FailedConsole Output

Started by upstream project "mango-prb" build number 834
originally caused by:
 GitHub pull request #494 of commit 2a6dfbaaa6dc79a7f5b26f9b0deca8aa54755b60 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-staging-worker-02 (ubuntu staging-02 staging) in workspace /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/pull/*:refs/remotes/origin/pr/*
Checking out Revision 1edf11fb172c57fbbe2f4178da4596eed4d18027 (origin/pr/494/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 1edf11fb172c57fbbe2f4178da4596eed4d18027
 > git rev-list c90580069db7be603bb69fc3ed517f972d2571b7 # timeout=10
[ubuntu] $ /bin/bash /tmp/hudson8111980170016860199.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/mangoTestMvnpmmz3Bo

# 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/mangoTestMvnpmmz3Bo: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 ${BASH_SOURCE[0]} 
+++ dirname /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../pom.xml
++ head -2
++ sed 's/ *<version>//g'
++ tail -1
++ sed 's/<\/version>//g'
+ VERSION=0.0.3-SNAPSHOT

# 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 2.3.3 ]]

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 0.0.3-SNAPSHOT on Spark 2.3.3 and Hadoop 2.7.5'
Testing MANGO version 0.0.3-SNAPSHOT on Spark 2.3.3 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...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-cli:[unknown-version], /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/pom.xml, line 39, column 15
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango
[INFO] mango: CORE
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.0.0:clean (default-clean) @ mango-parent ---
[INFO] Deleting /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CORE 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.0.0:clean (default-clean) @ mango-core ---
[INFO] Deleting /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CLI 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.0.0:clean (default-clean) @ mango-cli ---
[INFO] Deleting /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Assembly 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.0.0:clean (default-clean) @ mango-assembly ---
[INFO] Deleting /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  0.220 s]
[INFO] mango: CORE ........................................ SUCCESS [  0.095 s]
[INFO] mango: CLI ......................................... SUCCESS [  0.516 s]
[INFO] Mango: Assembly .................................... SUCCESS [  0.055 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.166 s
[INFO] Finished at: 2019-05-10T14:51:08-07:00
[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 494 ]]
+ COVERALLS_PRB_OPTION=-DpullRequest=494

# 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...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-cli:[unknown-version], /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/pom.xml, line 39, column 15
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango
[INFO] mango: CORE
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.3-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 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://oss.sonatype.org/content/repositories/snapshots/commons-codec/commons-codec/maven-metadata.xml
Downloading: https://repository.apache.org/snapshots/commons-codec/commons-codec/maven-metadata.xml
Downloading: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml
672/672 B   
            
Downloaded: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml (672 B at 2.0 KB/sec)
            
