SuccessConsole Output

Started by upstream project "mango" build number 4536
originally caused by:
 Started by timer
[EnvInject] - Loading node environment variables.
Building remotely on research-jenkins-worker-07 (research-07 ubuntu) in workspace /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/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/heads/*:refs/remotes/origin/*
Checking out Revision 126d6b2fbb6773804f1d53a298b69a2cf355e35a (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 126d6b2fbb6773804f1d53a298b69a2cf355e35a
 > git rev-list 126d6b2fbb6773804f1d53a298b69a2cf355e35a # timeout=10
[ubuntu] $ /bin/bash /tmp/hudson1019415992408555500.sh
+ set -e
+ export JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ export CONDA_BIN=/home/anaconda/bin/
+ CONDA_BIN=/home/anaconda/bin/
+ export PATH=/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ set +x
+ /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test

# make a tempdir for writing maven cruft to
MANGO_MVN_TMP_DIR=$(mktemp -d -t mangoTestMvnXXXXXXX)
mktemp -d -t mangoTestMvnXXXXXXX
++ mktemp -d -t mangoTestMvnXXXXXXX
+ MANGO_MVN_TMP_DIR=/tmp/mangoTestMvn1mQYoFF

# make a temp directory for installing/downloading jars to
MANGO_TMP_DIR=$(mktemp -d -t mangoTestXXXXXXX)
mktemp -d -t mangoTestXXXXXXX
++ mktemp -d -t mangoTestXXXXXXX
+ MANGO_TMP_DIR=/tmp/mangoTestV15zb3b

MANGO_TMP_DIR=$MANGO_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
+ MANGO_TMP_DIR=/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded
mkdir $MANGO_TMP_DIR
+ mkdir /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded

# 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/mangoTestMvn1mQYoFF:g' '{}' ';'
find . -name "*.bak" -exec rm {} \;
+ find . -name '*.bak' -exec rm '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
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'
DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )
 cd $( dirname ${BASH_SOURCE[0]} ) && pwd 
 dirname ${BASH_SOURCE[0]} 
+++ dirname /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/..
VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g'
++ grep '<version>' /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.0.4-SNAPSHOT

# unique identifier for conda env
PYTHON_UUID=$(uuidgen)
uuidgen
++ uuidgen
+ PYTHON_UUID=a97b34cf-f97e-4130-9fb9-9e2e0f026bbe

# function that deletes conda environments and temporary environments
function clean_up {
    # deactivate and remove all mango associated conda envs
    source deactivate
    # delete conda env, if it exists
    conda remove -y --force --name mango-build-${PYTHON_UUID} --all || \
        echo "conda ENV mango-build-${PYTHON_UUID} does not exist"

    # delete tmp directories
    rm -rf ${MANGO_TMP_DIR}
    rm -rf ${MANGO_MVN_TMP_DIR}
}
trap clean_up EXIT
+ trap clean_up EXIT

# is the hadoop version set?
if ! [[ ${HADOOP_VERSION} ]];
then
    echo "HADOOP_VERSION environment variable is not set."
    echo "Please set this variable before running."

    exit 1
fi
+ [[ -n 2.7.5 ]]

# is the spark version set?
if ! [[ ${SPARK_VERSION} ]];
then
    echo "SPARK_VERSION environment variable is not set."
    echo "Please set this variable before running."

    exit 1
fi
+ [[ -n 2.4.4 ]]

set -e
+ set -e

# are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first
if [ ${SCALAVER} == 2.11 ];
then
    # shouldn't be able to move to scala 2.11 twice
    set +e
    ./scripts/move_to_scala_2.11.sh
    if [[ $? == 0 ]];
    then
        echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)."
        exit 1
    fi
    set -e
fi
+ '[' 2.11 == 2.11 ']'
+ set +e
+ ./scripts/move_to_scala_2.11.sh
Scala version is already set to 2.11 (Scala artifacts have _2.11 version suffix in artifact name).
Cowardly refusing to move to Scala 2.11 a second time...
+ [[ 1 == 0 ]]
+ set -e

# print versions
echo "Testing MANGO version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing MANGO version 0.0.4-SNAPSHOT on Spark 2.4.4 and Hadoop 2.7.5'
Testing MANGO version 0.0.4-SNAPSHOT on Spark 2.4.4 and Hadoop 2.7.5

# clean the targets first
mvn clean
+ mvn clean
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango
[INFO] mango: CORE
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ mango-parent ---
[INFO] Deleting /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CORE 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ mango-core ---
[INFO] Deleting /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CLI 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ mango-cli ---
[INFO] Deleting /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Assembly 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ mango-assembly ---
[INFO] Deleting /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  0.354 s]
[INFO] mango: CORE ........................................ SUCCESS [  0.040 s]
[INFO] mango: CLI ......................................... SUCCESS [  0.296 s]
[INFO] Mango: Assembly .................................... SUCCESS [  0.068 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.948 s
[INFO] Finished at: 2019-12-08T06:02:41-08:00
[INFO] Final Memory: 22M/1472M
[INFO] ------------------------------------------------------------------------

# clear distribution in case there are residual jars
rm -rf mango-distribution/target/
+ rm -rf mango-distribution/target/

# if this is a pull request, we need to set the coveralls pr id
if [[ ! -z $ghprbPullId ]];
then
    COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}"
fi
+ [[ ! -z '' ]]

# coveralls token should not be visible
set +x +v
+ set +x +v
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango
[INFO] mango: CORE
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent ---
[INFO] Modified 0 of 39 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-parent >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent ---
[INFO] Modified 0 of 39 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-parent ---
[INFO] Skipping SCoverage execution for project with packaging type 'pom'
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-parent ---
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-parent <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-parent ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CORE 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/classes at 1575813772208
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class AlignmentRecordMaterialization(@transient sc: SparkContext,
[WARNING]                                       ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class FeatureMaterialization(@transient sc: SparkContext,
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]                                                              @transient sc: SparkContext,
[WARNING]                                                               ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class VariantContextMaterialization(@transient sc: SparkContext,
[WARNING]                                      ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
[WARNING]     try {
[WARNING]     ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/converters/SAMRecordConverter.scala:145: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]       builder.setPrimaryAlignment(!samRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                              ^
[WARNING] warning: there were four feature warnings; re-run with -feature for details
[WARNING] 7 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 12 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala:-1: info: compiling
[INFO] Compiling 13 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes at 1575813786768
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala/org/bdgenomics/mango/models/LazyMaterializationSuite.scala:77: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class LazyDummy(@transient sc: SparkContext,
[WARNING]                  ^
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-core ---
Discovery starting.
Discovery completed in 477 milliseconds.
Run starting. Expected test count is: 72
DiscoverySuite:
2019-12-08 06:03:16 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2019-12-08 06:03:16 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-08 06:03:17 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-08 06:03:19 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed.idx...
- correctly gathers regions of occupancy from Feature file
- does not fail when no regions discovered
VariantContextMaterializationSuite:
2019-12-08 06:03:19 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
- Fetch from 1 vcf file with genotypes
- gets sample information
- Can extract json
2019-12-08 06:03:26 WARN  Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf.
- Can read Partitioned Parquet Genotypes
- correctly reassigns referenceName
2019-12-08 06:03:33 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf.idx...
- returns from file without genotypes
- more than 1 vcf file
- Should handle chromosomes with different prefixes
- fetches multiple regions from load
GenomeConfigSuite:
- Should read in genome path
- Should parse chrom sizes file
- Should parse refSeq.txt file
- Should fail when genome file does not exist
- should build genome
BamReaderSuite:
- Should load local bam file
- Gets file header
- loads all data when region is not specified
- Fails on files that are not bam or sam
- Should return empty on invalid chromosome
- Should return no data on empty dictionary
- Should load local sam file
- Should load local bam files with incorrect prefixes file
- Should load data from HDFS using Spark
- Should load http bam file
RefSeqSuite:
- Should convert refseq file to GA4GH genes
GA4GHutilSuite:
- create JSON from AlignmentRecordDataset
- create JSON from AlignmentRecordDataset with 1 sample
- create JSON from AlignmentRecordDataset with more than 1 sample
- create JSON with genotypes from VCF using GenotypeDataset
- create JSON without genotypes from VCF using VariantDataset
- create JSON from FeatureDataset
LazyMaterializationSuite:
- Should correctly reassigns chr prefix
2019-12-08 06:03:46 WARN  Bookkeep:66 - bookkeeping queue is empty
2019-12-08 06:03:46 WARN  LazyDummy:247 - memory limit exceeded. Dropping null from cache
2019-12-08 06:03:46 WARN  LazyDummy:247 - memory limit exceeded. Dropping chrM from cache
- Should check and clear memory
FeatureMaterializationSuite:
- assert raw data returns from one block
2019-12-08 06:03:47 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed.idx...
- can fetch multiple files
- Should handle chromosomes with different prefixes
- fetches multiple regions from load
BookkeepSuite:
- remembers new regions
- adds new regions to existing chromosomes
- adds new chromosome
- merges regions
- saves sequence dictionary
- get and put region where region equals chunk size
AlignmentRecordMaterializationSuite:
- create new AlignmentRecordMaterialization
- return raw data from AlignmentRecordMaterialization
- can process stringified data
- Read Partitioned Data
- fetches multiple regions from load
- Should handle chromosomes with different prefixes
- should get data from unindexed file when referenceName predicates do not match
2019-12-08 06:04:07 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak.idx...
BedReaderSuite:
- Should load local bed file
- Should load all records when region is not specified
- Fails on files that are not bed format
- Should return empty on invalid chromosome
- Should load local narrowPeak file
- Should load local bed files with incorrect prefixes file
- Should load data from HDFS using Spark
- Should load remote bed file
2019-12-08 06:04:08 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz.tbi...
VcfReaderSuite:
- Should load local vcf file
- Gets file header
2019-12-08 06:04:08 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz.tbi...
2019-12-08 06:04:08 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.idx...
- Should load bgz file
2019-12-08 06:04:08 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz.tbi...
- Should load compressed bgz file
- Should load all records when region is not defined
- Fails on files that are not vcf or vcf.gz
- Should return empty on invalid chromosome
- Should load local vcf files with incorrect prefixes file
- Should load genotypes
- loads gzipped vcfs
2019-12-08 06:04:09 WARN  VCFInputFormat:410 - No tabix index file found for file:/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.tbi, splits will not be filtered, which may be very inefficient
- Should load data from HDFS using Spark
- Should load http vcf file
Run completed in 58 seconds, 342 milliseconds.
Total number of tests run: 72
Suites: completed 13, aborted 0
Tests: succeeded 72, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-core >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-core ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/scoverage-classes at 1575813856242
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class AlignmentRecordMaterialization(@transient sc: SparkContext,
[WARNING]                                       ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class FeatureMaterialization(@transient sc: SparkContext,
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]                                                              @transient sc: SparkContext,
[WARNING]                                                               ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class VariantContextMaterialization(@transient sc: SparkContext,
[WARNING]                                      ^
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
[WARNING]     try {
[WARNING]     ^
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [1611 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scoverage-data]
[WARNING] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/converters/SAMRecordConverter.scala:145: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]       builder.setPrimaryAlignment(!samRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                              ^
[WARNING] warning: there were four feature warnings; re-run with -feature for details
[WARNING] 7 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 10 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-core ---
Discovery starting.
Discovery completed in 434 milliseconds.
Run starting. Expected test count is: 72
DiscoverySuite:
2019-12-08 06:04:28 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2019-12-08 06:04:28 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-08 06:04:29 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-08 06:04:30 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed.idx...
- correctly gathers regions of occupancy from Feature file
- does not fail when no regions discovered
VariantContextMaterializationSuite:
2019-12-08 06:04:30 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
- Fetch from 1 vcf file with genotypes
- gets sample information
- Can extract json
2019-12-08 06:04:35 WARN  Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf.
- Can read Partitioned Parquet Genotypes
- correctly reassigns referenceName
2019-12-08 06:04:42 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf.idx...
- returns from file without genotypes
- more than 1 vcf file
- Should handle chromosomes with different prefixes
- fetches multiple regions from load
GenomeConfigSuite:
- Should read in genome path
- Should parse chrom sizes file
- Should parse refSeq.txt file
- Should fail when genome file does not exist
- should build genome
BamReaderSuite:
- Should load local bam file
- Gets file header
- loads all data when region is not specified
- Fails on files that are not bam or sam
- Should return empty on invalid chromosome
- Should return no data on empty dictionary
- Should load local sam file
- Should load local bam files with incorrect prefixes file
- Should load data from HDFS using Spark
- Should load http bam file
RefSeqSuite:
- Should convert refseq file to GA4GH genes
GA4GHutilSuite:
- create JSON from AlignmentRecordDataset
- create JSON from AlignmentRecordDataset with 1 sample
- create JSON from AlignmentRecordDataset with more than 1 sample
- create JSON with genotypes from VCF using GenotypeDataset
- create JSON without genotypes from VCF using VariantDataset
- create JSON from FeatureDataset
LazyMaterializationSuite:
- Should correctly reassigns chr prefix
2019-12-08 06:05:01 WARN  Bookkeep:66 - bookkeeping queue is empty
2019-12-08 06:05:01 WARN  LazyDummy:247 - memory limit exceeded. Dropping null from cache
2019-12-08 06:05:01 WARN  LazyDummy:247 - memory limit exceeded. Dropping chrM from cache
- Should check and clear memory
FeatureMaterializationSuite:
- assert raw data returns from one block
2019-12-08 06:05:01 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed.idx...
- can fetch multiple files
- Should handle chromosomes with different prefixes
- fetches multiple regions from load
BookkeepSuite:
- remembers new regions
- adds new regions to existing chromosomes
- adds new chromosome
- merges regions
- saves sequence dictionary
- get and put region where region equals chunk size
AlignmentRecordMaterializationSuite:
- create new AlignmentRecordMaterialization
- return raw data from AlignmentRecordMaterialization
- can process stringified data
- Read Partitioned Data
- fetches multiple regions from load
- Should handle chromosomes with different prefixes
- should get data from unindexed file when referenceName predicates do not match
2019-12-08 06:05:35 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak.idx...
BedReaderSuite:
- Should load local bed file
- Should load all records when region is not specified
- Fails on files that are not bed format
- Should return empty on invalid chromosome
- Should load local narrowPeak file
- Should load local bed files with incorrect prefixes file
- Should load data from HDFS using Spark
- Should load remote bed file
2019-12-08 06:05:36 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz.tbi...
VcfReaderSuite:
- Should load local vcf file
- Gets file header
2019-12-08 06:05:36 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz.tbi...
2019-12-08 06:05:36 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.idx...
- Should load bgz file
2019-12-08 06:05:36 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz.tbi...
- Should load compressed bgz file
- Should load all records when region is not defined
- Fails on files that are not vcf or vcf.gz
- Should return empty on invalid chromosome
- Should load local vcf files with incorrect prefixes file
- Should load genotypes
- loads gzipped vcfs
2019-12-08 06:05:37 WARN  VCFInputFormat:410 - No tabix index file found for file:/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.tbi, splits will not be filtered, which may be very inefficient
- Should load data from HDFS using Spark
- Should load http vcf file
Run completed in 1 minute, 13 seconds.
Total number of tests run: 72
Suites: completed 13, aborted 0
Tests: succeeded 72, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-core <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-core ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CLI 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/classes at 1575813944359
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes at 1575813952594
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
Discovery starting.
Discovery completed in 709 milliseconds.
Run starting. Expected test count is: 31
MangoMainSuite:
- default command groups is non empty
- module provides default command groups
- inject default command groups when called via main
- command groups is empty when called via apply
- single command group
- add new command group to default command groups
- module restores default command groups when called via apply
- custom module with single command group
- custom module with new command group added to default command groups
VizReadsSuite:
2019-12-08 06:06:03 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2019-12-08 06:06:03 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-08 06:06:03 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-08 06:06:06 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
2019-12-08 06:06:06 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx...
2019-12-08 06:06:06 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx...
- Should pass for discovery mode
Could not load resource: [/WEB-INF/layouts/browser.ssp]
Could not load resource: [/WEB-INF/layouts/overall.ssp]
- Should get browser and overall template information
- should return reads
- Should throw error when reads do not exist
- Reads should throw NotFound error on invalid reference
- should not return reads with invalid key
- /variants/:key/:ref
- should not return variants with invalid key
- Should throw error when variants do not exist
- /features/:key/:ref
- should not return features with invalid key
- Should throw error when features do not exist
- Features should throw out of bounds error on invalid reference
- gets coverage from feature endpoint
- should not return coverage with invalid key
- Should return coverage and features
- gets genes
- Coverage should throw out of bounds error on invalid reference
- Should trigger requests for http files
2019-12-08 06:06:48 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.idx...
- should run example files
MakeGenomeSuite:
Exception in thread "Thread-124" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-136" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
2019-12-08 06:06:54 WARN  GenomeConfig:141 - No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1
- creates genome
- fails with invalid genome
Run completed in 56 seconds, 218 milliseconds.
Total number of tests run: 31
Suites: completed 4, aborted 0
Tests: succeeded 31, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-cli >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-cli ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/scoverage-classes at 1575814018053
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [895 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
Discovery starting.
Discovery completed in 606 milliseconds.
Run starting. Expected test count is: 31
MangoMainSuite:
- default command groups is non empty
- module provides default command groups
- inject default command groups when called via main
- command groups is empty when called via apply
- single command group
- add new command group to default command groups
- module restores default command groups when called via apply
- custom module with single command group
- custom module with new command group added to default command groups
VizReadsSuite:
2019-12-08 06:07:08 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2019-12-08 06:07:08 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-08 06:07:08 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-08 06:07:11 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
2019-12-08 06:07:12 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx...
2019-12-08 06:07:12 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx...
- Should pass for discovery mode
Could not load resource: [/WEB-INF/layouts/browser.ssp]
Could not load resource: [/WEB-INF/layouts/overall.ssp]
- Should get browser and overall template information
- should return reads
- Should throw error when reads do not exist
- Reads should throw NotFound error on invalid reference
- should not return reads with invalid key
- /variants/:key/:ref
- should not return variants with invalid key
- Should throw error when variants do not exist
- /features/:key/:ref
- should not return features with invalid key
- Should throw error when features do not exist
- Features should throw out of bounds error on invalid reference
- gets coverage from feature endpoint
- should not return coverage with invalid key
- Should return coverage and features
- gets genes
- Coverage should throw out of bounds error on invalid reference
- Should trigger requests for http files
2019-12-08 06:08:21 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.idx...
- should run example files
MakeGenomeSuite:
Exception in thread "Thread-124" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-136" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
2019-12-08 06:08:25 WARN  GenomeConfig:141 - No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1
- creates genome
- fails with invalid genome
Run completed in 1 minute, 22 seconds.
Total number of tests run: 31
Suites: completed 4, aborted 0
Tests: succeeded 31, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-cli <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-cli ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Assembly 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scala-2.11.12/classes at 1575814112211
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-assembly >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-assembly ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scala-2.11.12/scoverage-classes at 1575814114158
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [0 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-assembly ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-assembly <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-assembly ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ mango-parent ---
[INFO] Starting Coveralls job for jenkins (4536 / https://amplab.cs.berkeley.edu/jenkins/job/mango/HADOOP_VERSION=2.7.5,SCALAVER=2.11,SPARK_VERSION=2.4.4,label=ubuntu/4536/)
[INFO] Using repository token <secret>
[INFO] Git commit 126d6b2 in master
[INFO] Writing Coveralls data to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/target/coveralls.json...
[INFO] Processing coverage report from /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 156ms
[INFO] Gathered code coverage metrics for 21 source files with 4008 lines of code:
[INFO] - 1110 relevant lines
[INFO] - 890 covered lines
[INFO] - 220 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 525ms for Job #4536.1
[INFO] https://coveralls.io/jobs/56606479
[INFO] *** It might take hours for Coveralls to update the actual coverage numbers for a job
[INFO]     If you see question marks in the report, please be patient
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  1.517 s]
[INFO] mango: CORE ........................................ SUCCESS [02:56 min]
[INFO] mango: CLI ......................................... SUCCESS [02:46 min]
[INFO] Mango: Assembly .................................... SUCCESS [  7.111 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:56 min
[INFO] Finished at: 2019-12-08T06:08:38-08:00
[INFO] Final Memory: 63M/1470M
[INFO] ------------------------------------------------------------------------

