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/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/._SUCCESS.crc
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/._metadata.crc
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/._header.crc
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/._references.avro.crc
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/_SUCCESS
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/_metadata
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/_common_metadata
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/_references.avro
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/_header
/tmp/adamTestMvnZqujfIH/1715338759302682983/variants.lex.adam/._common_metadata.crc
/tmp/adamTestMvnZqujfIH/TempSuite2029452261792419931.sam
/tmp/adamTestMvnZqujfIH/TempSuite2029452261792419931.sam/part-r-00000.sam
/tmp/adamTestMvnZqujfIH/TempSuite2029452261792419931.sam/._SUCCESS.crc
/tmp/adamTestMvnZqujfIH/TempSuite2029452261792419931.sam/_SUCCESS
/tmp/adamTestMvnZqujfIH/TempSuite2029452261792419931.sam/.part-r-00000.sam.crc
/tmp/adamTestMvnZqujfIH/TempSuite3802829974368125231.sam
/tmp/adamTestMvnZqujfIH/SequenceDatasetSuite3644822628416184499.fasta
/tmp/adamTestMvnZqujfIH/TempSuite3711697505418328876
/tmp/adamTestMvnZqujfIH/TempSuite4130299486875724612
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/._SUCCESS.crc
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/part-00000-1f419c3f-44d2-459e-aa7d-1f506adec9a1-c000.snappy.parquet
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/._references.avro.crc
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/part-00001-1f419c3f-44d2-459e-aa7d-1f506adec9a1-c000.snappy.parquet
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/_SUCCESS
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/.part-00001-1f419c3f-44d2-459e-aa7d-1f506adec9a1-c000.snappy.parquet.crc
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/.part-00002-1f419c3f-44d2-459e-aa7d-1f506adec9a1-c000.snappy.parquet.crc
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/_references.avro
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/part-00002-1f419c3f-44d2-459e-aa7d-1f506adec9a1-c000.snappy.parquet
/tmp/adamTestMvnZqujfIH/TempSuite2716448577396271266.adam/.part-00000-1f419c3f-44d2-459e-aa7d-1f506adec9a1-c000.snappy.parquet.crc
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/._SUCCESS.crc
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/._metadata.crc
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/._processingSteps.avro.crc
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/._references.avro.crc
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/_SUCCESS
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/_metadata
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/._readGroups.avro.crc
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/_common_metadata
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/_references.avro
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/_processingSteps.avro
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/_readGroups.avro
/tmp/adamTestMvnZqujfIH/javaAC799344774696085322/testRdd.fragment.adam/._common_metadata.crc
/tmp/adamTestMvnZqujfIH/TempSuite4657576564102549216
/tmp/adamTestMvnZqujfIH/TempSuite3802829974368125231
/tmp/adamTestMvnZqujfIH/TempSuite4715099569724921521
/tmp/adamTestMvnZqujfIH/TempSuite6999228720011403738.bed
/tmp/adamTestMvnZqujfIH/TempSuite6999228720011403738.bed/._SUCCESS.crc
/tmp/adamTestMvnZqujfIH/TempSuite6999228720011403738.bed/.part-00000.crc
/tmp/adamTestMvnZqujfIH/TempSuite6999228720011403738.bed/part-00000
/tmp/adamTestMvnZqujfIH/TempSuite6999228720011403738.bed/_SUCCESS
/tmp/adamTestMvnZqujfIH/.TempSuite3521205548866066038.bam.crc
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/.part-00001.crc
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/.part-00003.crc
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/._SUCCESS.crc
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/part-00003
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/.part-00000.crc
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/part-00000
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/part-00002
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/_SUCCESS
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/part-00001
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite1268179272451852214.interval_list/.part-00002.crc
/tmp/adamTestMvnZqujfIH/TempSuite487423772063951504
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite3519255885174505319
/tmp/adamTestMvnZqujfIH/TempSuite3921321162544996033.bed
/tmp/adamTestMvnZqujfIH/TempSuite3921321162544996033.bed/._SUCCESS.crc
/tmp/adamTestMvnZqujfIH/TempSuite3921321162544996033.bed/.part-00000.crc
/tmp/adamTestMvnZqujfIH/TempSuite3921321162544996033.bed/part-00000
/tmp/adamTestMvnZqujfIH/TempSuite3921321162544996033.bed/_SUCCESS
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/.part-00001.crc
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/.part-00003.crc
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/._SUCCESS.crc
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/part-00003
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/.part-00000.crc
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/part-00000
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/part-00002
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/_SUCCESS
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/part-00001
/tmp/adamTestMvnZqujfIH/FeatureDatasetFunctionsSuite8908899759602532077.gff3/.part-00002.crc
/tmp/adamTestMvnZqujfIH/ordered.sam3918452418379867360.sam
rm -rf ${ADAM_MVN_TMP_DIR}
+ rm -rf /tmp/adamTestMvnZqujfIH

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/adamTestMvnZqujfIH: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/adamTestVmYb8t2

# Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR
ADAM_TMP_DIR=$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
+ ADAM_TMP_DIR=/tmp/adamTestVmYb8t2/deleteMePleaseThisIsNoLongerNeeded
mkdir $ADAM_TMP_DIR
+ mkdir /tmp/adamTestVmYb8t2/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/adamTestVmYb8t2/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/adamTestVmYb8t2/deleteMePleaseThisIsNoLongerNeeded

pushd $PROJECT_ROOT
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu

# Copy the jar into our temp space for testing
cp -r . $ADAM_TMP_DIR
+ cp -r . /tmp/adamTestVmYb8t2/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/label/ubuntu

pushd $ADAM_TMP_DIR
+ pushd /tmp/adamTestVmYb8t2/deleteMePleaseThisIsNoLongerNeeded
/tmp/adamTestVmYb8t2/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.5/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-2.4.5
    
# 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-2.4.5/spark-2.4.5-bin-without-hadoop-scala-2.12.tgz' -o spark-2.4.5-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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
curl: (60) SSL certificate problem: certificate has expired
More details here: https://curl.haxx.se/docs/sslcerts.html

curl performs SSL certificate verification by default, using a "bundle"
 of Certificate Authority (CA) public keys (CA certs). If the default
 bundle file isn't adequate, you can specify an alternate file
 using the --cacert option.
If this HTTPS server uses a certificate signed by a CA represented in
 the bundle, the certificate verification probably failed due to a
 problem with the certificate (it might be expired, or the name might
 not match the domain name in the URL).
If you'd like to turn off curl's verification of the certificate, use
 the -k (or --insecure) option.
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/aae35c9dae7d4ce6d90026a18937ae0fc9b4d685
Finished: FAILURE