tgz
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curl: (28) Connection timed out after 300193 milliseconds
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/0173e7feb1e06030b4052d9acaeb3853650f42ea
Finished: FAILURE