# if those pass, build the distribution package
mvn -U \
    -P distribution \
    package \
    -DskipTests \
    -Dhadoop.version=${HADOOP_VERSION} \
    -Dspark.version=${SPARK_VERSION} \
    -DargLine=${MANGO_MVN_TMP_DIR}
+ mvn -U -P distribution package -DskipTests -Dhadoop.version=2.7.5 -Dspark.version=2.4.4 -DargLine=/tmp/mangoTestMvn1mQYoFF
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango
[INFO] mango: CORE
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO] mango: Distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent ---
[INFO] Modified 0 of 39 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CORE 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-core ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-core ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-core >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-core <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class AlignmentRecordMaterialization(@transient sc: SparkContext,
                                      ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class FeatureMaterialization(@transient sc: SparkContext,
                              ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
                                                             @transient sc: SparkContext,
                                                              ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class VariantContextMaterialization(@transient sc: SparkContext,
                                     ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
    try {
    ^
warning: there were four feature warnings; re-run with -feature for details
model contains 42 documentable templates
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/RefSeq.scala:29: warning: Variable GENOME undefined in comment for object RefSeqFile in object RefSeqFile
 * Processes refSeq file, downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                     ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                  ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                                    ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:51: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz
                                                                                   ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:52: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - refSeq.txt file: downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                 ^
11 warnings found
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CLI 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- sass-maven-plugin:3.7.1:update-stylesheets (default) @ mango-cli ---
[INFO] Checked 0 files for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/sass
[INFO] Checked 0 filtered (**/*.css) files for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT/css
[INFO] Compiling Sass templates
[INFO] Queueing Sass template for compile: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets => /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets
Ignoring eventmachine-1.2.7 because its extensions are not built. Try: gem pristine eventmachine --version 1.2.7
Ignoring ffi-1.9.25 because its extensions are not built. Try: gem pristine ffi --version 1.9.25
Ignoring http_parser.rb-0.6.0 because its extensions are not built. Try: gem pristine http_parser.rb --version 0.6.0
[INFO]     >> /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.scss => /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.css
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (Run `npm install`) @ mango-cli ---
npm WARN mango-cli@0.0.2 No repository field.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:copy-resources (copy-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8760 resources
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-cli ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-cli ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-cli ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-cli >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-cli <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
model contains 26 documentable templates
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- appassembler-maven-plugin:1.10:assemble (default) @ mango-cli ---
[INFO] Installing artifact /home/jenkins/.m2/repository/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro/1.8.2/avro-1.8.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro/1.8.2/avro-1.8.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/tukaani/xz/1.5/xz-1.5.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-codec/commons-codec/1.4/commons-codec-1.4.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-pool/commons-pool/1.6/commons-pool-1.6.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-pool/commons-pool/1.6/commons-pool-1.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli-spark2_2.11/0.29.0/adam-cli-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli-spark2_2.11/0.29.0/adam-cli-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-apis-spark2_2.11/0.29.0/adam-apis-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis-spark2_2.11/0.29.0/adam-apis-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/args4j/args4j/2.33/args4j-2.33.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/args4j/args4j/2.33/args4j-2.33.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/guice/4.2.0/guice-4.2.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/inject/guice/4.2.0/guice-4.2.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/javax/inject/javax.inject/1/javax.inject-1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/aopalliance/aopalliance/1.0/aopalliance-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-core-spark2_2.11/0.29.0/adam-core-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core-spark2_2.11/0.29.0/adam-core-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/objenesis/objenesis/2.1/objenesis-2.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/objenesis/objenesis/2.1/objenesis-2.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-io/commons-io/2.6/commons-io-2.6.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-io/commons-io/2.6/commons-io-2.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.29.0/adam-codegen-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.29.0/adam-codegen-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.14.0/bdg-formats-0.14.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.14.0/bdg-formats-0.14.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar
[INFO] Installing artifact /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-ga4gh/0.8.0/convert-ga4gh-0.8.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.8.0/convert-ga4gh-0.8.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.8.0/convert-htsjdk-0.8.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.8.0/convert-htsjdk-0.8.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.8.0/convert-0.8.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.8.0/convert-0.8.0.jar
[INFO] Installing artifact /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli/0.0.4-SNAPSHOT/mango-cli-0.0.4-SNAPSHOT.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Assembly 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ mango-assembly ---
[INFO] Including org.bdgenomics.mango:mango-cli:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.3 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.14.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
[INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra.rl:rl_2.11:jar:0.4.10 in the shaded jar.
[INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar.
[INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar.
[INFO] Including joda-time:joda-time:jar:2.9.1 in the shaded jar.
[INFO] Including org.joda:joda-convert:jar:1.8.1 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.5 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.11.12 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.8.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.8.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.8.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.8.1 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] mango-cli-0.0.4-SNAPSHOT.jar, adam-cli-spark2_2.11-0.29.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar with /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: Distribution 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.4.1:single (default) @ mango-distribution ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
[INFO] Building tar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  3.517 s]
[INFO] mango: CORE ........................................ SUCCESS [ 16.089 s]
[INFO] mango: CLI ......................................... SUCCESS [ 29.629 s]
[INFO] Mango: Assembly .................................... SUCCESS [ 21.155 s]
[INFO] mango: Distribution ................................ SUCCESS [ 27.749 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:38 min
[INFO] Finished at: 2019-12-08T06:10:18-08:00
[INFO] Final Memory: 93M/1490M
[INFO] ------------------------------------------------------------------------

# make sure that the distribution package contains an assembly jar
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzvf mango-distribution/target/mango-distribution*-bin.tar.gz | \
    grep mango-assembly | \
    grep jar | \
    grep -v -e sources -e javadoc
+ grep mango-assembly
+ tar tzvf mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
+ grep jar
+ grep -v -e sources -e javadoc
-rw-r--r-- jenkins/jenkins 93389288 2019-12-08 06:09 mango-distribution-0.0.4-SNAPSHOT/repo/mango-assembly-0.0.4-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvn1mQYoFF
/tmp/mangoTestMvn1mQYoFF
/tmp/mangoTestMvn1mQYoFF/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvn1mQYoFF/5528208307459449753
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877
/tmp/mangoTestMvn1mQYoFF/283464730722645427
/tmp/mangoTestMvn1mQYoFF/283464730722645427/anoGam1.genome
/tmp/mangoTestMvn1mQYoFF/3347076886879908130
/tmp/mangoTestMvn1mQYoFF/3347076886879908130/anoGam1.genome
/tmp/mangoTestMvn1mQYoFF/invalidBuild.genome606334396618787128
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/_SUCCESS
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/._references.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/referenceName=1
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/referenceName=1/positionBin=0/part-00000-a2f5b7c7-34fa-4c73-b7e3-b349fb27b12d.c000.snappy.parquet
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/referenceName=1/positionBin=0/.part-00000-a2f5b7c7-34fa-4c73-b7e3-b349fb27b12d.c000.snappy.parquet.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/._samples.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/_partitionedByStartPos
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/_references.avro
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/._header.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/._SUCCESS.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/_samples.avro
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459.adam/_header
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/_SUCCESS
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/._references.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/referenceName=1
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/referenceName=1/positionBin=0/.part-00000-7c2df2de-8f63-49b1-b39b-f791e5ddc8e6.c000.snappy.parquet.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/referenceName=1/positionBin=0/part-00000-7c2df2de-8f63-49b1-b39b-f791e5ddc8e6.c000.snappy.parquet
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/._samples.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/_partitionedByStartPos
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/_references.avro
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/._header.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/._SUCCESS.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/_samples.avro
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497.adam/_header
/tmp/mangoTestMvn1mQYoFF/invalidBuild.genome3195532210785163279
/tmp/mangoTestMvn1mQYoFF/genomes2630983282036510008
/tmp/mangoTestMvn1mQYoFF/genomes2630983282036510008/hg19.genome
/tmp/mangoTestMvn1mQYoFF/mmbroken6416022689827956995.genome
/tmp/mangoTestMvn1mQYoFF/TempSuite6825886412586488497
/tmp/mangoTestMvn1mQYoFF/genomes1464431821665068596
/tmp/mangoTestMvn1mQYoFF/genomes1464431821665068596/hg19.genome
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/_SUCCESS
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/._references.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=1
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=1/positionBin=26/.part-00000-ed041238-9ae9-48cb-9d2a-980bb2dd21e5.c000.snappy.parquet.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=1/positionBin=26/part-00000-ed041238-9ae9-48cb-9d2a-980bb2dd21e5.c000.snappy.parquet
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=1/positionBin=240/.part-00000-ed041238-9ae9-48cb-9d2a-980bb2dd21e5.c000.snappy.parquet.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=1/positionBin=240/part-00000-ed041238-9ae9-48cb-9d2a-980bb2dd21e5.c000.snappy.parquet
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/_readGroups.avro
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/_partitionedByStartPos
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/_references.avro
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/._SUCCESS.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/._readGroups.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=2
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=2/positionBin=189/.part-00000-ed041238-9ae9-48cb-9d2a-980bb2dd21e5.c000.snappy.parquet.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/referenceName=2/positionBin=189/part-00000-ed041238-9ae9-48cb-9d2a-980bb2dd21e5.c000.snappy.parquet
/tmp/mangoTestMvn1mQYoFF/TempSuite5660462503481748877.adam/_processingSteps.avro
/tmp/mangoTestMvn1mQYoFF/mmbroken3915532221606893738.genome
/tmp/mangoTestMvn1mQYoFF/TempSuite5541074068897557459
/tmp/mangoTestMvn1mQYoFF/4968407140995771513
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/_SUCCESS
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/._references.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=1
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=1/positionBin=26/.part-00000-ba2a23f0-f7f1-4c2d-a7ea-cce3d340dec9.c000.snappy.parquet.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=1/positionBin=26/part-00000-ba2a23f0-f7f1-4c2d-a7ea-cce3d340dec9.c000.snappy.parquet
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=1/positionBin=240/.part-00000-ba2a23f0-f7f1-4c2d-a7ea-cce3d340dec9.c000.snappy.parquet.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=1/positionBin=240/part-00000-ba2a23f0-f7f1-4c2d-a7ea-cce3d340dec9.c000.snappy.parquet
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/_readGroups.avro
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/_partitionedByStartPos
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/_references.avro
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/._SUCCESS.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/._readGroups.avro.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=2
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=2/positionBin=189/.part-00000-ba2a23f0-f7f1-4c2d-a7ea-cce3d340dec9.c000.snappy.parquet.crc
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/referenceName=2/positionBin=189/part-00000-ba2a23f0-f7f1-4c2d-a7ea-cce3d340dec9.c000.snappy.parquet
/tmp/mangoTestMvn1mQYoFF/TempSuite2570326039475510559.adam/_processingSteps.avro
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvn1mQYoFF

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${MANGO_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/mangoTestMvn1mQYoFF:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

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

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

    pushd $PROJECT_ROOT

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

    pushd $MANGO_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=${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}

    # create a conda environment for python build, if necessary
    pythons=( 3.6 )
    for python in ${pythons[*]}
    do
        conda create -y -q -n mango-build-${PYTHON_UUID} python=${python} pip
        source activate mango-build-${PYTHON_UUID}

        # install npm and node in the venv for mango-viz
        conda install -y nodejs

        # prepare mango python
        pushd mango-python
        make prepare
        popd

        # we can run the python build, now that we have a spark executable
        mvn -U \
            -P python,distribution \
            package \
            -DskipTests \
            -Dhadoop.version=${HADOOP_VERSION} \
            -Dspark.version=${SPARK_VERSION}

        # clean mango python
        pushd mango-python
        make clean
        popd

        # prepare mango viz
        pushd mango-viz
        make prepare
        popd

        # run the widgets tests (mango-viz)
        mvn -P widgets test

        # clean mango viz
        pushd mango-viz
        make clean
        popd

        # 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 mango-distribution/target/mango-distribution*-bin.tar.gz | \
            grep bdgenomics.mango | \
            grep egg

        # test mango notebook, output to temporary log file
        MANGO_NOTEBOOK_LOGS=${MANGO_TMP_DIR}/mango-notebook.log
        bash -xv ${PROJECT_ROOT}/bin/mango-notebook  &> ${MANGO_NOTEBOOK_LOGS} &

        # sleep for 2 seconds to let mango-notebook start up
        sleep 2

        # if mango-notebook fails, then trying to kill the process will fail
        if kill $! ; then
            echo "Mango Notebook Succeeded"
        else
            echo "Mango Notebook failed with logs:"
            cat ${MANGO_NOTEBOOK_LOGS}
            exit 1
        fi

        # copy python targets back
        cp -r mango-python/target ${PROJECT_ROOT}/mango-python/

        # deactivate and remove the conda env
        source deactivate
        conda remove -y --name mango-build-${PYTHON_UUID} --all

    done

    # test mango submit
    MANGO_BROWSER_LOGS=${MANGO_TMP_DIR}/mango-submit.log
    bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS} &

    # sleep for 10 seconds to let mango-browser start up
    sleep 10

    # make sure server responds to POST for reads and variants
    curl -s -N \
    --header "Content-type: application/json" \
    --request POST \
    --data "{\"pageToken\":null,\"pageSize\":200,\"readGroupIds\":[\"chr17_7500000-7515000_sam\"],\"referenceId\":\"chr17\",\"start\":1,\"end\":100}"  \
    http://localhost:8080/reads/search | grep alignments

    if [[ $? != 0 ]]; then
        echo "invalid alignments"
        exit 1
    fi

    curl -s -N \
        --header "Content-type: application/json" \
        --request POST \
        --data "{\"variantSetId\":\"ALL_chr17_7500000-7515000_phase3_shapeit2_mvncall_integrated_v5a_20130502_genotypes_vcf\",\"pageToken\":null,\"pageSize\":400,\"referenceName\":\"chr17\",\"callSetIds\":[],\"start\":7500000,\"end\":7515000}"  \
        http://localhost:8080/variants/search | grep variants

    if [[ $? != 0 ]]; then
        echo "invalid variants"
        exit 1
    fi

    # get processes with mango prefix
    PROCESSES=( $(ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }') )

    # There should be processes running for mango-browser
    if [ "${#PROCESSES[@]}" -gt 0 ] ; then
        echo "Mango Browser Succeeded"
        # kill all Mango Browser related processes
        kill ${PROCESSES}; 
    else
        echo "Mango Browser failed with logs:"
        cat ${MANGO_BROWSER_LOGS}
        exit 1
    fi

    # test genome builds
    TEST_GENOME="anoGam1"
    bash -xv ${PROJECT_ROOT}/bin/make_genome ${TEST_GENOME} ${MANGO_TMP_DIR}

    unzip ${MANGO_TMP_DIR}/${TEST_GENOME}.genome -d ${MANGO_TMP_DIR}/${TEST_GENOME}

    pushd ${MANGO_TMP_DIR}/${TEST_GENOME}
    cat properties.txt
    cat ${TEST_GENOME}.chrom.sizes
    popd
fi
+ [[ 2.11 == 2.11 ]]
+ export TMPDIR=/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded
+ pushd /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/..
~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ cp -r . /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded
+ popd
~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ pushd /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ [[ 2.7.5 =~ ^2\.6 ]]
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7
+ SPARK=spark-2.4.4
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.4/spark-2.4.4-bin-hadoop2.7.tgz' -o spark-2.4.4-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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

