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/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/._processing.avro.crc
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/.part-r-00001.gz.parquet.crc
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/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/._seqdict.avro.crc
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/_processing.avro
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/_SUCCESS
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/.part-r-00003.gz.parquet.crc
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/part-r-00003.gz.parquet
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/._metadata.crc
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/_rgdict.avro
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/_seqdict.avro
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/part-r-00001.gz.parquet
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/.part-r-00002.gz.parquet.crc
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/_metadata
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/._SUCCESS.crc
/tmp/adamTestMvnrnkJLLv/TempSuite3373747976960770658.adam/._common_metadata.crc
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite3776328390474544276
/tmp/adamTestMvnrnkJLLv/TempSuite6967921096721658454
/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam
/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam/._seqdict.avro.crc
/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam/_SUCCESS
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/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam/_seqdict.avro
/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam/_samples.avro
/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam/._SUCCESS.crc
/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam/._samples.avro.crc
/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam/._header.crc
/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam/_header
/tmp/adamTestMvnrnkJLLv/TempSuite5348942128209423884.adam/.part-00000-d7586d0e-42ec-44a8-b712-20ea3fc7f67f-c000.snappy.parquet.crc
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/_common_metadata
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/._rgdict.avro.crc
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/._processing.avro.crc
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/._seqdict.avro.crc
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/_processing.avro
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/_SUCCESS
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/._metadata.crc
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/_rgdict.avro
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/_seqdict.avro
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/_metadata
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/._SUCCESS.crc
/tmp/adamTestMvnrnkJLLv/TempSuite4718678525939326163.adam/._common_metadata.crc
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/.part-00003.crc
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/.part-00000.crc
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/_SUCCESS
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/part-00003
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/part-00000
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/part-00002
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/._SUCCESS.crc
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/.part-00002.crc
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/part-00001
/tmp/adamTestMvnrnkJLLv/FeatureRDDFunctionsSuite1241525699347320491.interval_list/.part-00001.crc
/tmp/adamTestMvnrnkJLLv/TempSuite4683620873629598445.bed
/tmp/adamTestMvnrnkJLLv/TempSuite4683620873629598445.bed/.part-00000.crc
/tmp/adamTestMvnrnkJLLv/TempSuite4683620873629598445.bed/_SUCCESS
/tmp/adamTestMvnrnkJLLv/TempSuite4683620873629598445.bed/part-00000
/tmp/adamTestMvnrnkJLLv/TempSuite4683620873629598445.bed/._SUCCESS.crc
/tmp/adamTestMvnrnkJLLv/1933248526255088905
/tmp/adamTestMvnrnkJLLv/1933248526255088905/ordered.sam
/tmp/adamTestMvnrnkJLLv/1933248526255088905/.ordered.sam.crc
/tmp/adamTestMvnrnkJLLv/2528104392410734631
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/_common_metadata
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/._rgdict.avro.crc
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/._processing.avro.crc
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/._seqdict.avro.crc
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/_processing.avro
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/_SUCCESS
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/._metadata.crc
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/_rgdict.avro
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/_seqdict.avro
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/_metadata
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/._SUCCESS.crc
/tmp/adamTestMvnrnkJLLv/2528104392410734631/predicate.2.adam/._common_metadata.crc
/tmp/adamTestMvnrnkJLLv/TempSuite1810490377302027737.adam
/tmp/adamTestMvnrnkJLLv/TempSuite1810490377302027737.adam/part-00000-f900d7fd-0cae-4e8e-a54a-3e19ecd48609-c000.snappy.parquet
/tmp/adamTestMvnrnkJLLv/TempSuite1810490377302027737.adam/.part-00000-f900d7fd-0cae-4e8e-a54a-3e19ecd48609-c000.snappy.parquet.crc
/tmp/adamTestMvnrnkJLLv/TempSuite1810490377302027737.adam/._seqdict.avro.crc
/tmp/adamTestMvnrnkJLLv/TempSuite1810490377302027737.adam/_SUCCESS
/tmp/adamTestMvnrnkJLLv/TempSuite1810490377302027737.adam/_seqdict.avro
/tmp/adamTestMvnrnkJLLv/TempSuite1810490377302027737.adam/._SUCCESS.crc
/tmp/adamTestMvnrnkJLLv/TempSuite1810490377302027737.adam/._header.crc
/tmp/adamTestMvnrnkJLLv/TempSuite1810490377302027737.adam/_header
rm -rf ${ADAM_MVN_TMP_DIR}
+ rm -rf /tmp/adamTestMvnrnkJLLv