            
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.0.1:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/classes at 1557525078660
[WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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] warning: there were three inliner warnings; re-run with -Yinline-warnings for details
[WARNING] 8 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 18 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 20 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/test/scala:-1: info: compiling
[INFO] Compiling 13 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes at 1557525099638
[WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.5.1:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-core ---
Discovery starting.
Discovery completed in 615 milliseconds.
Run starting. Expected test count is: 70
DiscoverySuite:
2019-05-10 14:51:49 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2019-05-10 14:51:49 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-05-10 14:51:49 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-05-10 14:51:51 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:
2019-05-10 14:51:51 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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
2019-05-10 14:51:57 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
2019-05-10 14:52:04 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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
2019-05-10 14:52:18 WARN  Bookkeep:66 - bookkeeping queue is empty
2019-05-10 14:52:18 WARN  LazyDummy:247 - memory limit exceeded. Dropping null from cache
2019-05-10 14:52:18 WARN  LazyDummy:247 - memory limit exceeded. Dropping chrM from cache
- Should check and clear memory
FeatureMaterializationSuite:
- assert raw data returns from one block
2019-05-10 14:52:18 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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
2019-05-10 14:52:43 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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
VcfReaderSuite:
- Should load local vcf file
2019-05-10 14:52:45 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz.tbi...
- Gets file header
- 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
2019-05-10 14:52:45 WARN  VCFInputFormat:410 - No tabix index file found for file:/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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, 2 seconds.
Total number of tests run: 70
Suites: completed 13, aborted 0
Tests: succeeded 70, 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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.0.1:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/scoverage-classes at 1557525173306
[WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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.
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[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
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[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [1609 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scoverage-data]
[WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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] warning: there were three inliner warnings; re-run with -Yinline-warnings for details
[WARNING] 8 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 24 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 20 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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:3.5.1:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-core ---
Discovery starting.
Discovery completed in 626 milliseconds.
Run starting. Expected test count is: 70
DiscoverySuite:
2019-05-10 14:53:20 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2019-05-10 14:53:20 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-05-10 14:53:21 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-05-10 14:53:22 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:
2019-05-10 14:53:23 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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
2019-05-10 14:53:28 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
2019-05-10 14:53:35 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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
2019-05-10 14:53:52 WARN  Bookkeep:66 - bookkeeping queue is empty
2019-05-10 14:53:52 WARN  LazyDummy:247 - memory limit exceeded. Dropping null from cache
2019-05-10 14:53:52 WARN  LazyDummy:247 - memory limit exceeded. Dropping chrM from cache
- Should check and clear memory
FeatureMaterializationSuite:
- assert raw data returns from one block
2019-05-10 14:53:52 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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
2019-05-10 14:54:27 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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
2019-05-10 14:54:28 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz.tbi...
VcfReaderSuite:
- Should load local vcf file
- Gets file header
- 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
2019-05-10 14:54:29 WARN  VCFInputFormat:410 - No tabix index file found for file:/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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, 14 seconds.
Total number of tests run: 70
Suites: completed 13, aborted 0
Tests: succeeded 70, 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 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml
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[INFO] 
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[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.0.1:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2855 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/classes at 1557525280758
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[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-compiler-plugin:3.5.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1: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 ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes at 1557525290619
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-cli ---
Discovery starting.
Discovery completed in 720 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:
2019-05-10 14:55:01 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2019-05-10 14:55:01 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-05-10 14:55:02 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-05-10 14:55:04 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
2019-05-10 14:55:05 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx...
2019-05-10 14:55:05 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx...
- Should pass for discovery mode
scala/reflect/io/JavaToolsPlatformArchive
scala/reflect/io/JavaToolsPlatformArchive
- 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
2019-05-10 14:55:49 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-100" 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$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-112" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$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)
2019-05-10 14:55:52 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 55 seconds, 816 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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.0.1:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2855 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/scoverage-classes at 1557525359114
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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 [872 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[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-compiler-plugin:3.5.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1: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 ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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:3.5.1:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-cli ---
Discovery starting.
Discovery completed in 896 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:
2019-05-10 14:56:13 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2019-05-10 14:56:13 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-05-10 14:56:13 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-05-10 14:56:16 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
2019-05-10 14:56:17 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx...
2019-05-10 14:56:17 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx...
- Should pass for discovery mode
scala/reflect/io/JavaToolsPlatformArchive
scala/reflect/io/JavaToolsPlatformArchive
- 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
2019-05-10 14:57:33 WARN  VcfReader:206 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-99" 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$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-111" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$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)
2019-05-10 14:57:37 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, 31 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 0.0.3-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:2.2.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.0.1:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/scala-2.11.12/classes at 1557525472417
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[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:3.5.1:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1: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:2.2.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.0.1:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/scala-2.11.12/scoverage-classes at 1557525490575
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from cloudera
[INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https
[INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org
[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:3.5.1:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1: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 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ mango-parent ---
[INFO] Starting Coveralls job for jenkins (834 / https://amplab.cs.berkeley.edu/jenkins/job/mango-prb/HADOOP_VERSION=2.7.5,SCALAVER=2.11,SPARK_VERSION=2.3.3,label=ubuntu/834/)
[INFO] Using repository token <secret>
[INFO] Git commit 1edf11f in optimize_http
[INFO] Writing Coveralls data to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/target/coveralls.json...
[INFO] Processing coverage report from /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 104ms
[INFO] Gathered code coverage metrics for 21 source files with 3984 lines of code:
[INFO] - 1100 relevant lines
[INFO] - 885 covered lines
[INFO] - 215 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 849ms for Job #834.1
[INFO] https://coveralls.io/jobs/48355691
[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 [  1.267 s]
[INFO] mango: CORE ........................................ SUCCESS [03:22 min]
[INFO] mango: CLI ......................................... SUCCESS [03:06 min]
[INFO] Mango: Assembly .................................... SUCCESS [ 39.424 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 07:12 min
[INFO] Finished at: 2019-05-10T14:58:22-07:00
[INFO] Final Memory: 65M/1509M
[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=2.3.3 -DargLine=/tmp/mangoTestMvnpmmz3Bo
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-cli:[unknown-version], /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/pom.xml, line 39, column 15
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[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 0.0.3-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-shade-plugin:3.1.0:shade (default) @ mango-parent ---
[INFO] Replacing original artifact with shaded artifact.
[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 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/repositories/snapshots/commons-codec/commons-codec/maven-metadata.xml
Downloading: https://repository.apache.org/snapshots/commons-codec/commons-codec/maven-metadata.xml
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Downloaded: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml (672 B at 2.9 KB/sec)
            