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+ tar xzvf spark-2.4.4-bin-hadoop2.7.tgz
spark-2.4.4-bin-hadoop2.7/
spark-2.4.4-bin-hadoop2.7/R/
spark-2.4.4-bin-hadoop2.7/R/lib/
spark-2.4.4-bin-hadoop2.7/R/lib/sparkr.zip
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/INDEX
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/html/
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/html/R.css
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/html/00Index.html
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/help/
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/help/aliases.rds
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/help/AnIndex
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdx
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdb
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/help/paths.rds
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/worker/
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/worker/worker.R
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/worker/daemon.R
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/tests/
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/tests/testthat/
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/tests/testthat/test_basic.R
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/profile/
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/profile/shell.R
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/profile/general.R
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/R/
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdx
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdb
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/R/SparkR
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/Meta/
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/Meta/nsInfo.rds
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/Meta/links.rds
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/Meta/hsearch.rds
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/Meta/Rd.rds
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/Meta/features.rds
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/Meta/package.rds
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/DESCRIPTION
spark-2.4.4-bin-hadoop2.7/R/lib/SparkR/NAMESPACE
spark-2.4.4-bin-hadoop2.7/sbin/
spark-2.4.4-bin-hadoop2.7/sbin/stop-shuffle-service.sh
spark-2.4.4-bin-hadoop2.7/sbin/start-thriftserver.sh
spark-2.4.4-bin-hadoop2.7/sbin/start-slave.sh
spark-2.4.4-bin-hadoop2.7/sbin/start-shuffle-service.sh
spark-2.4.4-bin-hadoop2.7/sbin/start-mesos-shuffle-service.sh
spark-2.4.4-bin-hadoop2.7/sbin/start-master.sh
spark-2.4.4-bin-hadoop2.7/sbin/start-history-server.sh
spark-2.4.4-bin-hadoop2.7/sbin/spark-config.sh
spark-2.4.4-bin-hadoop2.7/sbin/stop-thriftserver.sh
spark-2.4.4-bin-hadoop2.7/sbin/stop-slaves.sh
spark-2.4.4-bin-hadoop2.7/sbin/stop-slave.sh
spark-2.4.4-bin-hadoop2.7/sbin/stop-mesos-shuffle-service.sh
spark-2.4.4-bin-hadoop2.7/sbin/stop-mesos-dispatcher.sh
spark-2.4.4-bin-hadoop2.7/sbin/stop-master.sh
spark-2.4.4-bin-hadoop2.7/sbin/stop-history-server.sh
spark-2.4.4-bin-hadoop2.7/sbin/stop-all.sh
spark-2.4.4-bin-hadoop2.7/sbin/start-slaves.sh
spark-2.4.4-bin-hadoop2.7/sbin/start-mesos-dispatcher.sh
spark-2.4.4-bin-hadoop2.7/sbin/start-all.sh
spark-2.4.4-bin-hadoop2.7/sbin/spark-daemons.sh
spark-2.4.4-bin-hadoop2.7/sbin/spark-daemon.sh
spark-2.4.4-bin-hadoop2.7/sbin/slaves.sh
spark-2.4.4-bin-hadoop2.7/python/
spark-2.4.4-bin-hadoop2.7/python/dist/
spark-2.4.4-bin-hadoop2.7/python/pyspark.egg-info/
spark-2.4.4-bin-hadoop2.7/python/pyspark.egg-info/SOURCES.txt
spark-2.4.4-bin-hadoop2.7/python/pyspark.egg-info/dependency_links.txt
spark-2.4.4-bin-hadoop2.7/python/pyspark.egg-info/top_level.txt
spark-2.4.4-bin-hadoop2.7/python/pyspark.egg-info/PKG-INFO
spark-2.4.4-bin-hadoop2.7/python/pyspark.egg-info/requires.txt
spark-2.4.4-bin-hadoop2.7/python/README.md
spark-2.4.4-bin-hadoop2.7/python/MANIFEST.in
spark-2.4.4-bin-hadoop2.7/python/setup.py
spark-2.4.4-bin-hadoop2.7/python/run-tests.py
spark-2.4.4-bin-hadoop2.7/python/run-tests-with-coverage
spark-2.4.4-bin-hadoop2.7/python/test_support/
spark-2.4.4-bin-hadoop2.7/python/test_support/userlibrary.py
spark-2.4.4-bin-hadoop2.7/python/test_support/userlib-0.1.zip
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/text-test.txt
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/streaming/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/streaming/text-test.txt
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/people_array_utf16le.json
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/people_array.json
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/people1.json
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/people.json
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/part-r-00007.gz.parquet
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/.part-r-00007.gz.parquet.crc
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/part-r-00005.gz.parquet
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/.part-r-00005.gz.parquet.crc
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/part-r-00004.gz.parquet
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/part-r-00002.gz.parquet
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/.part-r-00004.gz.parquet.crc
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/.part-r-00002.gz.parquet.crc
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/part-r-00008.gz.parquet
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/.part-r-00008.gz.parquet.crc
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/_metadata
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/_common_metadata
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/_SUCCESS
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/c=1/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/c=1/part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/c=1/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/c=0/
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/c=0/part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/c=0/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/orc_partitioned/_SUCCESS
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/ages_newlines.csv
spark-2.4.4-bin-hadoop2.7/python/test_support/sql/ages.csv
spark-2.4.4-bin-hadoop2.7/python/test_support/hello/
spark-2.4.4-bin-hadoop2.7/python/test_support/hello/sub_hello/
spark-2.4.4-bin-hadoop2.7/python/test_support/hello/sub_hello/sub_hello.txt
spark-2.4.4-bin-hadoop2.7/python/test_support/hello/hello.txt
spark-2.4.4-bin-hadoop2.7/python/test_support/SimpleHTTPServer.py
spark-2.4.4-bin-hadoop2.7/python/test_coverage/
spark-2.4.4-bin-hadoop2.7/python/test_coverage/sitecustomize.py
spark-2.4.4-bin-hadoop2.7/python/test_coverage/coverage_daemon.py
spark-2.4.4-bin-hadoop2.7/python/test_coverage/conf/
spark-2.4.4-bin-hadoop2.7/python/test_coverage/conf/spark-defaults.conf
spark-2.4.4-bin-hadoop2.7/python/setup.cfg
spark-2.4.4-bin-hadoop2.7/python/run-tests
spark-2.4.4-bin-hadoop2.7/python/pyspark/
spark-2.4.4-bin-hadoop2.7/python/pyspark/python/
spark-2.4.4-bin-hadoop2.7/python/pyspark/python/pyspark/
spark-2.4.4-bin-hadoop2.7/python/pyspark/python/pyspark/shell.py
spark-2.4.4-bin-hadoop2.7/python/pyspark/shuffle.py
spark-2.4.4-bin-hadoop2.7/python/pyspark/serializers.py
spark-2.4.4-bin-hadoop2.7/python/pyspark/rdd.py
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spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/CosineSimilarity.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/CorrelationsExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/Correlations.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/ChiSqSelectorExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/BisectingKMeansExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/BinaryClassificationMetricsExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/AssociationRulesExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/AbstractParams.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/Word2VecExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnySVD.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnyPCA.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TFIDFExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SummaryStatisticsExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLogisticRegression.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLinearRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingKMeansExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StratifiedSamplingExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StandardScalerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SparseNaiveBayes.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SimpleFPGrowth.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SampledRDDs.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SVMWithSGDExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SVDExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RegressionMetricsExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RecommendationExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomRDDGeneration.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestClassificationExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PrefixSpanExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PowerIterationClusteringExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PMMLModelExportExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnSourceVectorExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnRowMatrixExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/NormalizerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/NaiveBayesExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MultivariateSummarizer.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MulticlassMetricsExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MultiLabelMetricsExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LogisticRegressionWithLBFGSExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LinearRegressionWithSGDExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LatentDirichletAllocationExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LDAExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LBFGSExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/KernelDensityEstimationExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/KMeansExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/IsotonicRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/HypothesisTestingKolmogorovSmirnovTestExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/HypothesisTestingExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostingRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostingClassificationExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GaussianMixtureExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/FPGrowthExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RankingMetricsExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MovieLensALS.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LinearRegression.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostedTreesRunner.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/DecisionTreeRunner.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/BinaryClassification.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/Word2VecExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorSlicerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorSizeHintExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorIndexerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorAssemblerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/UnaryTransformerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/TokenizerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/TfIdfExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/SummarizerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/StringIndexerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/StopWordsRemoverExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/StandardScalerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/SQLTransformerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RandomForestRegressorExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RandomForestExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RFormulaExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/QuantileDiscretizerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PowerIterationClusteringExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PolynomialExpansionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PipelineExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PCAExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/OneVsRestExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/NormalizerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/NaiveBayesExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/NGramExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MultilayerPerceptronClassifierExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MulticlassLogisticRegressionWithElasticNetExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ModelSelectionViaTrainValidationSplitExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ModelSelectionViaCrossValidationExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MinMaxScalerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MinHashLSHExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MaxAbsScalerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LogisticRegressionWithElasticNetExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LogisticRegressionSummaryExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LogisticRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LinearSVCExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LinearRegressionWithElasticNetExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LinearRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LDAExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/KMeansExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/IsotonicRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/InteractionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/IndexToStringExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ImputerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GradientBoostedTreeRegressorExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GeneralizedLinearRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GaussianMixtureExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GBTExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/FeatureHasherExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/EstimatorTransformerParamExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ElementwiseProductExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DeveloperApiExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DataFrameExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DCTExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/CountVectorizerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/CorrelationExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ChiSquareTestExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ChiSqSelectorExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BucketizerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BucketedRandomProjectionLSHExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BinarizerExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ALSExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/AFTSurvivalRegressionExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RandomForestClassifierExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PrefixSpanExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/OneHotEncoderEstimatorExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GradientBoostedTreeClassifierExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/FPGrowthExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeClassificationExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BisectingKMeansExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/TriangleCountingExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/SynthBenchmark.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/SSSPExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/PageRankExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/LiveJournalPageRank.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/ConnectedComponentsExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/ComprehensiveExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/Analytics.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/AggregateMessagesExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkTC.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkRemoteFileTest.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkPi.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkPageRank.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkLR.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkKMeans.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkHdfsLR.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkALS.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SkewedGroupByTest.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SimpleSkewedGroupByTest.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/MultiBroadcastTest.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalPi.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalLR.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalKMeans.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalFileLR.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalALS.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/GroupByTest.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ExceptionHandlingTest.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/DriverSubmissionTest.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/BroadcastTest.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewStream.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewGenerator.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/StreamingExamples.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/StatefulNetworkWordCount.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/SqlNetworkWordCount.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/RecoverableNetworkWordCount.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/RawNetworkGrep.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/QueueStream.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/NetworkWordCount.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/HdfsWordCount.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/DirectKafkaWordCount.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/CustomReceiver.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredSessionization.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCountWindowed.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCount.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredKafkaWordCount.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/hive/
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/hive/SparkHiveExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedUntypedAggregation.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedTypedAggregation.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/RDDRelation.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/SparkSQLExample.scala
spark-2.4.4-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/SQLDataSourceExample.scala
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spark-2.4.4-bin-hadoop2.7/examples/src/main/r/ml/survreg.R
spark-2.4.4-bin-hadoop2.7/examples/src/main/r/ml/randomForest.R
spark-2.4.4-bin-hadoop2.7/examples/src/main/r/ml/naiveBayes.R
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spark-2.4.4-bin-hadoop2.7/examples/src/main/python/
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/wordcount.py
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spark-2.4.4-bin-hadoop2.7/examples/src/main/python/streaming/network_wordjoinsentiments.py
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spark-2.4.4-bin-hadoop2.7/examples/src/main/python/streaming/hdfs_wordcount.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/streaming/recoverable_network_wordcount.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/streaming/kafka_wordcount.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/streaming/flume_wordcount.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/streaming/direct_kafka_wordcount.py
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spark-2.4.4-bin-hadoop2.7/examples/src/main/python/sql/basic.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/sql/hive.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/sql/datasource.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/sql/arrow.py
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spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/tf_idf_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/svm_with_sgd_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/svd_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/summary_statistics_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/streaming_linear_regression_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/streaming_k_means_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/stratified_sampling_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/sampled_rdds.py
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spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/random_rdd_generation.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/random_forest_regression_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/random_forest_classification_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/power_iteration_clustering_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/pca_rowmatrix_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/normalizer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/naive_bayes_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/multi_label_metrics_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/logistic_regression_with_lbfgs_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/logistic_regression.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/linear_regression_with_sgd_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/latent_dirichlet_allocation_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/kmeans.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/kernel_density_estimation_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/k_means_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/hypothesis_testing_kolmogorov_smirnov_test_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/hypothesis_testing_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/gradient_boosting_regression_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/gradient_boosting_classification_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/gaussian_mixture_model.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/gaussian_mixture_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/fpgrowth_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/elementwise_product_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/decision_tree_regression_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/decision_tree_classification_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/correlations_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/correlations.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/binary_classification_metrics_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/standard_scaler_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/ranking_metrics_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/multi_class_metrics_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/isotonic_regression_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/mllib/bisecting_k_means_example.py
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spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/word2vec_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/vector_slicer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/vector_size_hint_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/vector_indexer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/vector_assembler_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/train_validation_split.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/tokenizer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/tf_idf_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/summarizer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/string_indexer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/stopwords_remover_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/standard_scaler_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/sql_transformer.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/rformula_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/random_forest_regressor_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/random_forest_classifier_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/quantile_discretizer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/prefixspan_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/polynomial_expansion_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/pipeline_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/pca_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/one_vs_rest_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/normalizer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/naive_bayes_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/n_gram_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/multilayer_perceptron_classification.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/multiclass_logistic_regression_with_elastic_net.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/min_max_scaler_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/min_hash_lsh_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/max_abs_scaler_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/logistic_regression_with_elastic_net.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/logistic_regression_summary_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/linearsvc.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/linear_regression_with_elastic_net.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/lda_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/kmeans_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/isotonic_regression_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/index_to_string_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/imputer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/gradient_boosted_tree_regressor_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/gradient_boosted_tree_classifier_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/generalized_linear_regression_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/gaussian_mixture_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/fpgrowth_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/feature_hasher_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/estimator_transformer_param_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/elementwise_product_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/decision_tree_regression_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/decision_tree_classification_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/dct_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/dataframe_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/cross_validator.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/count_vectorizer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/correlation_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/chisq_selector_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/chi_square_test_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/bucketizer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/bucketed_random_projection_lsh_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/binarizer_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/als_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/aft_survival_regression.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/onehot_encoder_estimator_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/ml/bisecting_k_means_example.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/logistic_regression.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/kmeans.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/avro_inputformat.py
spark-2.4.4-bin-hadoop2.7/examples/src/main/python/als.py
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spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaMulticlassClassificationMetricsExample.java
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spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLogisticRegressionWithLBFGSExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLinearRegressionWithSGDExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLatentDirichletAllocationExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLBFGSExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaKernelDensityEstimationExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaKMeansExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaIsotonicRegressionExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaHypothesisTestingKolmogorovSmirnovTestExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaHypothesisTestingExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaGradientBoostingRegressionExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaGradientBoostingClassificationExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaGaussianMixtureExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaElementwiseProductExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaDecisionTreeRegressionExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaDecisionTreeClassificationExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaChiSqSelectorExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaBisectingKMeansExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaBinaryClassificationMetricsExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaAssociationRulesExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaALS.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRankingMetricsExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRandomForestClassificationExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaCorrelationsExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaWord2VecExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorSlicerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorSizeHintExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorIndexerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorAssemblerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaTokenizerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaTfIdfExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaSummarizerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaStringIndexerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaStopWordsRemoverExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaStandardScalerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaSQLTransformerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaRandomForestRegressorExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaRFormulaExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaQuantileDiscretizerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPowerIterationClusteringExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPolynomialExpansionExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPipelineExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPCAExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaOneVsRestExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaNormalizerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaNaiveBayesExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaNGramExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMultilayerPerceptronClassifierExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMulticlassLogisticRegressionWithElasticNetExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaModelSelectionViaTrainValidationSplitExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaModelSelectionViaCrossValidationExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMinMaxScalerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMinHashLSHExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMaxAbsScalerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionWithElasticNetExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionSummaryExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLinearSVCExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLinearRegressionWithElasticNetExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLabeledDocument.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLDAExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaKMeansExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaIsotonicRegressionExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaInteractionExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaIndexToStringExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaImputerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeRegressorExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGeneralizedLinearRegressionExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGaussianMixtureExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaFeatureHasherExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaFPGrowthExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaEstimatorTransformerParamExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaElementwiseProductExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDocument.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDecisionTreeRegressionExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDCTExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaCountVectorizerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaCorrelationExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaChiSquareTestExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaChiSqSelectorExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBucketizerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBucketedRandomProjectionLSHExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBinarizerExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaRandomForestClassifierExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPrefixSpanExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaOneHotEncoderEstimatorExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeClassifierExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDecisionTreeClassificationExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBisectingKMeansExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaALSExample.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaWordCount.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaStatusTrackerDemo.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaSparkPi.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaPageRank.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaLogQuery.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaHdfsLR.java
spark-2.4.4-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaTC.java
spark-2.4.4-bin-hadoop2.7/examples/jars/
spark-2.4.4-bin-hadoop2.7/examples/jars/spark-examples_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/examples/jars/scopt_2.11-3.7.0.jar
spark-2.4.4-bin-hadoop2.7/kubernetes/
spark-2.4.4-bin-hadoop2.7/kubernetes/tests/
spark-2.4.4-bin-hadoop2.7/kubernetes/tests/pyfiles.py
spark-2.4.4-bin-hadoop2.7/kubernetes/tests/worker_memory_check.py
spark-2.4.4-bin-hadoop2.7/kubernetes/tests/py_container_checks.py
spark-2.4.4-bin-hadoop2.7/kubernetes/dockerfiles/
spark-2.4.4-bin-hadoop2.7/kubernetes/dockerfiles/spark/
spark-2.4.4-bin-hadoop2.7/kubernetes/dockerfiles/spark/entrypoint.sh
spark-2.4.4-bin-hadoop2.7/kubernetes/dockerfiles/spark/Dockerfile
spark-2.4.4-bin-hadoop2.7/kubernetes/dockerfiles/spark/bindings/
spark-2.4.4-bin-hadoop2.7/kubernetes/dockerfiles/spark/bindings/python/
spark-2.4.4-bin-hadoop2.7/kubernetes/dockerfiles/spark/bindings/python/Dockerfile
spark-2.4.4-bin-hadoop2.7/kubernetes/dockerfiles/spark/bindings/R/
spark-2.4.4-bin-hadoop2.7/kubernetes/dockerfiles/spark/bindings/R/Dockerfile
spark-2.4.4-bin-hadoop2.7/yarn/
spark-2.4.4-bin-hadoop2.7/yarn/spark-2.4.4-yarn-shuffle.jar
spark-2.4.4-bin-hadoop2.7/jars/
spark-2.4.4-bin-hadoop2.7/jars/jackson-mapper-asl-1.9.13.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-jaxrs-1.9.13.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-dataformat-yaml-2.6.7.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-databind-2.6.7.1.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-core-asl-1.9.13.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-core-2.6.7.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-annotations-2.6.7.jar
spark-2.4.4-bin-hadoop2.7/jars/ivy-2.4.0.jar
spark-2.4.4-bin-hadoop2.7/jars/httpcore-4.4.10.jar
spark-2.4.4-bin-hadoop2.7/jars/httpclient-4.5.6.jar
spark-2.4.4-bin-hadoop2.7/jars/htrace-core-3.1.0-incubating.jar
spark-2.4.4-bin-hadoop2.7/jars/hppc-0.7.2.jar
spark-2.4.4-bin-hadoop2.7/jars/hk2-utils-2.4.0-b34.jar
spark-2.4.4-bin-hadoop2.7/jars/hk2-locator-2.4.0-b34.jar
spark-2.4.4-bin-hadoop2.7/jars/hk2-api-2.4.0-b34.jar
spark-2.4.4-bin-hadoop2.7/jars/hive-metastore-1.2.1.spark2.jar
spark-2.4.4-bin-hadoop2.7/jars/hive-jdbc-1.2.1.spark2.jar
spark-2.4.4-bin-hadoop2.7/jars/hive-exec-1.2.1.spark2.jar
spark-2.4.4-bin-hadoop2.7/jars/hive-cli-1.2.1.spark2.jar
spark-2.4.4-bin-hadoop2.7/jars/hive-beeline-1.2.1.spark2.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-yarn-server-web-proxy-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-yarn-server-common-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-yarn-common-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-yarn-client-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-yarn-api-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-mapreduce-client-shuffle-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-mapreduce-client-jobclient-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-mapreduce-client-core-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-mapreduce-client-common-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-mapreduce-client-app-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-hdfs-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-common-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-client-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-auth-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/hadoop-annotations-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/guice-servlet-3.0.jar
spark-2.4.4-bin-hadoop2.7/jars/guice-3.0.jar
spark-2.4.4-bin-hadoop2.7/jars/guava-14.0.1.jar
spark-2.4.4-bin-hadoop2.7/jars/gson-2.2.4.jar
spark-2.4.4-bin-hadoop2.7/jars/generex-1.0.1.jar
spark-2.4.4-bin-hadoop2.7/jars/flatbuffers-1.2.0-3f79e055.jar
spark-2.4.4-bin-hadoop2.7/jars/eigenbase-properties-1.1.5.jar
spark-2.4.4-bin-hadoop2.7/jars/derby-10.12.1.1.jar
spark-2.4.4-bin-hadoop2.7/jars/datanucleus-rdbms-3.2.9.jar
spark-2.4.4-bin-hadoop2.7/jars/datanucleus-core-3.2.10.jar
spark-2.4.4-bin-hadoop2.7/jars/datanucleus-api-jdo-3.2.6.jar
spark-2.4.4-bin-hadoop2.7/jars/curator-recipes-2.7.1.jar
spark-2.4.4-bin-hadoop2.7/jars/curator-framework-2.7.1.jar
spark-2.4.4-bin-hadoop2.7/jars/curator-client-2.7.1.jar
spark-2.4.4-bin-hadoop2.7/jars/core-1.1.2.jar
spark-2.4.4-bin-hadoop2.7/jars/compress-lzf-1.0.3.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-pool-1.5.4.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-net-3.1.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-math3-3.4.1.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-logging-1.1.3.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-lang3-3.5.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-lang-2.6.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-io-2.4.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-httpclient-3.1.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-digester-1.8.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-dbcp-1.4.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-crypto-1.0.0.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-configuration-1.6.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-compress-1.8.1.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-compiler-3.0.9.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-collections-3.2.2.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-codec-1.10.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-cli-1.2.jar
spark-2.4.4-bin-hadoop2.7/jars/commons-beanutils-1.9.3.jar
spark-2.4.4-bin-hadoop2.7/jars/chill_2.11-0.9.3.jar
spark-2.4.4-bin-hadoop2.7/jars/chill-java-0.9.3.jar
spark-2.4.4-bin-hadoop2.7/jars/calcite-linq4j-1.2.0-incubating.jar
spark-2.4.4-bin-hadoop2.7/jars/calcite-core-1.2.0-incubating.jar
spark-2.4.4-bin-hadoop2.7/jars/calcite-avatica-1.2.0-incubating.jar
spark-2.4.4-bin-hadoop2.7/jars/breeze_2.11-0.13.2.jar
spark-2.4.4-bin-hadoop2.7/jars/breeze-macros_2.11-0.13.2.jar
spark-2.4.4-bin-hadoop2.7/jars/bonecp-0.8.0.RELEASE.jar
spark-2.4.4-bin-hadoop2.7/jars/avro-mapred-1.8.2-hadoop2.jar
spark-2.4.4-bin-hadoop2.7/jars/avro-ipc-1.8.2.jar
spark-2.4.4-bin-hadoop2.7/jars/avro-1.8.2.jar
spark-2.4.4-bin-hadoop2.7/jars/automaton-1.11-8.jar
spark-2.4.4-bin-hadoop2.7/jars/arrow-vector-0.10.0.jar
spark-2.4.4-bin-hadoop2.7/jars/arrow-memory-0.10.0.jar
spark-2.4.4-bin-hadoop2.7/jars/arrow-format-0.10.0.jar
spark-2.4.4-bin-hadoop2.7/jars/arpack_combined_all-0.1.jar
spark-2.4.4-bin-hadoop2.7/jars/api-util-1.0.0-M20.jar
spark-2.4.4-bin-hadoop2.7/jars/api-asn1-api-1.0.0-M20.jar
spark-2.4.4-bin-hadoop2.7/jars/apacheds-kerberos-codec-2.0.0-M15.jar
spark-2.4.4-bin-hadoop2.7/jars/apacheds-i18n-2.0.0-M15.jar
spark-2.4.4-bin-hadoop2.7/jars/apache-log4j-extras-1.2.17.jar
spark-2.4.4-bin-hadoop2.7/jars/aopalliance-repackaged-2.4.0-b34.jar
spark-2.4.4-bin-hadoop2.7/jars/aopalliance-1.0.jar
spark-2.4.4-bin-hadoop2.7/jars/antlr4-runtime-4.7.jar
spark-2.4.4-bin-hadoop2.7/jars/antlr-runtime-3.4.jar
spark-2.4.4-bin-hadoop2.7/jars/antlr-2.7.7.jar
spark-2.4.4-bin-hadoop2.7/jars/aircompressor-0.10.jar
spark-2.4.4-bin-hadoop2.7/jars/activation-1.1.1.jar
spark-2.4.4-bin-hadoop2.7/jars/ST4-4.0.4.jar
spark-2.4.4-bin-hadoop2.7/jars/RoaringBitmap-0.7.45.jar
spark-2.4.4-bin-hadoop2.7/jars/JavaEWAH-0.3.2.jar
spark-2.4.4-bin-hadoop2.7/jars/zstd-jni-1.3.2-2.jar
spark-2.4.4-bin-hadoop2.7/jars/zookeeper-3.4.6.jar
spark-2.4.4-bin-hadoop2.7/jars/zjsonpatch-0.3.0.jar
spark-2.4.4-bin-hadoop2.7/jars/xz-1.5.jar
spark-2.4.4-bin-hadoop2.7/jars/xmlenc-0.52.jar
spark-2.4.4-bin-hadoop2.7/jars/xercesImpl-2.9.1.jar
spark-2.4.4-bin-hadoop2.7/jars/xbean-asm6-shaded-4.8.jar
spark-2.4.4-bin-hadoop2.7/jars/validation-api-1.1.0.Final.jar
spark-2.4.4-bin-hadoop2.7/jars/univocity-parsers-2.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/super-csv-2.2.0.jar
spark-2.4.4-bin-hadoop2.7/jars/stringtemplate-3.2.1.jar
spark-2.4.4-bin-hadoop2.7/jars/stream-2.7.0.jar
spark-2.4.4-bin-hadoop2.7/jars/stax-api-1.0.1.jar
spark-2.4.4-bin-hadoop2.7/jars/stax-api-1.0-2.jar
spark-2.4.4-bin-hadoop2.7/jars/spire_2.11-0.13.0.jar
spark-2.4.4-bin-hadoop2.7/jars/spire-macros_2.11-0.13.0.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-yarn_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-unsafe_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-tags_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-tags_2.11-2.4.4-tests.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-streaming_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-sql_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-sketch_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-repl_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-network-shuffle_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-network-common_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-mllib_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-mllib-local_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-mesos_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-launcher_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-kvstore_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-kubernetes_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-hive_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-hive-thriftserver_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-graphx_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-core_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/spark-catalyst_2.11-2.4.4.jar
spark-2.4.4-bin-hadoop2.7/jars/snappy-java-1.1.7.3.jar
spark-2.4.4-bin-hadoop2.7/jars/snappy-0.2.jar
spark-2.4.4-bin-hadoop2.7/jars/snakeyaml-1.15.jar
spark-2.4.4-bin-hadoop2.7/jars/slf4j-log4j12-1.7.16.jar
spark-2.4.4-bin-hadoop2.7/jars/slf4j-api-1.7.16.jar
spark-2.4.4-bin-hadoop2.7/jars/shims-0.7.45.jar
spark-2.4.4-bin-hadoop2.7/jars/shapeless_2.11-2.3.2.jar
spark-2.4.4-bin-hadoop2.7/jars/scala-xml_2.11-1.0.5.jar
spark-2.4.4-bin-hadoop2.7/jars/scala-reflect-2.11.12.jar
spark-2.4.4-bin-hadoop2.7/jars/scala-parser-combinators_2.11-1.1.0.jar
spark-2.4.4-bin-hadoop2.7/jars/scala-library-2.11.12.jar
spark-2.4.4-bin-hadoop2.7/jars/scala-compiler-2.11.12.jar
spark-2.4.4-bin-hadoop2.7/jars/pyrolite-4.13.jar
spark-2.4.4-bin-hadoop2.7/jars/py4j-0.10.7.jar
spark-2.4.4-bin-hadoop2.7/jars/protobuf-java-2.5.0.jar
spark-2.4.4-bin-hadoop2.7/jars/parquet-jackson-1.10.1.jar
spark-2.4.4-bin-hadoop2.7/jars/parquet-hadoop-bundle-1.6.0.jar
spark-2.4.4-bin-hadoop2.7/jars/parquet-hadoop-1.10.1.jar
spark-2.4.4-bin-hadoop2.7/jars/parquet-format-2.4.0.jar
spark-2.4.4-bin-hadoop2.7/jars/parquet-encoding-1.10.1.jar
spark-2.4.4-bin-hadoop2.7/jars/parquet-common-1.10.1.jar
spark-2.4.4-bin-hadoop2.7/jars/parquet-column-1.10.1.jar
spark-2.4.4-bin-hadoop2.7/jars/paranamer-2.8.jar
spark-2.4.4-bin-hadoop2.7/jars/osgi-resource-locator-1.0.1.jar
spark-2.4.4-bin-hadoop2.7/jars/oro-2.0.8.jar
spark-2.4.4-bin-hadoop2.7/jars/orc-shims-1.5.5.jar
spark-2.4.4-bin-hadoop2.7/jars/orc-mapreduce-1.5.5-nohive.jar
spark-2.4.4-bin-hadoop2.7/jars/orc-core-1.5.5-nohive.jar
spark-2.4.4-bin-hadoop2.7/jars/opencsv-2.3.jar
spark-2.4.4-bin-hadoop2.7/jars/okio-1.13.0.jar
spark-2.4.4-bin-hadoop2.7/jars/okhttp-3.8.1.jar
spark-2.4.4-bin-hadoop2.7/jars/objenesis-2.5.1.jar
spark-2.4.4-bin-hadoop2.7/jars/netty-all-4.1.17.Final.jar
spark-2.4.4-bin-hadoop2.7/jars/netty-3.9.9.Final.jar
spark-2.4.4-bin-hadoop2.7/jars/minlog-1.3.0.jar
spark-2.4.4-bin-hadoop2.7/jars/metrics-jvm-3.1.5.jar
spark-2.4.4-bin-hadoop2.7/jars/metrics-json-3.1.5.jar
spark-2.4.4-bin-hadoop2.7/jars/metrics-graphite-3.1.5.jar
spark-2.4.4-bin-hadoop2.7/jars/metrics-core-3.1.5.jar
spark-2.4.4-bin-hadoop2.7/jars/mesos-1.4.0-shaded-protobuf.jar
spark-2.4.4-bin-hadoop2.7/jars/macro-compat_2.11-1.1.1.jar
spark-2.4.4-bin-hadoop2.7/jars/machinist_2.11-0.6.1.jar
spark-2.4.4-bin-hadoop2.7/jars/lz4-java-1.4.0.jar
spark-2.4.4-bin-hadoop2.7/jars/logging-interceptor-3.12.0.jar
spark-2.4.4-bin-hadoop2.7/jars/log4j-1.2.17.jar
spark-2.4.4-bin-hadoop2.7/jars/libthrift-0.9.3.jar
spark-2.4.4-bin-hadoop2.7/jars/libfb303-0.9.3.jar
spark-2.4.4-bin-hadoop2.7/jars/leveldbjni-all-1.8.jar
spark-2.4.4-bin-hadoop2.7/jars/kubernetes-model-common-4.1.2.jar
spark-2.4.4-bin-hadoop2.7/jars/kubernetes-model-4.1.2.jar
spark-2.4.4-bin-hadoop2.7/jars/kubernetes-client-4.1.2.jar
spark-2.4.4-bin-hadoop2.7/jars/kryo-shaded-4.0.2.jar
spark-2.4.4-bin-hadoop2.7/jars/jul-to-slf4j-1.7.16.jar
spark-2.4.4-bin-hadoop2.7/jars/jtransforms-2.4.0.jar
spark-2.4.4-bin-hadoop2.7/jars/jta-1.1.jar
spark-2.4.4-bin-hadoop2.7/jars/jsr305-1.3.9.jar
spark-2.4.4-bin-hadoop2.7/jars/jsp-api-2.1.jar
spark-2.4.4-bin-hadoop2.7/jars/json4s-scalap_2.11-3.5.3.jar
spark-2.4.4-bin-hadoop2.7/jars/json4s-jackson_2.11-3.5.3.jar
spark-2.4.4-bin-hadoop2.7/jars/json4s-core_2.11-3.5.3.jar
spark-2.4.4-bin-hadoop2.7/jars/json4s-ast_2.11-3.5.3.jar
spark-2.4.4-bin-hadoop2.7/jars/jpam-1.1.jar
spark-2.4.4-bin-hadoop2.7/jars/jodd-core-3.5.2.jar
spark-2.4.4-bin-hadoop2.7/jars/joda-time-2.9.3.jar
spark-2.4.4-bin-hadoop2.7/jars/jline-2.14.6.jar
spark-2.4.4-bin-hadoop2.7/jars/jetty-util-6.1.26.jar
spark-2.4.4-bin-hadoop2.7/jars/jetty-6.1.26.jar
spark-2.4.4-bin-hadoop2.7/jars/jersey-server-2.22.2.jar
spark-2.4.4-bin-hadoop2.7/jars/jersey-media-jaxb-2.22.2.jar
spark-2.4.4-bin-hadoop2.7/jars/jersey-guava-2.22.2.jar
spark-2.4.4-bin-hadoop2.7/jars/jersey-container-servlet-core-2.22.2.jar
spark-2.4.4-bin-hadoop2.7/jars/jersey-container-servlet-2.22.2.jar
spark-2.4.4-bin-hadoop2.7/jars/jersey-common-2.22.2.jar
spark-2.4.4-bin-hadoop2.7/jars/jersey-client-2.22.2.jar
spark-2.4.4-bin-hadoop2.7/jars/jdo-api-3.0.1.jar
spark-2.4.4-bin-hadoop2.7/jars/jcl-over-slf4j-1.7.16.jar
spark-2.4.4-bin-hadoop2.7/jars/jaxb-api-2.2.2.jar
spark-2.4.4-bin-hadoop2.7/jars/javolution-5.5.1.jar
spark-2.4.4-bin-hadoop2.7/jars/javax.ws.rs-api-2.0.1.jar
spark-2.4.4-bin-hadoop2.7/jars/javax.servlet-api-3.1.0.jar
spark-2.4.4-bin-hadoop2.7/jars/javax.inject-2.4.0-b34.jar
spark-2.4.4-bin-hadoop2.7/jars/javax.inject-1.jar
spark-2.4.4-bin-hadoop2.7/jars/javax.annotation-api-1.2.jar
spark-2.4.4-bin-hadoop2.7/jars/javassist-3.18.1-GA.jar
spark-2.4.4-bin-hadoop2.7/jars/janino-3.0.9.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-xc-1.9.13.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-module-scala_2.11-2.6.7.1.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-module-paranamer-2.7.9.jar
spark-2.4.4-bin-hadoop2.7/jars/jackson-module-jaxb-annotations-2.6.7.jar
spark-2.4.4-bin-hadoop2.7/RELEASE
+ export SPARK_HOME=/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7
+ SPARK_HOME=/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7
+ pythons=(3.6)
+ for python in '${pythons[*]}'
+ conda create -y -q -n mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe python=3.6 pip