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/adamTestMvnrnkJLLv:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

if test -n "$(git status --porcelain)"
then
    echo "Applying move_to_xyz script marred a pom.xml file."
    echo "Exiting..."
    exit 1
fi
git status --porcelain
++ git status --porcelain
+ test -n ''

# run integration tests
# prebuilt spark distributions are scala 2.11 for spark 2.x
if [[ ( ${SPARK_VERSION} == 2.2.1 && ${SCALAVER} == 2.11 ) ]];
then

    # make a temp directory
    ADAM_TMP_DIR=$(mktemp -d -t adamTestXXXXXXX)

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

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

    pushd $PROJECT_ROOT

    # Copy the jar into our temp space for testing
    cp -r . $ADAM_TMP_DIR
    popd

    pushd $ADAM_TMP_DIR

    # 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

    # set spark artifact string for downloading assembly
    SPARK=spark-${SPARK_VERSION}
    
    # download prepackaged spark assembly
    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}
    
    # set the path to the adam submit script
    ADAM=./bin/adam-submit

    # test running adam-shell
    ./bin/adam-shell -i scripts/jenkins-test-adam-shell.scala
    
    # add pyspark to the python path
    PY4J_ZIP="$(ls -1 "${SPARK_HOME}/python/lib" | grep py4j)"
    export PYTHONPATH=${SPARK_HOME}/python:${SPARK_HOME}/python/lib/${PY4J_ZIP}:${PYTHONPATH}

    # put adam jar on the pyspark path
    ASSEMBLY_DIR="${ADAM_TMP_DIR}/adam-assembly/target"
    ASSEMBLY_JAR="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
    export PYSPARK_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} pyspark-shell"

    # create a conda environment for python build, if necessary
    pythons=( 2.7 3.6 )

    for python in ${pythons[*]}
    do
	uuid=$(uuidgen)
	conda create -q -n adam-build-${uuid} python=2.7 anaconda
	source activate adam-build-${uuid}
	
	
	# we only support SparkR on Spark 2.x
	if [ ${SPARK_VERSION} == 2.2.1 ];
	then
	    
	    # make a directory to install SparkR into, and set the R user libs path
	    export R_LIBS_USER=${SPARK_HOME}/local_R_libs
	    mkdir -p ${R_LIBS_USER}
	    R CMD INSTALL \
	      -l ${R_LIBS_USER} \
	      ${SPARK_HOME}/R/lib/SparkR/
	    
	    export SPARKR_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} sparkr-shell"
	    
            # we can run the python build, now that we have a spark executable
	    # -DskipTests appears to skip the python/r tests?
	    mvn -U \
		-P python,r,distribution \
		package \
		-Dsuites=select.no.suites\* \
		-Dhadoop.version=${HADOOP_VERSION} \
		-Dspark.version=${SPARK_VERSION}

	    # make sure that the distribution package contains an egg
	    # if no assembly jar is found, this will exit with code 1 and fail the build
	    tar tzvf adam-distribution/target/adam-distribution*-bin.tar.gz | \
		grep bdgenomics.adam | \
		grep egg
	fi
	
	# run pyadam test
	./bin/pyadam < scripts/jenkins-test-pyadam.py
	
	# deactivate and remove the conda env
	source deactivate
	conda remove -n adam-build-${uuid} --all

	# copy python targets back
	cp -r adam-python/target ${PROJECT_ROOT}/adam-python/
    done
	
    # define filenames
    BAM=mouse_chrM.bam
    READS=${BAM}.reads.adam
    SORTED_READS=${BAM}.reads.sorted.adam
    FRAGMENTS=${BAM}.fragments.adam
    