Package plan for installation in environment /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe:

The following NEW packages will be INSTALLED:

    _libgcc_mutex:   0.1-main               
    ca-certificates: 2019.11.27-0           
    certifi:         2019.11.28-py36_0      
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       9.1.0-hdf63c60_0       
    libstdcxx-ng:    9.1.0-hdf63c60_0       
    ncurses:         6.1-he6710b0_1         
    openssl:         1.1.1d-h7b6447c_3      
    pip:             19.3.1-py36_0          
    python:          3.6.9-h265db76_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      42.0.2-py36_0          
    sqlite:          3.30.1-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.6-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-h7b6447c_3      


+ source activate mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/anaconda/bin/activate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/anaconda/bin/activate
++ _CONDA_DIR=/home/anaconda/bin

if [ $# -gt 1 ]; then
    (>&2 echo "Error: did not expect more than one argument.")
    (>&2 echo "    (Got $@)")
    return 1
fi
++ '[' 1 -gt 1 ']'

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        # ignore any windows backup paths from bat-based activation
        if [ "${CONDA_PATH_BACKUP:0:1}" != "/"  ]; then
           unset CONDA_PATH_BACKUP
        fi
        export _CONDA_PYTHON="$_CONDA_DIR/../python"
        ;;
    *)
        EXT=""
        export _CONDA_PYTHON="$_CONDA_DIR/python"
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=
++ export _CONDA_PYTHON=/home/anaconda/bin/python
++ _CONDA_PYTHON=/home/anaconda/bin/python

# Ensure that this script is sourced, not executed
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "activate" ]]; then
    (>&2 echo "Error: activate must be sourced. Run 'source activate envname'
instead of 'activate envname'.
")
    "$_CONDA_DIR/conda" ..activate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \a\c\t\i\v\a\t\e ]]

if [ "$#" -eq "0" ]; then
    args=('root')
else
    args=$@
fi
++ '[' 1 -eq 0 ']'
++ args=mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe

"$_CONDA_DIR/conda" ..checkenv $_SHELL$EXT "$args"
++ /home/anaconda/bin/conda ..checkenv bash mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe
if (( $? != 0 )); then
    return 1
fi
++ ((  0 != 0  ))

# Ensure we deactivate any scripts from the old env
_CONDA_HOLD=true
++ _CONDA_HOLD=true
source "$_CONDA_DIR/deactivate"
++ source /home/anaconda/bin/deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
+++ [[ -n 4.3.48(1)-release ]]
+++ _SCRIPT_LOCATION=/home/anaconda/bin/deactivate
+++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
++++ dirname /home/anaconda/bin/deactivate
+++ _CONDA_DIR=/home/anaconda/bin

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
+++ case "$(uname -s)" in
uname -s
++++ uname -s
+++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
+++ [[ 1 > 0 ]]
+++ key=mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe
+++ case $key in
+++ shift
+++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
+++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
++++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test
+++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
+++ [[ -z '' ]]
+++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
++++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test
+++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]
+++ return 0
unset _CONDA_HOLD
++ unset _CONDA_HOLD

_NEW_PART=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$args")
"$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$args"
+++ /home/anaconda/bin/conda ..activate bash mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe
++ _NEW_PART=/home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin
if (( $? == 0 )); then
    export CONDA_PATH_BACKUP="$PATH"
    # export this to restore it upon deactivation
    export CONDA_PS1_BACKUP="$PS1"

    # look if the deactivate script left a placeholder for us
    if [[ $PATH == *"CONDA_PATH_PLACEHOLDER"* ]]; then
        # If it did, replace it with our _NEW_PART
        export PATH="$($_CONDA_PYTHON -c "import re; print(re.sub(r'CONDA_PATH_PLACEHOLDER', r'$_NEW_PART', '$PATH', 1))")"
    else
        export PATH="$_NEW_PART:$PATH"
    fi

    # CONDA_DEFAULT_ENV is the shortest representation of how conda recognizes your env.
    #    It can be an env name, or a full path.
    #    Last date of change: 2016-06-21
    # If the string contains / it's a path
    if [[ "$@" == */* ]]; then
        export CONDA_DEFAULT_ENV=$(get_abs_filename "$args")
    else
        export CONDA_DEFAULT_ENV="$args"
    fi
    # CONDA_PREFIX is always the full path to the activated environment.  It is not set
    #    when no environment is active.
    # Legacy support: CONDA_DEFAULT_ENV is either env name or full path if given as path.
    #    CONDA_PREFIX is always the full path, for consistency.
    #    Last date of change: 2016-06-21
    firstpath=${_NEW_PART%%:*}
    export CONDA_PREFIX="$(echo ${firstpath} | sed "s|/bin$||")" &>/dev/null

    # if CONDA_DEFAULT_ENV not in PS1, prepend it with parentheses
    if [ $("$_CONDA_DIR/conda" ..changeps1) = "1" ]; then
        if ! $(grep -q CONDA_DEFAULT_ENV <<<$PS1); then
            if ! $(grep -q "POWERLINE" <<<$PS1); then
                export PS1="(${CONDA_DEFAULT_ENV}) $PS1"
            fi
        fi
    fi

    # Load any of the scripts found $PREFIX/etc/conda/activate.d AFTER activation
    _CONDA_D="${CONDA_PREFIX}/etc/conda/activate.d"
    if [[ -d "$_CONDA_D" ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi
    unset _CONDA_PYTHON
else
    unset _CONDA_PYTHON
    return $?
fi
++ ((  0 == 0  ))
++ export CONDA_PATH_BACKUP=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ CONDA_PATH_BACKUP=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ export CONDA_PS1_BACKUP=
++ CONDA_PS1_BACKUP=
++ [[ /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games == *\C\O\N\D\A\_\P\A\T\H\_\P\L\A\C\E\H\O\L\D\E\R* ]]
++ export PATH=/home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ PATH=/home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ [[ '' == */* ]]
++ export CONDA_DEFAULT_ENV=mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe
++ CONDA_DEFAULT_ENV=mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe
++ firstpath=/home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin
echo ${firstpath} | sed "s|/bin$||"
+++ echo /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe
"$_CONDA_DIR/conda" ..changeps1
+++ /home/anaconda/bin/conda ..changeps1
++ '[' 1 = 1 ']'
grep -q CONDA_DEFAULT_ENV <<<$PS1
+++ grep -q CONDA_DEFAULT_ENV
grep -q "POWERLINE" <<<$PS1
+++ grep -q POWERLINE
++ export 'PS1=(mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe) '
++ PS1='(mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe) '
++ _CONDA_D=/home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/etc/conda/activate.d
++ [[ -d /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/etc/conda/activate.d ]]
++ unset _CONDA_PYTHON

unset CONDA_PATH
++ unset CONDA_PATH

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ conda install -y nodejs
Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe:

The following NEW packages will be INSTALLED:

    nodejs: 10.13.0-he6710b0_0

+ pushd mango-python
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ make prepare
pip install pytest==3.9.1
Collecting pytest==3.9.1
  Using cached https://files.pythonhosted.org/packages/bf/14/a16e1ac03aeb9776d98374bb76495a6623d56dff0f7b815ed5a1e04d893e/pytest-3.9.1-py2.py3-none-any.whl
Collecting attrs>=17.4.0
  Using cached https://files.pythonhosted.org/packages/a2/db/4313ab3be961f7a763066401fb77f7748373b6094076ae2bda2806988af6/attrs-19.3.0-py2.py3-none-any.whl
Collecting py>=1.5.0
  Using cached https://files.pythonhosted.org/packages/76/bc/394ad449851729244a97857ee14d7cba61ddb268dce3db538ba2f2ba1f0f/py-1.8.0-py2.py3-none-any.whl
Collecting more-itertools>=4.0.0
  Downloading https://files.pythonhosted.org/packages/68/03/0604cec1ea13c9f063dd50f900d1a36160334dd3cfb01fd0e638f61b46ba/more_itertools-8.0.2-py3-none-any.whl (40kB)
Collecting pluggy>=0.7
  Using cached https://files.pythonhosted.org/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pytest==3.9.1) (42.0.2.post20191203)
Collecting atomicwrites>=1.0
  Using cached https://files.pythonhosted.org/packages/52/90/6155aa926f43f2b2a22b01be7241be3bfd1ceaf7d0b3267213e8127d41f4/atomicwrites-1.3.0-py2.py3-none-any.whl
Collecting six>=1.10.0
  Using cached https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl
Collecting importlib-metadata>=0.12; python_version < "3.8"
  Downloading https://files.pythonhosted.org/packages/e7/59/cc2a91f71957dfb32f25e6b19d8c6dfdbe524e0998e7f7a58a75126ce0cd/importlib_metadata-1.2.0-py2.py3-none-any.whl
Collecting zipp>=0.5
  Using cached https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl
Installing collected packages: attrs, py, more-itertools, zipp, importlib-metadata, pluggy, atomicwrites, six, pytest
Successfully installed atomicwrites-1.3.0 attrs-19.3.0 importlib-metadata-1.2.0 more-itertools-8.0.2 pluggy-0.13.1 py-1.8.0 pytest-3.9.1 six-1.13.0 zipp-0.6.0
# ipython version required for python 2.7
pip install jupyter_contrib_nbextensions
Collecting jupyter_contrib_nbextensions
  Using cached https://files.pythonhosted.org/packages/33/f0/6e2c00afda860f655fbf0f795f7310bdbf12122846344dfdc803fc7455d5/jupyter_contrib_nbextensions-0.5.1-py2.py3-none-any.whl
Collecting nbconvert>=4.2
  Using cached https://files.pythonhosted.org/packages/79/6c/05a569e9f703d18aacb89b7ad6075b404e8a4afde2c26b73ca77bb644b14/nbconvert-5.6.1-py2.py3-none-any.whl
Processing /home/jenkins/.cache/pip/wheels/0d/71/2a/164491997299b9f2479a251e254323fe35d946779e18f27956/jupyter_latex_envs-1.4.6-py2.py3-none-any.whl
Collecting traitlets>=4.1
  Using cached https://files.pythonhosted.org/packages/ca/ab/872a23e29cec3cf2594af7e857f18b687ad21039c1f9b922fac5b9b142d5/traitlets-4.3.3-py2.py3-none-any.whl
Collecting jupyter-contrib-core>=0.3.3
  Using cached https://files.pythonhosted.org/packages/e6/8f/04a752a8b66a66e7092c035e5d87d2502ac7ec07f9fb6059059b6c0dc272/jupyter_contrib_core-0.3.3-py2.py3-none-any.whl
Processing /home/jenkins/.cache/pip/wheels/15/df/fe/2a74fe34709e7fdc5ae153a768675d9fda93cc7d5133ed1fb0/jupyter_nbextensions_configurator-0.4.1-py2.py3-none-any.whl
Collecting jupyter-core
  Using cached https://files.pythonhosted.org/packages/fb/82/86437f661875e30682e99d04c13ba6c216f86f5f6ca6ef212d3ee8b6ca11/jupyter_core-4.6.1-py2.py3-none-any.whl
Processing /home/jenkins/.cache/pip/wheels/84/bf/40/2f6ef700f48401ca40e5e3dd7d0e3c0a90e064897b7fe5fc08/tornado-6.0.3-cp36-cp36m-linux_x86_64.whl
Collecting ipython-genutils
  Using cached https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl
Collecting pyyaml
  Downloading https://files.pythonhosted.org/packages/8d/c9/e5be955a117a1ac548cdd31e37e8fd7b02ce987f9655f5c7563c656d5dcb/PyYAML-5.2.tar.gz (265kB)
Collecting lxml
  Using cached https://files.pythonhosted.org/packages/68/30/affd16b77edf9537f5be051905f33527021e20d563d013e8c42c7fd01949/lxml-4.4.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting notebook>=4.0
  Using cached https://files.pythonhosted.org/packages/f5/69/d2ffaf7efc20ce47469187e3a41e6e03e17b45de5a6559f4e7ab3eace5e1/notebook-6.0.2-py3-none-any.whl
Collecting jupyter-highlight-selected-word>=0.1.1
  Using cached https://files.pythonhosted.org/packages/50/d7/19ab7cfd60bf268d2abbacc52d4295a40f52d74dfc0d938e4761ee5e598b/jupyter_highlight_selected_word-0.2.0-py2.py3-none-any.whl
Collecting defusedxml
  Using cached https://files.pythonhosted.org/packages/06/74/9b387472866358ebc08732de3da6dc48e44b0aacd2ddaa5cb85ab7e986a2/defusedxml-0.6.0-py2.py3-none-any.whl
Collecting jinja2>=2.4
  Using cached https://files.pythonhosted.org/packages/65/e0/eb35e762802015cab1ccee04e8a277b03f1d8e53da3ec3106882ec42558b/Jinja2-2.10.3-py2.py3-none-any.whl
Collecting mistune<2,>=0.8.1
  Using cached https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl
Processing /home/jenkins/.cache/pip/wheels/39/01/56/f1b08a6275acc59e846fa4c1e1b65dbc1919f20157d9e66c20/pandocfilters-1.4.2-cp36-none-any.whl
Collecting pygments
  Using cached https://files.pythonhosted.org/packages/be/39/32da3184734730c0e4d3fa3b2b5872104668ad6dc1b5a73d8e477e5fe967/Pygments-2.5.2-py2.py3-none-any.whl
Collecting testpath
  Using cached https://files.pythonhosted.org/packages/1b/9e/1a170feaa54f22aeb5a5d16c9015e82234275a3c8ab630b552493f9cb8a9/testpath-0.4.4-py2.py3-none-any.whl
Collecting entrypoints>=0.2.2
  Using cached https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl
Collecting bleach
  Using cached https://files.pythonhosted.org/packages/ab/05/27e1466475e816d3001efb6e0a85a819be17411420494a1e602c36f8299d/bleach-3.1.0-py2.py3-none-any.whl
Collecting nbformat>=4.4
  Using cached https://files.pythonhosted.org/packages/da/27/9a654d2b6cc1eaa517d1c5a4405166c7f6d72f04f6e7eea41855fe808a46/nbformat-4.4.0-py2.py3-none-any.whl
Collecting ipython
  Downloading https://files.pythonhosted.org/packages/00/17/c3e3dd337cc601b47c599441786fd4e888b587a2a512d38ac752274fd0bc/ipython-7.10.1-py3-none-any.whl (778kB)
Collecting decorator
  Using cached https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-py2.py3-none-any.whl
Requirement already satisfied: six in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from traitlets>=4.1->jupyter_contrib_nbextensions) (1.13.0)
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter-contrib-core>=0.3.3->jupyter_contrib_nbextensions) (42.0.2.post20191203)
Collecting pyzmq>=17
  Using cached https://files.pythonhosted.org/packages/94/07/cee3d328a2e13f9de1c2b62cced7a389b61ac81424f2e377f3dc9d668282/pyzmq-18.1.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting jupyter-client>=5.3.4
  Using cached https://files.pythonhosted.org/packages/13/81/fe0eee1bcf949851a120254b1f530ae1e01bdde2d3ab9710c6ff81525061/jupyter_client-5.3.4-py2.py3-none-any.whl
Collecting ipykernel
  Using cached https://files.pythonhosted.org/packages/e1/92/8fec943b5b81078399f969f00557804d884c96fcd0bc296e81a2ed4fd270/ipykernel-5.1.3-py3-none-any.whl
Collecting terminado>=0.8.1
  Using cached https://files.pythonhosted.org/packages/ff/96/1d9a2c23990aea8f8e0b5c3b6627d03196a73771a17a2d9860bbe9823ab6/terminado-0.8.3-py2.py3-none-any.whl
Collecting Send2Trash
  Using cached https://files.pythonhosted.org/packages/49/46/c3dc27481d1cc57b9385aff41c474ceb7714f7935b1247194adae45db714/Send2Trash-1.5.0-py3-none-any.whl
Processing /home/jenkins/.cache/pip/wheels/1c/54/34/fd47cd9b308826cc4292b54449c1899a30251ef3b506bc91ea/prometheus_client-0.7.1-cp36-none-any.whl
Collecting MarkupSafe>=0.23
  Using cached https://files.pythonhosted.org/packages/b2/5f/23e0023be6bb885d00ffbefad2942bc51a620328ee910f64abe5a8d18dd1/MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting webencodings
  Using cached https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
Collecting jsonschema!=2.5.0,>=2.4
  Using cached https://files.pythonhosted.org/packages/c5/8f/51e89ce52a085483359217bc72cdbf6e75ee595d5b1d4b5ade40c7e018b8/jsonschema-3.2.0-py2.py3-none-any.whl
Processing /home/jenkins/.cache/pip/wheels/98/b0/dd/29e28ff615af3dda4c67cab719dd51357597eabff926976b45/backcall-0.1.0-cp36-none-any.whl
Collecting pexpect; sys_platform != "win32"
  Using cached https://files.pythonhosted.org/packages/0e/3e/377007e3f36ec42f1b84ec322ee12141a9e10d808312e5738f52f80a232c/pexpect-4.7.0-py2.py3-none-any.whl
Collecting jedi>=0.10
  Using cached https://files.pythonhosted.org/packages/55/54/da994f359e4e7da4776a200e76dbc85ba5fc319eefc22e33d55296d95a1d/jedi-0.15.1-py2.py3-none-any.whl
Collecting pickleshare
  Using cached https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl
Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
  Using cached https://files.pythonhosted.org/packages/7f/1f/e145dd467dc9b0e6f1e64232c03119498dfec497e383f1e8be9f83eaa97e/prompt_toolkit-3.0.2-py3-none-any.whl
Collecting python-dateutil>=2.1
  Using cached https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl
Collecting ptyprocess; os_name != "nt"
  Using cached https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert>=4.2->jupyter_contrib_nbextensions) (1.2.0)
Processing /home/jenkins/.cache/pip/wheels/83/89/d3/1712b9c33c9b9c0911b188a86aeff2a9a05e113f986cf79d92/pyrsistent-0.15.6-cp36-cp36m-linux_x86_64.whl
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert>=4.2->jupyter_contrib_nbextensions) (19.3.0)
Collecting parso>=0.5.0
  Using cached https://files.pythonhosted.org/packages/a3/bd/bf4e5bd01d79906e5b945a7af033154da49fd2b0d5b5c705a21330323305/parso-0.5.1-py2.py3-none-any.whl
Collecting wcwidth
  Using cached https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl
Requirement already satisfied: zipp>=0.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert>=4.2->jupyter_contrib_nbextensions) (0.6.0)
Requirement already satisfied: more-itertools in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from zipp>=0.5->importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert>=4.2->jupyter_contrib_nbextensions) (8.0.2)
Building wheels for collected packages: pyyaml
  Building wheel for pyyaml (setup.py): started
  Building wheel for pyyaml (setup.py): finished with status 'done'
  Created wheel for pyyaml: filename=PyYAML-5.2-cp36-cp36m-linux_x86_64.whl size=44209 sha256=864ff989228b01f3c9032ccbdbe37f031c4079b376fc3ce60443027f78e26bd2
  Stored in directory: /home/jenkins/.cache/pip/wheels/54/b7/c7/2ada654ee54483c9329871665aaf4a6056c3ce36f29cf66e67
Successfully built pyyaml
Installing collected packages: defusedxml, MarkupSafe, jinja2, mistune, pandocfilters, pygments, testpath, decorator, ipython-genutils, traitlets, jupyter-core, entrypoints, webencodings, bleach, pyrsistent, jsonschema, nbformat, nbconvert, backcall, ptyprocess, pexpect, parso, jedi, pickleshare, wcwidth, prompt-toolkit, ipython, pyzmq, tornado, python-dateutil, jupyter-client, ipykernel, terminado, Send2Trash, prometheus-client, notebook, jupyter-latex-envs, jupyter-contrib-core, pyyaml, jupyter-nbextensions-configurator, lxml, jupyter-highlight-selected-word, jupyter-contrib-nbextensions
Successfully installed MarkupSafe-1.1.1 Send2Trash-1.5.0 backcall-0.1.0 bleach-3.1.0 decorator-4.4.1 defusedxml-0.6.0 entrypoints-0.3 ipykernel-5.1.3 ipython-7.10.1 ipython-genutils-0.2.0 jedi-0.15.1 jinja2-2.10.3 jsonschema-3.2.0 jupyter-client-5.3.4 jupyter-contrib-core-0.3.3 jupyter-contrib-nbextensions-0.5.1 jupyter-core-4.6.1 jupyter-highlight-selected-word-0.2.0 jupyter-latex-envs-1.4.6 jupyter-nbextensions-configurator-0.4.1 lxml-4.4.2 mistune-0.8.4 nbconvert-5.6.1 nbformat-4.4.0 notebook-6.0.2 pandocfilters-1.4.2 parso-0.5.1 pexpect-4.7.0 pickleshare-0.7.5 prometheus-client-0.7.1 prompt-toolkit-3.0.2 ptyprocess-0.6.0 pygments-2.5.2 pyrsistent-0.15.6 python-dateutil-2.8.1 pyyaml-5.2 pyzmq-18.1.1 terminado-0.8.3 testpath-0.4.4 tornado-6.0.3 traitlets-4.3.3 wcwidth-0.1.7 webencodings-0.5.1
pip install -r requirements.txt
Processing /home/jenkins/.cache/pip/wheels/eb/c0/e6/f0f525ada263f7f72f4b3efcc7f5b3c12a372f07f55a2d687d/cigar-0.1.3-cp36-none-any.whl
Collecting matplotlib==2.0.2
  Using cached https://files.pythonhosted.org/packages/60/d4/6b6d8a7a6bc69a1602ab372f6fc6e88ef88a8a96398a1a25edbac636295b/matplotlib-2.0.2-cp36-cp36m-manylinux1_x86_64.whl
Collecting ipython==7.8.0
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Collecting jupyter==1.0.0
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Processing /home/jenkins/.cache/pip/wheels/c7/22/3a/f4974d7fd9a0af6699bc047075a66335f607057f072a797543/bdgenomics.adam-0.30.0a0-cp36-none-any.whl
Processing /home/jenkins/.cache/pip/wheels/ec/df/8e/7e6efc45fd34e2850763a5ec5ac7f27052424d26105f12f971/bdgenomics.mango.pileup-0.0.6a0-cp36-none-any.whl
Collecting ipywidgets==7.0.0
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Processing /home/jenkins/.cache/pip/wheels/52/41/b0/bf50409fe2b1d3b79afa3eed71b54b3e30fe5b695db2c7ba2e/psutil-5.6.7-cp36-cp36m-linux_x86_64.whl
Requirement already satisfied: python-dateutil in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.8.1)
Collecting pytz
  Using cached https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl
Collecting numpy>=1.7.1
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Requirement already satisfied: six>=1.10 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.13.0)
Collecting pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6
  Using cached https://files.pythonhosted.org/packages/c0/0c/fc2e007d9a992d997f04a80125b0f183da7fb554f1de701bbb70a8e7d479/pyparsing-2.4.5-py2.py3-none-any.whl
Collecting cycler>=0.10
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (2.5.2)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (4.7.0)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.7.5)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.15.1)
Requirement already satisfied: backcall in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.1.0)
Requirement already satisfied: traitlets>=4.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (4.3.3)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (4.4.1)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (42.0.2.post20191203)
Collecting prompt-toolkit<2.1.0,>=2.0.0
  Using cached https://files.pythonhosted.org/packages/87/61/2dfea88583d5454e3a64f9308a686071d58d59a55db638268a6413e1eb6d/prompt_toolkit-2.0.10-py3-none-any.whl
Collecting qtconsole
  Using cached https://files.pythonhosted.org/packages/7c/57/3528b84ffa753e2089908bbf74bb5ae60653eb7a63797b6234e88b847d67/qtconsole-4.6.0-py2.py3-none-any.whl
Collecting jupyter-console
  Using cached https://files.pythonhosted.org/packages/cb/ee/6374ae8c21b7d0847f9c3722dcdfac986b8e54fa9ad9ea66e1eb6320d2b8/jupyter_console-6.0.0-py2.py3-none-any.whl
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (6.0.2)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.1.3)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.6.1)
Processing /home/jenkins/.cache/pip/wheels/ab/09/4d/0d184230058e654eb1b04467dbc1292f00eaa186544604b471/pyspark-2.4.4-py2.py3-none-any.whl
Collecting pytest==2.8.3
  Using cached https://files.pythonhosted.org/packages/b0/7b/7aa01fa919ca0d038cdf8744ba9fd0416b04ec1878a68bfd77f39534e408/pytest-2.8.3-py2.py3-none-any.whl
Collecting modin[ray]==0.6.1
  Using cached https://files.pythonhosted.org/packages/4f/62/dbea5f16c685aa1bab65787562f4990d5b78caa915c7d323b47013c454ad/modin-0.6.1-py3-none-any.whl
Collecting widgetsnbextension~=3.0.0
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Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 7)) (4.4.0)
Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython==7.8.0->-r requirements.txt (line 3)) (0.6.0)
Requirement already satisfied: parso>=0.5.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jedi>=0.10->ipython==7.8.0->-r requirements.txt (line 3)) (0.5.1)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from traitlets>=4.2->ipython==7.8.0->-r requirements.txt (line 3)) (0.2.0)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->ipython==7.8.0->-r requirements.txt (line 3)) (0.1.7)
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Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.3)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (18.1.1)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.7.1)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.5.0)
Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (2.10.3)
Requirement already satisfied: tornado>=5.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (6.0.3)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.4.4)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.4)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.4.2)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.3)
Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.1.0)
Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.6.0)
Collecting py4j==0.10.7
  Using cached https://files.pythonhosted.org/packages/e3/53/c737818eb9a7dc32a7cd4f1396e787bd94200c3997c72c1dbe028587bd76/py4j-0.10.7-py2.py3-none-any.whl
Requirement already satisfied: py>=1.4.29 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pytest==2.8.3->bdgenomics.mango.pileup==0.0.6a0->-r requirements.txt (line 6)) (1.8.0)
Collecting pandas==0.25.1
  Using cached https://files.pythonhosted.org/packages/73/9b/52e228545d14f14bb2a1622e225f38463c8726645165e1cb7dde95bfe6d4/pandas-0.25.1-cp36-cp36m-manylinux1_x86_64.whl
Collecting ray==0.7.3; extra == "ray"
  Using cached https://files.pythonhosted.org/packages/a7/21/de080b8458de41fd8ac20dd96547418c0ed94eab4359e5885f4041d61337/ray-0.7.3-cp36-cp36m-manylinux1_x86_64.whl
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (3.2.0)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jinja2->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.1.1)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5.1)
Requirement already satisfied: pyyaml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->-r requirements.txt (line 6)) (5.2)
Collecting protobuf>=3.8.0
  Downloading https://files.pythonhosted.org/packages/b8/be/438a8b90701aacfd7d741541571a236edbcf46f772caa25fcb27c4937e9e/protobuf-3.11.1-cp36-cp36m-manylinux1_x86_64.whl (1.3MB)
Collecting funcsigs
  Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting click
  Using cached https://files.pythonhosted.org/packages/fa/37/45185cb5abbc30d7257104c434fe0b07e5a195a6847506c074527aa599ec/Click-7.0-py2.py3-none-any.whl
Collecting redis
  Using cached https://files.pythonhosted.org/packages/32/ae/28613a62eea0d53d3db3147f8715f90da07667e99baeedf1010eb400f8c0/redis-3.3.11-py2.py3-none-any.whl
Collecting colorama
  Downloading https://files.pythonhosted.org/packages/c9/dc/45cdef1b4d119eb96316b3117e6d5708a08029992b2fee2c143c7a0a5cc5/colorama-0.4.3-py2.py3-none-any.whl
Collecting filelock
  Using cached https://files.pythonhosted.org/packages/93/83/71a2ee6158bb9f39a90c0dea1637f81d5eef866e188e1971a1b1ab01a35a/filelock-3.0.12-py3-none-any.whl
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (0.15.6)
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (1.2.0)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (19.3.0)
Requirement already satisfied: zipp>=0.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (0.6.0)
Requirement already satisfied: more-itertools in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from zipp>=0.5->importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (8.0.2)
ERROR: bdgenomics-mango-pileup 0.0.6a0 has requirement six==1.11.0, but you'll have six 1.13.0 which is incompatible.
Installing collected packages: cigar, pytz, numpy, pyparsing, cycler, matplotlib, prompt-toolkit, ipython, widgetsnbextension, ipywidgets, qtconsole, jupyter-console, jupyter, py4j, pyspark, bdgenomics.adam, pytest, pandas, protobuf, funcsigs, click, redis, colorama, filelock, ray, modin, bdgenomics.mango.pileup, psutil
  Found existing installation: prompt-toolkit 3.0.2
    Uninstalling prompt-toolkit-3.0.2:
      Successfully uninstalled prompt-toolkit-3.0.2
  Found existing installation: ipython 7.10.1
    Uninstalling ipython-7.10.1:
      Successfully uninstalled ipython-7.10.1
  Found existing installation: pytest 3.9.1
    Uninstalling pytest-3.9.1:
      Successfully uninstalled pytest-3.9.1
Successfully installed bdgenomics.adam-0.30.0a0 bdgenomics.mango.pileup-0.0.6a0 cigar-0.1.3 click-7.0 colorama-0.4.3 cycler-0.10.0 filelock-3.0.12 funcsigs-1.0.2 ipython-7.8.0 ipywidgets-7.0.0 jupyter-1.0.0 jupyter-console-6.0.0 matplotlib-2.0.2 modin-0.6.1 numpy-1.17.4 pandas-0.25.1 prompt-toolkit-2.0.10 protobuf-3.11.1 psutil-5.6.7 py4j-0.10.7 pyparsing-2.4.5 pyspark-2.4.4 pytest-2.8.3 pytz-2019.3 qtconsole-4.6.0 ray-0.7.3 redis-3.3.11 widgetsnbextension-3.0.8
+ popd
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ mvn -U -P python,distribution package -DskipTests -Dhadoop.version=2.7.5 -Dspark.version=2.4.4
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
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[INFO] Reactor Build Order:
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[INFO] mango
[INFO] mango: CORE
[INFO] Mango: Python APIs
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO] mango: Distribution
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[INFO] Building mango 0.0.4-SNAPSHOT
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
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[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent ---
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[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent >>>
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[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
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[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CORE 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/scala-2.11.12/classes at 1575814692715
[WARNING] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class AlignmentRecordMaterialization(@transient sc: SparkContext,
[WARNING]                                       ^
[WARNING] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class FeatureMaterialization(@transient sc: SparkContext,
[WARNING]                               ^
[WARNING] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]                                                              @transient sc: SparkContext,
[WARNING]                                                               ^
[WARNING] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class VariantContextMaterialization(@transient sc: SparkContext,
[WARNING]                                      ^
[WARNING] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
[WARNING]     try {
[WARNING]     ^
[WARNING] warning: there was one deprecation warning; re-run with -deprecation for details
[WARNING] warning: there were four feature warnings; re-run with -feature for details
[WARNING] 7 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 9 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core ---
[INFO] Test Source directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala:-1: info: compiling
[INFO] Compiling 13 source files to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/scala-2.11.12/test-classes at 1575814703823
[WARNING] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala/org/bdgenomics/mango/models/LazyMaterializationSuite.scala:77: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class LazyDummy(@transient sc: SparkContext,
[WARNING]                  ^
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-core ---
[INFO] Building jar: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core ---
[INFO] Building jar: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-core ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-core >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-core <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class AlignmentRecordMaterialization(@transient sc: SparkContext,
                                      ^
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class FeatureMaterialization(@transient sc: SparkContext,
                              ^
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
                                                             @transient sc: SparkContext,
                                                              ^
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class VariantContextMaterialization(@transient sc: SparkContext,
                                     ^
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
    try {
    ^
warning: there were four feature warnings; re-run with -feature for details
model contains 42 documentable templates
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/RefSeq.scala:29: warning: Variable GENOME undefined in comment for object RefSeqFile in object RefSeqFile
 * Processes refSeq file, downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                     ^
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                  ^
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                                    ^
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:51: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz
                                                                                   ^
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:52: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - refSeq.txt file: downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                 ^
11 warnings found
[INFO] Building jar: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.4-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Python APIs 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-python ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-python ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-python ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-python ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-python ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (dev-python) @ mango-python ---
pip install -e .
Obtaining file:///tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-python
Requirement already satisfied: cigar==0.1.3 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (0.1.3)
Requirement already satisfied: matplotlib==2.0.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (2.0.2)
Requirement already satisfied: ipython==7.8.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (7.8.0)
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (1.0.0)
Requirement already satisfied: bdgenomics.adam==0.30.0a0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (0.30.0a0)
Requirement already satisfied: bdgenomics.mango.pileup==0.0.6a0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (0.0.6a0)
Requirement already satisfied: ipywidgets==7.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (7.0.0)
Requirement already satisfied: psutil in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango==0.0.6a2) (5.6.7)
Requirement already satisfied: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (2.4.5)
Requirement already satisfied: pytz in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (2019.3)
Requirement already satisfied: cycler>=0.10 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (0.10.0)
Requirement already satisfied: python-dateutil in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (2.8.1)
Requirement already satisfied: six>=1.10 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (1.13.0)
Requirement already satisfied: numpy>=1.7.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.6a2) (1.17.4)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (4.4.1)
Requirement already satisfied: traitlets>=4.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (4.3.3)
Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (2.0.10)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.15.1)
Requirement already satisfied: backcall in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.1.0)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (42.0.2.post20191203)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.7.5)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (4.7.0)
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython==7.8.0->bdgenomics.mango==0.0.6a2) (2.5.2)
Requirement already satisfied: jupyter-console in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (6.0.0)
Requirement already satisfied: qtconsole in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (4.6.0)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (5.6.1)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (5.1.3)
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (6.0.2)
Requirement already satisfied: pyspark>=1.6.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.adam==0.30.0a0->bdgenomics.mango==0.0.6a2) (2.4.4)
Requirement already satisfied: modin[ray]==0.6.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (0.6.1)
Requirement already satisfied: pytest==2.8.3 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (2.8.3)
Requirement already satisfied: widgetsnbextension~=3.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (3.0.8)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (4.4.0)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from traitlets>=4.2->ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.2.0)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.1.7)
Requirement already satisfied: parso>=0.5.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jedi>=0.10->ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.5.1)
Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython==7.8.0->bdgenomics.mango==0.0.6a2) (0.6.0)
Requirement already satisfied: jupyter-client in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter-console->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (5.3.4)
Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (4.6.1)
Requirement already satisfied: jinja2>=2.4 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (2.10.3)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.4.4)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.8.4)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.3)
Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (3.1.0)
Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.6.0)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.4.2)
Requirement already satisfied: tornado>=4.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipykernel->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (6.0.3)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (18.1.1)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.5.0)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.7.1)
Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.8.3)
Requirement already satisfied: py4j==0.10.7 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pyspark>=1.6.0->bdgenomics.adam==0.30.0a0->bdgenomics.mango==0.0.6a2) (0.10.7)
Requirement already satisfied: pandas==0.25.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (0.25.1)
Requirement already satisfied: ray==0.7.3; extra == "ray" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (0.7.3)
Requirement already satisfied: py>=1.4.29 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pytest==2.8.3->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (1.8.0)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (3.2.0)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jinja2>=2.4->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (1.1.1)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.6a2) (0.5.1)
Requirement already satisfied: protobuf>=3.8.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (3.11.1)
Requirement already satisfied: click in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (7.0)
Requirement already satisfied: colorama in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (0.4.3)
Requirement already satisfied: filelock in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (3.0.12)
Requirement already satisfied: funcsigs in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (1.0.2)
Requirement already satisfied: redis in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (3.3.11)
Requirement already satisfied: pyyaml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->bdgenomics.mango==0.0.6a2) (5.2)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (0.15.6)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (19.3.0)
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (1.2.0)
Requirement already satisfied: zipp>=0.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (0.6.0)
Requirement already satisfied: more-itertools in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from zipp>=0.5->importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.6a2) (8.0.2)
Installing collected packages: bdgenomics.mango
  Running setup.py develop for bdgenomics.mango
Successfully installed bdgenomics.mango
python setup.py sdist bdist_egg
running sdist
running egg_info
writing bdgenomics.mango.egg-info/PKG-INFO
writing dependency_links to bdgenomics.mango.egg-info/dependency_links.txt
writing requirements to bdgenomics.mango.egg-info/requires.txt
writing top-level names to bdgenomics.mango.egg-info/top_level.txt
reading manifest file 'bdgenomics.mango.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no files found matching '*.jar' under directory 'deps/jars'
writing manifest file 'bdgenomics.mango.egg-info/SOURCES.txt'
running check
creating bdgenomics.mango-0.0.6a2
creating bdgenomics.mango-0.0.6a2/bdgenomics
creating bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
creating bdgenomics.mango-0.0.6a2/bdgenomics/mango
creating bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying files to bdgenomics.mango-0.0.6a2...
copying MANIFEST.in -> bdgenomics.mango-0.0.6a2
copying README.md -> bdgenomics.mango-0.0.6a2
copying requirements.txt -> bdgenomics.mango-0.0.6a2
copying setup.py -> bdgenomics.mango-0.0.6a2
copying version.py -> bdgenomics.mango-0.0.6a2
copying bdgenomics/__init__.py -> bdgenomics.mango-0.0.6a2/bdgenomics
copying bdgenomics.mango.egg-info/PKG-INFO -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/SOURCES.txt -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/dependency_links.txt -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/requires.txt -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/top_level.txt -> bdgenomics.mango-0.0.6a2/bdgenomics.mango.egg-info
copying bdgenomics/mango/__init__.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/alignments.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/coverage.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/distribution.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/features.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/genotypes.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/utils.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/variants.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango
copying bdgenomics/mango/test/__init__.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/alignment_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/coverage_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/distribution_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/feature_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/genotypes_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/notebook_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
copying bdgenomics/mango/test/variant_test.py -> bdgenomics.mango-0.0.6a2/bdgenomics/mango/test
Writing bdgenomics.mango-0.0.6a2/setup.cfg
creating dist
Creating tar archive
removing 'bdgenomics.mango-0.0.6a2' (and everything under it)
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/mango
copying bdgenomics/mango/utils.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/alignments.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/features.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/genotypes.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/variants.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/__init__.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/coverage.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/distribution.py -> build/lib/bdgenomics/mango
creating build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/notebook_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/alignment_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/genotypes_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/feature_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/distribution_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/__init__.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/variant_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/coverage_test.py -> build/lib/bdgenomics/mango/test
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/utils.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/alignments.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/features.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/genotypes.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/variants.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/notebook_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/alignment_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/genotypes_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/feature_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/distribution_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/variant_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/coverage_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/coverage.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/distribution.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/utils.py to utils.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/alignments.py to alignments.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/features.py to features.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/genotypes.py to genotypes.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/variants.py to variants.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/notebook_test.py to notebook_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/alignment_test.py to alignment_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/genotypes_test.py to genotypes_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/feature_test.py to feature_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/distribution_test.py to distribution_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/variant_test.py to variant_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/coverage_test.py to coverage_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/coverage.py to coverage.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/distribution.py to distribution.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.cpython-36.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
bdgenomics.__pycache__.__init__.cpython-36: module references __path__
bdgenomics.mango.__pycache__.__init__.cpython-36: module references __path__
creating 'dist/bdgenomics.mango-0.0.6a2-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-python ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-python ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-python/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-python ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (test-python) @ mango-python ---
pushd ../example-files/notebooks \
	&& jupyter nbconvert --to python mango-python-coverage.ipynb \
	&& jupyter nbconvert --to python mango-python-alignment.ipynb \
	&& jupyter nbconvert --to python mango-viz.ipynb \
	&& jupyter nbconvert --to python mango-python-variants.ipynb
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/example-files/notebooks /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-python
[NbConvertApp] Converting notebook mango-python-coverage.ipynb to python
[NbConvertApp] Writing 1051 bytes to mango-python-coverage.py
[NbConvertApp] Converting notebook mango-python-alignment.ipynb to python
[NbConvertApp] Writing 2194 bytes to mango-python-alignment.py
[NbConvertApp] Converting notebook mango-viz.ipynb to python
[NbConvertApp] Writing 2140 bytes to mango-viz.py
[NbConvertApp] Converting notebook mango-python-variants.ipynb to python
[NbConvertApp] Writing 1941 bytes to mango-python-variants.py
mkdir -p target
export PYTHONPATH=/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/python:/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip:${PYTHONPATH} \
&& export PYSPARK_SUBMIT_ARGS="--jars ../mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar --driver-class-path ../mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar pyspark-shell" \
&& python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux -- Python 3.6.9, pytest-2.8.3, py-1.8.0, pluggy-0.3.1 -- /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin/python
cachedir: .cache
rootdir: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-python, inifile: 
collecting ... collected 25 items

bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_coverage_distribution PASSED
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_fragment_distribution PASSED
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution PASSED
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_maximal_bin_size PASSED
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_no_elements PASSED
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_mapq_distribution PASSED
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_visualize_alignments PASSED
bdgenomics/mango/test/coverage_test.py::CoverageTest::test_coverage_distribution PASSED
bdgenomics/mango/test/coverage_test.py::CoverageTest::test_example_coverage PASSED
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_cumulative_count_distribution PASSED
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_fail_on_invalid_sample PASSED
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_normalized_count_distribution PASSED
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_sampling PASSED
bdgenomics/mango/test/feature_test.py::FeatureTest::test_visualize_features PASSED
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeCallRatesDistribution PASSED
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeSummary PASSED
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_HetHomRatioDistribution PASSED
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistribution PASSED
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistributionSampling PASSED
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_visualize_genotypes PASSED
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_alignment_example PASSED
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_coverage_example PASSED
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_example PASSED
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_variants_example PASSED
bdgenomics/mango/test/variant_test.py::VariantTest::test_visualize_variants PASSED

- generated xml file: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-python/target/pytest-reports/tests.xml -
========================= 25 passed in 106.87 seconds ==========================
pushd ../example-files/notebooks \
	&& rm mango-python-coverage.py \
	&& rm mango-python-alignment.py \
	&& rm mango-viz.py \
	&& rm mango-python-variants.py
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/example-files/notebooks /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-python
exit
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-python ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-python ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-python ---
[WARNING] JAR will be empty - no content was marked for inclusion!
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-python ---
[INFO] No sources in project. Archive not created.
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-python ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-python >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-python ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-python ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-python <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-python ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CLI 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/scala-2.11.12/classes at 1575814837217
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/scala-2.11.12/test-classes at 1575814844577
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- sass-maven-plugin:3.7.1:update-stylesheets (default) @ mango-cli ---
[INFO] Checked 0 files for /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/sass
[INFO] Checked 0 filtered (**/*.css) files for /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.4-SNAPSHOT/css
[INFO] Compiling Sass templates
[INFO] Queueing Sass template for compile: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets => /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets
Ignoring eventmachine-1.2.7 because its extensions are not built. Try: gem pristine eventmachine --version 1.2.7
Ignoring ffi-1.9.25 because its extensions are not built. Try: gem pristine ffi --version 1.9.25
Ignoring http_parser.rb-0.6.0 because its extensions are not built. Try: gem pristine http_parser.rb --version 0.6.0
[INFO]     >> /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets/main.scss => /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets/main.css
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (Run `npm install`) @ mango-cli ---
npm notice created a lockfile as package-lock.json. You should commit this file.
npm WARN mango-cli@0.0.2 No repository field.

audited 140 packages in 1.959s
found 0 vulnerabilities

[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:copy-resources (copy-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8761 resources
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-cli ---
[INFO] Building jar: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-cli ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-cli ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-cli >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-cli <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
model contains 26 documentable templates
[INFO] Building jar: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- appassembler-maven-plugin:1.10:assemble (default) @ mango-cli ---
[INFO] Installing artifact /home/jenkins/.m2/repository/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro/1.8.2/avro-1.8.2.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/avro/avro/1.8.2/avro-1.8.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/tukaani/xz/1.5/xz-1.5.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-codec/commons-codec/1.4/commons-codec-1.4.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-pool/commons-pool/1.6/commons-pool-1.6.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/commons-pool/commons-pool/1.6/commons-pool-1.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli-spark2_2.11/0.29.0/adam-cli-spark2_2.11-0.29.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli-spark2_2.11/0.29.0/adam-cli-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-apis-spark2_2.11/0.29.0/adam-apis-spark2_2.11-0.29.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis-spark2_2.11/0.29.0/adam-apis-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/args4j/args4j/2.33/args4j-2.33.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/args4j/args4j/2.33/args4j-2.33.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/guice/4.2.0/guice-4.2.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/inject/guice/4.2.0/guice-4.2.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/javax/inject/javax.inject/1/javax.inject-1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/aopalliance/aopalliance/1.0/aopalliance-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-core-spark2_2.11/0.29.0/adam-core-spark2_2.11-0.29.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core-spark2_2.11/0.29.0/adam-core-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/objenesis/objenesis/2.1/objenesis-2.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/objenesis/objenesis/2.1/objenesis-2.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-io/commons-io/2.6/commons-io-2.6.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/commons-io/commons-io/2.6/commons-io-2.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.29.0/adam-codegen-spark2_2.11-0.29.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.29.0/adam-codegen-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.14.0/bdg-formats-0.14.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.14.0/bdg-formats-0.14.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar
[INFO] Installing artifact /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-ga4gh/0.8.0/convert-ga4gh-0.8.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.8.0/convert-ga4gh-0.8.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.8.0/convert-htsjdk-0.8.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.8.0/convert-htsjdk-0.8.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.8.0/convert-0.8.0.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.8.0/convert-0.8.0.jar
[INFO] Installing artifact /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli/0.0.4-SNAPSHOT/mango-cli-0.0.4-SNAPSHOT.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Assembly 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/scala-2.11.12/classes at 1575814874338
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly ---
[INFO] Test Source directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-assembly ---
[INFO] Building jar: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ mango-assembly ---
[INFO] Including org.bdgenomics.mango:mango-cli:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.3 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.14.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
[INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra.rl:rl_2.11:jar:0.4.10 in the shaded jar.
[INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar.
[INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar.
[INFO] Including joda-time:joda-time:jar:2.9.1 in the shaded jar.
[INFO] Including org.joda:joda-convert:jar:1.8.1 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.5 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.11.12 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.8.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.8.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.8.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.8.1 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] mango-cli-0.0.4-SNAPSHOT.jar, adam-cli-spark2_2.11-0.29.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar with /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: Distribution 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.4.1:single (default) @ mango-distribution ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
[INFO] Building tar: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  4.595 s]
[INFO] mango: CORE ........................................ SUCCESS [ 33.180 s]
[INFO] Mango: Python APIs ................................. SUCCESS [01:54 min]
[INFO] mango: CLI ......................................... SUCCESS [ 36.084 s]
[INFO] Mango: Assembly .................................... SUCCESS [ 22.382 s]
[INFO] mango: Distribution ................................ SUCCESS [ 27.046 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:57 min
[INFO] Finished at: 2019-12-08T06:22:02-08:00
[INFO] Final Memory: 88M/1495M
[INFO] ------------------------------------------------------------------------
+ pushd mango-python
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ make clean
pip uninstall -y bdgenomics.mango
Uninstalling bdgenomics.mango-0.0.6a2:
  Successfully uninstalled bdgenomics.mango-0.0.6a2
rm -rf src/*.egg-info
rm -rf build/
+ popd
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ pushd mango-viz
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ make prepare
pip install -r requirements.txt
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.0.0)
Requirement already satisfied: ipywidgets==7.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from -r requirements.txt (line 2)) (7.0.0)
Collecting six==1.11.0
  Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Requirement already satisfied: modin[ray]==0.6.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from -r requirements.txt (line 4)) (0.6.1)
Requirement already satisfied: pytest==2.8.3 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from -r requirements.txt (line 5)) (2.8.3)
Requirement already satisfied: jupyter_contrib_nbextensions==0.5.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from -r requirements.txt (line 6)) (0.5.1)
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (6.0.2)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (5.1.3)
Requirement already satisfied: jupyter-console in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (6.0.0)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (5.6.1)
Requirement already satisfied: qtconsole in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (4.6.0)
Requirement already satisfied: traitlets>=4.3.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 2)) (4.3.3)
Requirement already satisfied: widgetsnbextension~=3.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 2)) (3.0.8)
Requirement already satisfied: ipython>=4.0.0; python_version >= "3.3" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 2)) (7.8.0)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 2)) (4.4.0)
Requirement already satisfied: pandas==0.25.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from modin[ray]==0.6.1->-r requirements.txt (line 4)) (0.25.1)
Requirement already satisfied: ray==0.7.3; extra == "ray" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from modin[ray]==0.6.1->-r requirements.txt (line 4)) (0.7.3)
Requirement already satisfied: py>=1.4.29 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pytest==2.8.3->-r requirements.txt (line 5)) (1.8.0)
Requirement already satisfied: jupyter-contrib-core>=0.3.3 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (0.3.3)
Requirement already satisfied: lxml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (4.4.2)
Requirement already satisfied: tornado in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (6.0.3)
Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (4.6.1)
Requirement already satisfied: pyyaml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (5.2)
Requirement already satisfied: jupyter-highlight-selected-word>=0.1.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (0.2.0)
Requirement already satisfied: jupyter-latex-envs>=1.3.8 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (1.4.6)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (0.2.0)
Requirement already satisfied: jupyter-nbextensions-configurator>=0.4.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (0.4.1)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (18.1.1)
Requirement already satisfied: jupyter-client>=5.3.4 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (5.3.4)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (1.5.0)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (0.7.1)
Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (2.10.3)
Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (0.8.3)
Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter-console->jupyter==1.0.0->-r requirements.txt (line 1)) (2.0.10)
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter-console->jupyter==1.0.0->-r requirements.txt (line 1)) (2.5.2)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.4.4)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.8.4)
Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.6.0)
Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (3.1.0)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (1.4.2)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.3)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from traitlets>=4.3.1->ipywidgets==7.0.0->-r requirements.txt (line 2)) (4.4.1)
Requirement already satisfied: backcall in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.1.0)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.7.5)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.15.1)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (42.0.2.post20191203)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (4.7.0)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (3.2.0)
Requirement already satisfied: pytz>=2017.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->-r requirements.txt (line 4)) (2019.3)
Requirement already satisfied: numpy>=1.13.3 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->-r requirements.txt (line 4)) (1.17.4)
Requirement already satisfied: python-dateutil>=2.6.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->-r requirements.txt (line 4)) (2.8.1)
Requirement already satisfied: filelock in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (3.0.12)
Requirement already satisfied: funcsigs in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (1.0.2)
Requirement already satisfied: colorama in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (0.4.3)
Requirement already satisfied: protobuf>=3.8.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (3.11.1)
Requirement already satisfied: redis in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (3.3.11)
Requirement already satisfied: click in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (7.0)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jinja2->notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (1.1.1)
Requirement already satisfied: ptyprocess; os_name != "nt" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from terminado>=0.8.1->notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (0.6.0)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->jupyter-console->jupyter==1.0.0->-r requirements.txt (line 1)) (0.1.7)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.5.1)
Requirement already satisfied: parso>=0.5.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.5.1)
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (1.2.0)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (19.3.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.15.6)
Requirement already satisfied: zipp>=0.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.6.0)
Requirement already satisfied: more-itertools in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from zipp>=0.5->importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (8.0.2)
Installing collected packages: six
  Found existing installation: six 1.13.0
    Uninstalling six-1.13.0:
      Successfully uninstalled six-1.13.0
Successfully installed six-1.11.0
# install node_modules
cd bdgenomics/mango/js; \
	npm install
npm WARN deprecated browserslist@1.7.7: Browserslist 2 could fail on reading Browserslist >3.0 config used in other tools.
npm WARN deprecated minimatch@2.0.10: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated minimatch@0.2.14: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated graceful-fs@1.2.3: please upgrade to graceful-fs 4 for compatibility with current and future versions of Node.js