    # fetch our input dataset
    echo "Fetching BAM file"
    rm -rf ${BAM}
    wget -q https://s3.amazonaws.com/bdgenomics-test/${BAM}

    # once fetched, convert BAM to ADAM
    echo "Converting BAM to ADAM read format"
    rm -rf ${READS}
    ${ADAM} transformAlignments ${BAM} ${READS}

    # then, sort the BAM
    echo "Converting BAM to ADAM read format with sorting"
    rm -rf ${SORTED_READS}
    ${ADAM} transformAlignments -sort_reads ${READS} ${SORTED_READS}

    # convert the reads to fragments to re-pair the reads
    echo "Converting read file to fragments"
    rm -rf ${FRAGMENTS}
    ${ADAM} transformFragments -load_as_reads ${READS} ${FRAGMENTS}

    # test that printing works
    echo "Printing reads and fragments"
    ${ADAM} print ${READS} 1>/dev/null 2>/dev/null
    ${ADAM} print ${FRAGMENTS} 1>/dev/null 2>/dev/null

    # run flagstat to verify that flagstat runs OK
    echo "Printing read statistics"
    ${ADAM} flagstat -print_metrics ${READS}
    rm -rf ${ADAM_TMP_DIR}
    popd
    
    # test that the source is formatted correctly
    # we had modified the poms to add a temp dir, so back out that modification first
    pushd ${PROJECT_ROOT}
    ./scripts/format-source
    if test -n "$(git status --porcelain)"
    then
        echo "Please run './scripts/format-source'"
        exit 1
    fi
    popd    
fi
+ [[ 2.2.1 == 2.2.1 ]]
+ [[ 2.11 == 2.11 ]]
mktemp -d -t adamTestXXXXXXX
++ mktemp -d -t adamTestXXXXXXX
+ ADAM_TMP_DIR=/tmp/adamTestLO0fYKr
+ ADAM_TMP_DIR=/tmp/adamTestLO0fYKr/deleteMePleaseThisIsNoLongerNeeded
+ mkdir /tmp/adamTestLO0fYKr/deleteMePleaseThisIsNoLongerNeeded
+ export TMPDIR=/tmp/adamTestLO0fYKr/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/adamTestLO0fYKr/deleteMePleaseThisIsNoLongerNeeded
+ pushd /home/jenkins/workspace/ADAM-ubuntu-testing/HADOOP_VERSION/2.7.3/SCALAVER/2.11/SPARK_VERSION/2.2.1/label/ubuntu/scripts/..
~/workspace/ADAM-ubuntu-testing/HADOOP_VERSION/2.7.3/SCALAVER/2.11/SPARK_VERSION/2.2.1/label/ubuntu ~/workspace/ADAM-ubuntu-testing/HADOOP_VERSION/2.7.3/SCALAVER/2.11/SPARK_VERSION/2.2.1/label/ubuntu
+ cp -r . /tmp/adamTestLO0fYKr/deleteMePleaseThisIsNoLongerNeeded
+ popd
~/workspace/ADAM-ubuntu-testing/HADOOP_VERSION/2.7.3/SCALAVER/2.11/SPARK_VERSION/2.2.1/label/ubuntu
+ pushd /tmp/adamTestLO0fYKr/deleteMePleaseThisIsNoLongerNeeded
/tmp/adamTestLO0fYKr/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-ubuntu-testing/HADOOP_VERSION/2.7.3/SCALAVER/2.11/SPARK_VERSION/2.2.1/label/ubuntu
+ [[ 2.7.3 =~ ^2\.6 ]]
+ [[ 2.7.3 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7
+ SPARK=spark-2.2.1
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.2.1/spark-2.2.1-bin-hadoop2.7.tgz' -o spark-2.2.1-bin-hadoop2.7.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   334  100   334    0     0   1052      0 --:--:-- --:--:-- --:--:--  1052
100   334  100   334    0     0   1052      0 --:--:-- --:--:-- --:--:--     0
+ tar xzvf spark-2.2.1-bin-hadoop2.7.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...
Finished: FAILURE