> spawn-sync@1.0.15 postinstall /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js/node_modules/spawn-sync
> node postinstall


> flow-bin@0.21.0 postinstall /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js/node_modules/flow-bin
> node lib/install.js

  ✔ flow binary test passed successfully
npm WARN prepublish-on-install As of npm@5, `prepublish` scripts are deprecated.
npm WARN prepublish-on-install Use `prepare` for build steps and `prepublishOnly` for upload-only.
npm WARN prepublish-on-install See the deprecation note in `npm help scripts` for more information.

> bdgenomics.mango.pileup@0.0.3-a0 prepublish /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js
> webpack

Hash: cc5171780dfef6f8f819330a8086a7bb1904b41b59f9ab4563f109013ebc
Version: webpack 1.15.0
Child
    Hash: cc5171780dfef6f8f819
    Version: webpack 1.15.0
    Time: 74ms
           Asset     Size  Chunks             Chunk Names
    extension.js  1.96 kB       0  [emitted]  main
       [0] ./src/extension.js 525 bytes {0} [built]
Child
    Hash: 330a8086a7bb1904b41b
    Version: webpack 1.15.0
    Time: 5663ms
           Asset     Size  Chunks             Chunk Names
        index.js  2.34 MB       0  [emitted]  main
    index.js.map   2.8 MB       0  [emitted]  main
       [0] ./src/index.js 957 bytes {0} [built]
       [7] ./src/pileupViewer.js 4.04 kB {0} [built]
     [526] ./src/utils.js 303 bytes {0} [built]
        + 525 hidden modules
Child
    Hash: 59f9ab4563f109013ebc
    Version: webpack 1.15.0
    Time: 5665ms
           Asset     Size  Chunks             Chunk Names
        index.js  2.32 MB       0  [emitted]  main
    index.js.map  2.77 MB       0  [emitted]  main
       [0] ./src/embed.js 576 bytes {0} [built]
       [1] ./src/pileupViewer.js 4.04 kB {0} [built]
     [520] ./src/utils.js 303 bytes {0} [built]
        + 519 hidden modules
npm notice created a lockfile as package-lock.json. You should commit this file.
npm WARN bdgenomics.mango.pileup@0.0.3-a0 No license field.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@1.2.9 (node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.9: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

added 759 packages from 697 contributors and audited 3136 packages in 90.127s
found 15 vulnerabilities (5 low, 2 moderate, 8 high)
  run `npm audit fix` to fix them, or `npm audit` for details
+ popd
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ mvn -P widgets test
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango
[INFO] Mango: Python visualization hooks
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent ---
[INFO] Modified 0 of 230 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Python visualization hooks 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-viz ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-viz ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-viz ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-viz ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (dev-python) @ mango-viz ---
rm -rf bdgenomics/mango/pileup/static
rm -rf bdgenomics/mango/js/dist
rm -rf bdgenomics.mango.pileup.egg-info/
pip install -v -e .
Created temporary directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/pip-ephem-wheel-cache-93xxi4aa
Created temporary directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9fftdiv1
Created requirements tracker '/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9fftdiv1'
Created temporary directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/pip-install-q9ggns_w
Obtaining file:///tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz
  Added file:///tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz to build tracker '/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9fftdiv1'
    Running setup.py (path:/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/setup.py) egg_info for package from file:///tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz
    Running command python setup.py egg_info
    running egg_info
    running jsdeps
    6.4.1
    6.4.1
    Installing build dependencies with npm.  This may take a while...
    npm WARN prepublish-on-install As of npm@5, `prepublish` scripts are deprecated.
    npm WARN prepublish-on-install Use `prepare` for build steps and `prepublishOnly` for upload-only.
    npm WARN prepublish-on-install See the deprecation note in `npm help scripts` for more information.

    > bdgenomics.mango.pileup@0.0.3-a0 prepublish /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js
    > webpack

    Hash: cc5171780dfef6f8f819330a8086a7bb1904b41b59f9ab4563f109013ebc
    Version: webpack 1.15.0
    Child
        Hash: cc5171780dfef6f8f819
        Version: webpack 1.15.0
        Time: 76ms
               Asset     Size  Chunks             Chunk Names
        extension.js  1.96 kB       0  [emitted]  main
           [0] ./src/extension.js 525 bytes {0} [built]
    Child
        Hash: 330a8086a7bb1904b41b
        Version: webpack 1.15.0
        Time: 5745ms
               Asset     Size  Chunks             Chunk Names
            index.js  2.34 MB       0  [emitted]  main
        index.js.map   2.8 MB       0  [emitted]  main
           [0] ./src/index.js 957 bytes {0} [built]
           [7] ./src/pileupViewer.js 4.04 kB {0} [built]
         [526] ./src/utils.js 303 bytes {0} [built]
            + 525 hidden modules
    Child
        Hash: 59f9ab4563f109013ebc
        Version: webpack 1.15.0
        Time: 5745ms
               Asset     Size  Chunks             Chunk Names
            index.js  2.32 MB       0  [emitted]  main
        index.js.map  2.77 MB       0  [emitted]  main
           [0] ./src/embed.js 576 bytes {0} [built]
           [1] ./src/pileupViewer.js 4.04 kB {0} [built]
         [520] ./src/utils.js 303 bytes {0} [built]
            + 519 hidden modules
    npm WARN bdgenomics.mango.pileup@0.0.3-a0 No license field.
    npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@1.2.9 (node_modules/fsevents):
    npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.9: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

    audited 3136 packages in 11.778s
    found 15 vulnerabilities (5 low, 2 moderate, 8 high)
      run `npm audit fix` to fix them, or `npm audit` for details
    creating bdgenomics.mango.pileup.egg-info
    writing bdgenomics.mango.pileup.egg-info/PKG-INFO
    writing dependency_links to bdgenomics.mango.pileup.egg-info/dependency_links.txt
    writing requirements to bdgenomics.mango.pileup.egg-info/requires.txt
    writing top-level names to bdgenomics.mango.pileup.egg-info/top_level.txt
    writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    reading manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
    warning: no previously-included files matching '__pycache__' found anywhere in distribution
    warning: no previously-included files matching '.DS_Store' found anywhere in distribution
    warning: no files found matching 'version.py'
    warning: no files found matching '*.*' under directory 'pileup/static'
    writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
  Source in /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz has version 0.0.6a1, which satisfies requirement bdgenomics.mango.pileup==0.0.6a1 from file:///tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz
  Removed bdgenomics.mango.pileup==0.0.6a1 from file:///tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz from build tracker '/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9fftdiv1'
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (1.0.0)
Requirement already satisfied: ipywidgets==7.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (7.0.0)
Requirement already satisfied: six==1.11.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (1.11.0)
Requirement already satisfied: modin[ray]==0.6.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (0.6.1)
  Installing extra requirements: 'ray'
Requirement already satisfied: pytest==2.8.3 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (2.8.3)
Requirement already satisfied: jupyter_contrib_nbextensions==0.5.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (5.6.1)
Requirement already satisfied: jupyter-console in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (6.0.0)
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (6.0.2)
Requirement already satisfied: qtconsole in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.6.0)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (5.1.3)
Requirement already satisfied: widgetsnbextension~=3.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (3.0.8)
Requirement already satisfied: traitlets>=4.3.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.3.3)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.4.0)
Requirement already satisfied: ipython>=4.0.0; python_version >= "3.3" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (7.8.0)
Requirement already satisfied: pandas==0.25.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (0.25.1)
Requirement already satisfied: ray==0.7.3; extra == "ray" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (0.7.3)
Requirement already satisfied: py>=1.4.29 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pytest==2.8.3->bdgenomics.mango.pileup==0.0.6a1) (1.8.0)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.2.0)
Requirement already satisfied: jupyter-latex-envs>=1.3.8 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (1.4.6)
Requirement already satisfied: lxml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (4.4.2)
Requirement already satisfied: jupyter-highlight-selected-word>=0.1.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.2.0)
Requirement already satisfied: jupyter-nbextensions-configurator>=0.4.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.4.1)
Requirement already satisfied: pyyaml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (5.2)
Requirement already satisfied: jupyter-contrib-core>=0.3.3 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.3.3)
Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (4.6.1)
Requirement already satisfied: tornado in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (6.0.3)
Requirement already satisfied: jinja2>=2.4 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (2.10.3)
Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.6.0)
Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (3.1.0)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.8.4)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.3)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.4.4)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.4.2)
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (2.5.2)
Requirement already satisfied: jupyter-client in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter-console->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (5.3.4)
Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jupyter-console->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (2.0.10)
Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.8.3)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.7.1)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (18.1.1)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.5.0)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from traitlets>=4.3.1->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.4.1)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (3.2.0)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.15.1)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.7.5)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (42.0.2.post20191203)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.7.0)
Requirement already satisfied: backcall in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.1.0)
Requirement already satisfied: python-dateutil>=2.6.1 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (2.8.1)
Requirement already satisfied: numpy>=1.13.3 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (1.17.4)
Requirement already satisfied: pytz>=2017.2 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (2019.3)
Requirement already satisfied: protobuf>=3.8.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (3.11.1)
Requirement already satisfied: filelock in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (3.0.12)
Requirement already satisfied: colorama in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (0.4.3)
Requirement already satisfied: click in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (7.0)
Requirement already satisfied: funcsigs in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (1.0.2)
Requirement already satisfied: redis in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (3.3.11)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jinja2>=2.4->nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.1.1)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->jupyter-console->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.1.7)
Requirement already satisfied: ptyprocess; os_name != "nt" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from terminado>=0.8.1->notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.6.0)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (19.3.0)
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.2.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.15.6)
Requirement already satisfied: parso>=0.5.0 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
Requirement already satisfied: zipp>=0.5 in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.6.0)
Requirement already satisfied: more-itertools in /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages (from zipp>=0.5->importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (8.0.2)
Installing collected packages: bdgenomics.mango.pileup
  Found existing installation: bdgenomics.mango.pileup 0.0.6a0
    Uninstalling bdgenomics.mango.pileup-0.0.6a0:
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages/~dgenomics.mango.pileup-0.0.6a0.dist-info
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages/bdgenomics.mango.pileup-0.0.6a0.dist-info/
      Created temporary directory: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/pip-uninstall-n_z5g4rz
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages/bdgenomics/__init__.py
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages/bdgenomics/~_pycache__
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages/bdgenomics/__pycache__/
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages/bdgenomics/~ango
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages/bdgenomics/mango/
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/share/jupyter/nbextensions/~ileup
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/share/jupyter/nbextensions/pileup/
      Successfully uninstalled bdgenomics.mango.pileup-0.0.6a0
  Running setup.py develop for bdgenomics.mango.pileup
    Running command /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/setup.py'"'"'; __file__='"'"'/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
    running develop
    running egg_info
    writing bdgenomics.mango.pileup.egg-info/PKG-INFO
    writing dependency_links to bdgenomics.mango.pileup.egg-info/dependency_links.txt
    writing requirements to bdgenomics.mango.pileup.egg-info/requires.txt
    writing top-level names to bdgenomics.mango.pileup.egg-info/top_level.txt
    reading manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
    warning: no previously-included files matching '__pycache__' found anywhere in distribution
    warning: no previously-included files matching '.DS_Store' found anywhere in distribution
    warning: no files found matching 'version.py'
    warning: no files found matching '*.*' under directory 'pileup/static'
    writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    running build_ext
    Creating /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/lib/python3.6/site-packages/bdgenomics.mango.pileup.egg-link (link to .)
    Adding bdgenomics.mango.pileup 0.0.6a1 to easy-install.pth file

    Installed /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz
Successfully installed bdgenomics.mango.pileup
Cleaning up...
Removed build tracker '/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9fftdiv1'
jupyter nbextension uninstall pileup
No installed extension 'pileup' found.
jupyter nbextension enable --py widgetsnbextension
Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: OK
jupyter nbextension install --py --symlink --user bdgenomics.mango.pileup
Installing /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/pileup/static -> pileup
Symlinking: /home/jenkins/.local/share/jupyter/nbextensions/pileup -> /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/pileup/static
- Validating: OK

    To initialize this nbextension in the browser every time the notebook (or other app) loads:
    
          jupyter nbextension enable bdgenomics.mango.pileup --user --py
    
jupyter nbextension enable bdgenomics.mango.pileup --py --user
Enabling notebook extension pileup/extension...
      - Validating: OK
python setup.py sdist bdist_egg
running sdist
running egg_info
writing bdgenomics.mango.pileup.egg-info/PKG-INFO
writing dependency_links to bdgenomics.mango.pileup.egg-info/dependency_links.txt
writing requirements to bdgenomics.mango.pileup.egg-info/requires.txt
writing top-level names to bdgenomics.mango.pileup.egg-info/top_level.txt
reading manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no files found matching 'version.py'
warning: no files found matching '*.*' under directory 'pileup/static'
writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
running check
creating bdgenomics.mango.pileup-0.0.6a1
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io/test
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/static
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying files to bdgenomics.mango.pileup-0.0.6a1...
copying MANIFEST.in -> bdgenomics.mango.pileup-0.0.6a1
copying README.md -> bdgenomics.mango.pileup-0.0.6a1
copying requirements.txt -> bdgenomics.mango.pileup-0.0.6a1
copying setup.py -> bdgenomics.mango.pileup-0.0.6a1
copying bdgenomics/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics
copying bdgenomics.mango.pileup.egg-info/PKG-INFO -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/SOURCES.txt -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/dependency_links.txt -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/not-zip-safe -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/requires.txt -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/top_level.txt -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics/mango/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango
copying bdgenomics/mango/io/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/bedfile.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/genomicfile.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/readers.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/utils.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/test/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io/test
copying bdgenomics/mango/io/test/test_bed.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io/test
copying bdgenomics/mango/pileup/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/_version.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/pileupViewer.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/sources.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/track.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/static/extension.js -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js.map -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/test/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_application.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_embed.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_notebook.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_types.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
Writing bdgenomics.mango.pileup-0.0.6a1/setup.cfg
creating dist
Creating tar archive
removing 'bdgenomics.mango.pileup-0.0.6a1' (and everything under it)
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/mango
copying bdgenomics/mango/__init__.py -> build/lib/bdgenomics/mango
creating build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/utils.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/bedfile.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/genomicfile.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/readers.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/__init__.py -> build/lib/bdgenomics/mango/io
creating build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/sources.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/pileupViewer.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/track.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/__init__.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/_version.py -> build/lib/bdgenomics/mango/pileup
creating build/lib/bdgenomics/mango/io/test
copying bdgenomics/mango/io/test/__init__.py -> build/lib/bdgenomics/mango/io/test
copying bdgenomics/mango/io/test/test_bed.py -> build/lib/bdgenomics/mango/io/test
creating build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_embed.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_types.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/__init__.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_application.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_notebook.py -> build/lib/bdgenomics/mango/pileup/test
creating build/lib/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/extension.js -> build/lib/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js -> build/lib/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js.map -> build/lib/bdgenomics/mango/pileup/static
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/mango
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/io/utils.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/io/bedfile.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/io/genomicfile.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/io/readers.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/io/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/io/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/io/test/test_bed.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/sources.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/static/index.js -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/static/extension.js -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/static/index.js.map -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/pileupViewer.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/track.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/_version.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_embed.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_types.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_application.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_notebook.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/utils.py to utils.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/bedfile.py to bedfile.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/genomicfile.py to genomicfile.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/readers.py to readers.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test/test_bed.py to test_bed.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/sources.py to sources.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/pileupViewer.py to pileupViewer.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/track.py to track.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/_version.py to _version.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/test_embed.py to test_embed.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/test_types.py to test_types.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/test_application.py to test_application.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/test_notebook.py to test_notebook.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.cpython-36.pyc
installing package data to build/bdist.linux-x86_64/egg
running install_data
creating build/bdist.linux-x86_64/egg/share
creating build/bdist.linux-x86_64/egg/share/jupyter
creating build/bdist.linux-x86_64/egg/share/jupyter/nbextensions
creating build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
copying bdgenomics/mango/pileup/static/extension.js -> build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
copying bdgenomics/mango/pileup/static/index.js -> build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
copying bdgenomics/mango/pileup/static/index.js.map -> build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/bdgenomics.mango.pileup-0.0.6a1-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-viz ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (test-python) @ mango-viz ---
pushd examples \
	&& jupyter nbconvert --to python pileup-tutorial.ipynb
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/examples /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz
[NbConvertApp] Converting notebook pileup-tutorial.ipynb to python
[NbConvertApp] Writing 2872 bytes to pileup-tutorial.py
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics/mango/
============================= test session starts ==============================
platform linux -- Python 3.6.9, pytest-2.8.3, py-1.8.0, pluggy-0.3.1 -- /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin/python
cachedir: .cache
rootdir: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz, inifile: 
collecting ... collected 28 items

bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_column_type PASSED
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_required_columns PASSED
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_to_json PASSED
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_validate_num_rows PASSED
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_visualization PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_features PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_genes PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_genotypes PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_pileup PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_toSVG PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_variants PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_zoomIn PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_zoomOut PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_embed_pileup PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_embed_data_two_widgets PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_snippet PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_minimal_pileup_html PASSED
bdgenomics/mango/pileup/test/test_notebook.py::MangoVizExampleTest::test_notebook_example PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_coverage PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_features PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_genes PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_genome PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_location PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_pileup PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_scale PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_variants PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_serialization PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_tracks_serialization PASSED

- generated xml file: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/target/pytest-reports/tests.xml -
========================== 28 passed in 8.20 seconds ===========================
# run lint and flow for js
pushd bdgenomics/mango/js \
	&& npm run lint
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz

> bdgenomics.mango.pileup@0.0.3-a0 lint /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js
> ./scripts/lint.sh

[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-viz ---
[INFO] Tests are skipped.
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  3.966 s]
[INFO] Mango: Python visualization hooks .................. SUCCESS [ 32.069 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 36.197 s
[INFO] Finished at: 2019-12-08T06:24:13-08:00
[INFO] Final Memory: 23M/1089M
[INFO] ------------------------------------------------------------------------
+ pushd mango-viz
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-viz /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ make clean
rm -rf bdgenomics/mango/js/dist
rm -rf bdgenomics.mango.pileup.egg-info/
rm -rf bdgenomics/mango/pileup/static/
rm -rf dist/
rm -rf bdgenomics/mango/js/node_modules
jupyter nbextension uninstall pileup
Removing: /home/jenkins/.local/share/jupyter/nbextensions/pileup
+ popd
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ grep bdgenomics.mango
+ tar tzvf mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
+ grep egg
drwxr-xr-x 0/0                    0 2019-12-08 06:18 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/
-rwxr-xr-x jenkins/jenkins       46 2019-12-08 06:18 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/dependency_links.txt
-rwxr-xr-x jenkins/jenkins      145 2019-12-08 06:18 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/requires.txt
-rwxr-xr-x jenkins/jenkins       11 2019-12-08 06:18 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/top_level.txt
-rwxr-xr-x jenkins/jenkins      827 2019-12-08 06:18 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/SOURCES.txt
-rwxr-xr-x jenkins/jenkins      798 2019-12-08 06:18 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/PKG-INFO
-rw-r--r-- jenkins/jenkins    51395 2019-12-08 06:18 mango-distribution-0.0.4-SNAPSHOT/repo/bdgenomics.mango-0.0.6a2-py3.6.egg
+ MANGO_NOTEBOOK_LOGS=/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-notebook.log
+ sleep 2
+ bash -xv /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/mango-notebook
+ kill 95680
+ echo 'Mango Notebook Succeeded'
Mango Notebook Succeeded
+ cp -r mango-python/target /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../mango-python/
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test: line 177: 95680 Terminated              bash -xv ${PROJECT_ROOT}/bin/mango-notebook &> ${MANGO_NOTEBOOK_LOGS}
+ source deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
++ [[ -z /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ]]

if (( $? == 0 )); then
    # Inverse of activation: run deactivate scripts prior to deactivating env
    _CONDA_D="${CONDA_PREFIX}/etc/conda/deactivate.d"
    if [[ -d $_CONDA_D ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi

#    # get the activation path that would have been provided for this prefix
#    _LAST_ACTIVATE_PATH=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$CONDA_PREFIX")
#
#    # in activate, we replace a placeholder so that conda keeps its place in the PATH order
#    # The activate script sets _CONDA_HOLD here to activate that behavior.
#    #   Otherwise, PATH is simply removed.
#    if [ -n "$_CONDA_HOLD" ]; then
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'CONDA_PATH_PLACEHOLDER\1', '$PATH', 1))")"
#    else
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'', '$PATH', 1))")"
#    fi
#
#    unset _LAST_ACTIVATE_PATH

    export PATH=$("$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX")

    unset CONDA_DEFAULT_ENV
    unset CONDA_PREFIX
    unset CONDA_PATH_BACKUP
    export PS1="$CONDA_PS1_BACKUP"
    unset CONDA_PS1_BACKUP
    unset _CONDA_PYTHON2
else
    unset _CONDA_PYTHON2
    return $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe
++ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ unset CONDA_DEFAULT_ENV
++ unset CONDA_PREFIX
++ unset CONDA_PATH_BACKUP
++ export PS1=
++ PS1=
++ unset CONDA_PS1_BACKUP
++ unset _CONDA_PYTHON2

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ conda remove -y --name mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe:

The following packages will be REMOVED:

    _libgcc_mutex:   0.1-main               
    ca-certificates: 2019.11.27-0           
    certifi:         2019.11.28-py36_0      
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       9.1.0-hdf63c60_0       
    libstdcxx-ng:    9.1.0-hdf63c60_0       
    ncurses:         6.1-he6710b0_1         
    nodejs:          10.13.0-he6710b0_0     
    openssl:         1.1.1d-h7b6447c_3      
    pip:             19.3.1-py36_0          
    python:          3.6.9-h265db76_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      42.0.2-py36_0          
    sqlite:          3.30.1-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.6-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-h7b6447c_3      

+ MANGO_BROWSER_LOGS=/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/mango-submit.log
+ sleep 10
+ bash -xv /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../example-files/browser-scripts/run-example.sh
+ curl -s -N --header 'Content-type: application/json' --request POST --data '{"pageToken":null,"pageSize":200,"readGroupIds":["chr17_7500000-7515000_sam"],"referenceId":"chr17","start":1,"end":100}' http://localhost:8080/reads/search
+ grep alignments
  "alignments": [],
+ [[ 0 != 0 ]]
+ grep variants
+ curl -s -N --header 'Content-type: application/json' --request POST --data '{"variantSetId":"ALL_chr17_7500000-7515000_phase3_shapeit2_mvncall_integrated_v5a_20130502_genotypes_vcf","pageToken":null,"pageSize":400,"referenceName":"chr17","callSetIds":[],"start":7500000,"end":7515000}' http://localhost:8080/variants/search
  "variants": [{
+ [[ 0 != 0 ]]
+ PROCESSES=($(ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }'))
ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }'
++ ps aux
++ grep -F browser-scripts/run-example.sh
++ grep -v -F grep
++ awk '{ print $2 }'
+ '[' 1 -gt 0 ']'
+ echo 'Mango Browser Succeeded'
Mango Browser Succeeded
+ kill 95770
+ TEST_GENOME=anoGam1
+ bash -xv /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/make_genome anoGam1 /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded
#!/usr/bin/env bash
#
# Licensed to Big Data Genomics (BDG) under one
# or more contributor license agreements.  See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership.  The BDG licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.  You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

# Runs MakeGenome, which generates a .genome file containing reference, genes, cytoband, and chromsizes.
# Requires 2 arguments: genome name and output file to save .genome file to.

SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})
dirname ${BASH_SOURCE[0]}
++ dirname /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/make_genome
+ SOURCE_DIR=/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin

# get Mango jar
MANGO_CLI_JAR=$(${SOURCE_DIR}/find-mango-assembly.sh)
${SOURCE_DIR}/find-mango-assembly.sh
++ /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/find-mango-assembly.sh
+ MANGO_CLI_JAR=/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar

SPARK_SUBMIT=$(${SOURCE_DIR}/find-spark.sh)
${SOURCE_DIR}/find-spark.sh
++ /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/find-spark.sh
+ SPARK_SUBMIT=/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit

# submit the job to Spark
"$SPARK_SUBMIT" \
  --class "org.bdgenomics.adam.cli.MangoMain" \
  --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
  --conf spark.kryo.registrator=org.bdgenomics.mango.serialization.MangoKryoRegistrator \
  $MANGO_CLI_JAR \
  "MakeGenome" "$@" \

+ /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit --class org.bdgenomics.adam.cli.MangoMain --conf spark.serializer=org.apache.spark.serializer.KryoSerializer --conf spark.kryo.registrator=org.bdgenomics.mango.serialization.MangoKryoRegistrator /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar MakeGenome anoGam1 /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded
19/12/08 06:24:32 WARN Utils: Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
19/12/08 06:24:32 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/12/08 06:24:32 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.MangoMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/12/08 06:24:32 INFO SparkContext: Running Spark version 2.4.4
19/12/08 06:24:32 INFO SparkContext: Submitted application: MakeGenome
19/12/08 06:24:32 INFO SecurityManager: Changing view acls to: jenkins
19/12/08 06:24:32 INFO SecurityManager: Changing modify acls to: jenkins
19/12/08 06:24:32 INFO SecurityManager: Changing view acls groups to: 
19/12/08 06:24:32 INFO SecurityManager: Changing modify acls groups to: 
19/12/08 06:24:32 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
19/12/08 06:24:33 INFO Utils: Successfully started service 'sparkDriver' on port 42007.
19/12/08 06:24:33 INFO SparkEnv: Registering MapOutputTracker
19/12/08 06:24:33 INFO SparkEnv: Registering BlockManagerMaster
19/12/08 06:24:33 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/12/08 06:24:33 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/12/08 06:24:33 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-bd9a019d-8bc2-4c62-accd-7d9cefa725eb
19/12/08 06:24:33 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/12/08 06:24:33 INFO SparkEnv: Registering OutputCommitCoordinator
19/12/08 06:24:33 WARN Utils: Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
19/12/08 06:24:33 INFO Utils: Successfully started service 'SparkUI' on port 4041.
19/12/08 06:24:33 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.27:4041
19/12/08 06:24:33 INFO SparkContext: Added JAR file:/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar at spark://192.168.10.27:42007/jars/mango-assembly-0.0.4-SNAPSHOT.jar with timestamp 1575815073549
19/12/08 06:24:33 INFO Executor: Starting executor ID driver on host localhost
19/12/08 06:24:33 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 35165.
19/12/08 06:24:33 INFO NettyBlockTransferService: Server created on 192.168.10.27:35165
19/12/08 06:24:33 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/12/08 06:24:33 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.27, 35165, None)
19/12/08 06:24:33 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.27:35165 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.27, 35165, None)
19/12/08 06:24:33 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.27, 35165, None)
19/12/08 06:24:33 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.27, 35165, None)
Exception in thread "Thread-28" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-40" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
19/12/08 06:24:37 WARN GenomeConfig: No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1
19/12/08 06:24:37 INFO MakeGenome: Saved genome anoGam1 to /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded
19/12/08 06:24:37 INFO MakeGenome: Overall Duration: 4.61 secs
19/12/08 06:24:37 INFO SparkContext: Invoking stop() from shutdown hook
19/12/08 06:24:37 INFO SparkUI: Stopped Spark web UI at http://192.168.10.27:4041
19/12/08 06:24:37 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/12/08 06:24:37 INFO MemoryStore: MemoryStore cleared
19/12/08 06:24:37 INFO BlockManager: BlockManager stopped
19/12/08 06:24:37 INFO BlockManagerMaster: BlockManagerMaster stopped
19/12/08 06:24:37 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/12/08 06:24:37 INFO SparkContext: Successfully stopped SparkContext
19/12/08 06:24:37 INFO ShutdownHookManager: Shutdown hook called
19/12/08 06:24:37 INFO ShutdownHookManager: Deleting directory /tmp/spark-b5816597-db8a-47f5-8e2e-a2c9b3c30c29
19/12/08 06:24:37 INFO ShutdownHookManager: Deleting directory /tmp/spark-4d1f2cec-77c0-4818-848e-13a96a5f2638
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test: line 301: 95770 Terminated              bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS}
+ unzip /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/anoGam1.genome -d /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/anoGam1
Archive:  /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/anoGam1.genome
  inflating: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/anoGam1/refGene.txt.gz  
  inflating: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/anoGam1/properties.txt  
  inflating: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/anoGam1/anoGam1.chrom.sizes  
  inflating: /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/anoGam1/cytoBand.txt.gz  
+ pushd /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/anoGam1
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded/anoGam1 /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ cat properties.txt
sequenceLocation=http://hgdownload.cse.ucsc.edu/goldenPath/anoGam1/bigZips/anoGam1.2bit
chromSizes=anoGam1.chrom.sizes
refGene=refGene.txt.gz
+ cat anoGam1.chrom.sizes
chr2L	48795086
chr2R	62725911
chr3L	41284009
chr3R	53272125
chrM	15363
chrU	59568033
chrX	22145176
+ popd
/tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

clean_up
+ clean_up
+ source deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/anaconda/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/anaconda/bin/deactivate
++ _CONDA_DIR=/home/anaconda/bin

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
++ [[ -z '' ]]
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]
++ return 0
+ conda remove -y --force --name mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe --all

CondaEnvironmentNotFoundError: Could not find environment: mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe .
You can list all discoverable environments with `conda info --envs`.

+ echo 'conda ENV mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe does not exist'
conda ENV mango-build-a97b34cf-f97e-4130-9fb9-9e2e0f026bbe does not exist
+ rm -rf /tmp/mangoTestV15zb3b/deleteMePleaseThisIsNoLongerNeeded
+ rm -rf /tmp/mangoTestMvn1mQYoFF
+ mvn --settings=/home/jenkins/workspace/settings.xml deploy -DskipTests -Pdistribution
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango
[INFO] mango: CORE
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO] mango: Distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent ---
[INFO] Modified 0 of 39 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ mango-parent ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ mango-parent ---
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/mango-parent-0.0.4-SNAPSHOT.pom
[INFO] 
[INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ mango-parent ---
Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/maven-metadata.xml
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Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/maven-metadata.xml (613 B at 1.1 KB/sec)
Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/mango-parent-0.0.4-20191208.142445-183.pom
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Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/maven-metadata.xml
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Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/maven-metadata.xml (432 B at 2.6 KB/sec)
Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/maven-metadata.xml
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[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CORE 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-core ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-core ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-core >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-core <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class AlignmentRecordMaterialization(@transient sc: SparkContext,
                                      ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class FeatureMaterialization(@transient sc: SparkContext,
                              ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
                                                             @transient sc: SparkContext,
                                                              ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class VariantContextMaterialization(@transient sc: SparkContext,
                                     ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
    try {
    ^
warning: there were four feature warnings; re-run with -feature for details
model contains 42 documentable templates
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/RefSeq.scala:29: warning: Variable GENOME undefined in comment for object RefSeqFile in object RefSeqFile
 * Processes refSeq file, downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                     ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                  ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                                    ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:51: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz
                                                                                   ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:52: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - refSeq.txt file: downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                 ^
11 warnings found
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ mango-core ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ mango-core ---
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-SNAPSHOT.jar
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-SNAPSHOT.pom
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-SNAPSHOT-sources.jar
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ mango-core ---
Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/maven-metadata.xml
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Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-20191208.142503-182.jar
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Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-20191208.142503-182.pom
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Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-20191208.142503-182-javadoc.jar
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[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CLI 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- sass-maven-plugin:3.7.1:update-stylesheets (default) @ mango-cli ---
[INFO] Checked 0 files for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/sass
[INFO] Checked 0 filtered (**/*.css) files for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT/css
[INFO] Compiling Sass templates
[INFO] Queueing Sass template for compile: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets => /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets
Ignoring eventmachine-1.2.7 because its extensions are not built. Try: gem pristine eventmachine --version 1.2.7
Ignoring ffi-1.9.25 because its extensions are not built. Try: gem pristine ffi --version 1.9.25
Ignoring http_parser.rb-0.6.0 because its extensions are not built. Try: gem pristine http_parser.rb --version 0.6.0
[INFO]     >> /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.scss => /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.css
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (Run `npm install`) @ mango-cli ---
npm WARN mango-cli@0.0.2 No repository field.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:copy-resources (copy-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8760 resources
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-cli ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-cli ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-cli ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-cli >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-cli <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
model contains 26 documentable templates
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- appassembler-maven-plugin:1.10:assemble (default) @ mango-cli ---
[INFO] Installing artifact /home/jenkins/.m2/repository/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro/1.8.2/avro-1.8.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro/1.8.2/avro-1.8.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/tukaani/xz/1.5/xz-1.5.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-codec/commons-codec/1.4/commons-codec-1.4.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-pool/commons-pool/1.6/commons-pool-1.6.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-pool/commons-pool/1.6/commons-pool-1.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli-spark2_2.11/0.29.0/adam-cli-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli-spark2_2.11/0.29.0/adam-cli-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-apis-spark2_2.11/0.29.0/adam-apis-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis-spark2_2.11/0.29.0/adam-apis-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/args4j/args4j/2.33/args4j-2.33.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/args4j/args4j/2.33/args4j-2.33.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/guice/4.2.0/guice-4.2.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/inject/guice/4.2.0/guice-4.2.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/javax/inject/javax.inject/1/javax.inject-1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/aopalliance/aopalliance/1.0/aopalliance-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-core-spark2_2.11/0.29.0/adam-core-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core-spark2_2.11/0.29.0/adam-core-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/objenesis/objenesis/2.1/objenesis-2.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/objenesis/objenesis/2.1/objenesis-2.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-io/commons-io/2.6/commons-io-2.6.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-io/commons-io/2.6/commons-io-2.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.29.0/adam-codegen-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.29.0/adam-codegen-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.14.0/bdg-formats-0.14.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.14.0/bdg-formats-0.14.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar
[INFO] Installing artifact /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-ga4gh/0.8.0/convert-ga4gh-0.8.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.8.0/convert-ga4gh-0.8.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.8.0/convert-htsjdk-0.8.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.8.0/convert-htsjdk-0.8.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.8.0/convert-0.8.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.8.0/convert-0.8.0.jar
[INFO] Installing artifact /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli/0.0.4-SNAPSHOT/mango-cli-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ mango-cli ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ mango-cli ---
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-cli/0.0.4-SNAPSHOT/mango-cli-0.0.4-SNAPSHOT.jar
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-cli/0.0.4-SNAPSHOT/mango-cli-0.0.4-SNAPSHOT.pom
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-cli/0.0.4-SNAPSHOT/mango-cli-0.0.4-SNAPSHOT-sources.jar
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-cli/0.0.4-SNAPSHOT/mango-cli-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ mango-cli ---
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[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Assembly 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ mango-assembly ---
[INFO] Including org.bdgenomics.mango:mango-cli:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.3 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.14.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
[INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra.rl:rl_2.11:jar:0.4.10 in the shaded jar.
[INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar.
[INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar.
[INFO] Including joda-time:joda-time:jar:2.9.1 in the shaded jar.
[INFO] Including org.joda:joda-convert:jar:1.8.1 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.5 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.11.12 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.8.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.8.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.8.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.8.1 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] mango-cli-0.0.4-SNAPSHOT.jar, adam-cli-spark2_2.11-0.29.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar with /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-shaded.jar
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ mango-assembly ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ mango-assembly ---
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-assembly/0.0.4-SNAPSHOT/mango-assembly-0.0.4-SNAPSHOT.jar
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-assembly/0.0.4-SNAPSHOT/mango-assembly-0.0.4-SNAPSHOT.pom
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-assembly/0.0.4-SNAPSHOT/mango-assembly-0.0.4-SNAPSHOT-sources.jar
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-assembly/0.0.4-SNAPSHOT/mango-assembly-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ mango-assembly ---
Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-assembly/0.0.4-SNAPSHOT/maven-metadata.xml
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Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-assembly/0.0.4-SNAPSHOT/maven-metadata.xml
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Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-assembly/0.0.4-SNAPSHOT/mango-assembly-0.0.4-20191208.142554-172.jar
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