            
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.0.1:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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:3.5.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 20 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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:3.5.1:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-core ---
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-core ---
[INFO] Including com.github.samtools:htsjdk:jar:2.16.1 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 org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 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 org.scala-lang:scala-compiler: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.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.curator:curator-client:jar:2.7.1 in the shaded jar.
[INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar.
[INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 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 commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar.
[INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar.
[INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar.
[INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar.
[INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar.
[INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar.
[INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar.
[INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar.
[INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar.
[INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar.
[INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar.
[INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar.
[INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar.
[INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar.
[INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar.
[INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar.
[INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar.
[INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar.
[INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar.
[INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar.
[INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar.
[INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar.
[INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar.
[INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar.
[INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar.
[INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar.
[INFO] Including oro:oro:jar:2.0.8 in the shaded jar.
[INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar.
[INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar.
[INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 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.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 org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 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:0.26.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.2 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:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.1 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.
[WARNING] minlog-1.3.0.jar, minlog-1.2.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[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] aopalliance-1.0.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: 
[WARNING]   - org.aopalliance.intercept.ConstructorInterceptor
[WARNING]   - org.aopalliance.intercept.MethodInvocation
[WARNING]   - org.aopalliance.intercept.MethodInterceptor
[WARNING]   - org.aopalliance.intercept.Invocation
[WARNING]   - org.aopalliance.aop.AspectException
[WARNING]   - org.aopalliance.intercept.Interceptor
[WARNING]   - org.aopalliance.intercept.Joinpoint
[WARNING]   - org.aopalliance.aop.Advice
[WARNING]   - org.aopalliance.intercept.ConstructorInvocation
[WARNING] javax.inject-2.4.0-b34.jar, javax.inject-1.jar define 6 overlapping classes: 
[WARNING]   - javax.inject.Inject
[WARNING]   - javax.inject.Singleton
[WARNING]   - javax.inject.Named
[WARNING]   - javax.inject.Scope
[WARNING]   - javax.inject.Provider
[WARNING]   - javax.inject.Qualifier
[WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, spark-tags_2.11-2.3.3.jar, spark-launcher_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, spark-kvstore_2.11-2.3.3.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: 
[WARNING]   - org.apache.spark.unused.UnusedStubClass
[WARNING] commons-logging-1.1.1.jar, jcl-over-slf4j-1.7.16.jar define 6 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING]   - org.apache.commons.logging.Log
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING] kryo-shaded-3.0.3.jar, kryo-2.24.0.jar define 193 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.BeanSerializer$1
[WARNING]   - com.esotericsoftware.kryo.Registration
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.kryo.util.IntMap$Values
[WARNING]   - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl
[WARNING]   - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField
[WARNING]   - com.esotericsoftware.kryo.serializers.JavaSerializer
[WARNING]   - 183 more...
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar with /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT-shaded.jar
[INFO] Dependency-reduced POM written at: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/dependency-reduced-pom.xml
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core ---
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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 ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/${GENOME}/database/refGene.txt.gz
                                                                                     ^
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                  ^
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                                    ^
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:51: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz
                                                                                   ^
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CLI 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml
741/741 B   
            
Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml (741 B at 60.3 KB/sec)
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.0.1:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2855 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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] --- 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-compiler-plugin:3.5.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1: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 ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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:3.5.1:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/sass
[INFO] Checked 0 filtered (**/*.css) files for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT/css
[INFO] Compiling Sass templates
[INFO] Queueing Sass template for compile: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets => /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-1.9.23 because its extensions are not built. Try: gem pristine ffi --version 1.9.23
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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.scss => /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.css
[INFO] 
[INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-cli ---
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-cli ---
[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 commons-logging:commons-logging:jar:1.1.3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.2.4 in the shaded jar.
[INFO] Including org.apache.curator:curator-client:jar:2.7.1 in the shaded jar.
[INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar.
[INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar.
[INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar.
[INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar.
[INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar.
[INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar.
[INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar.
[INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar.
[INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar.
[INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar.
[INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar.
[INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar.
[INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar.
[INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar.
[INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar.
[INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar.
[INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar.
[INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar.
[INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar.
[INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar.
[INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar.
[INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar.
[INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar.
[INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar.
[INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar.
[INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar.
[INFO] Including oro:oro:jar:2.0.8 in the shaded jar.
[INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar.
[INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar.
[INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.26.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.26.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 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.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 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.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:2.16.1 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 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:4.5.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 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:0.26.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.2 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.clapper:grizzled-slf4j_2.11:jar:1.0.2 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.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:0.0.3-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 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 org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar.
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, java-xmlbuilder-1.1.jar define 5 overlapping classes: 
[WARNING]   - com.jamesmurty.utils.NamespaceContextImpl
[WARNING]   - com.jamesmurty.utils.BaseXMLBuilder
[WARNING]   - com.jamesmurty.utils.XMLBuilder
[WARNING]   - com.jamesmurty.utils.XMLBuilder2
[WARNING]   - com.jamesmurty.utils.XMLBuilderRuntimeException
[WARNING] ngs-java-2.9.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 73 overlapping classes: 
[WARNING]   - ngs.itf.ReadItf
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.cause.JvmErrorCause
[WARNING]   - ngs.ReferenceIterator
[WARNING]   - gov.nih.nlm.ncbi.ngs.Manager$1
[WARNING]   - gov.nih.nlm.ncbi.ngs.LMProperties
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.LibraryLoadError
[WARNING]   - gov.nih.nlm.ncbi.ngs.LibDependencies
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.cause.ConnectionProblemCause
[WARNING]   - ngs.itf.PileupEventItf
[WARNING]   - gov.nih.nlm.ncbi.ngs.LibManager$Location
[WARNING]   - 63 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, args4j-2.0.31.jar define 71 overlapping classes: 
[WARNING]   - org.kohsuke.args4j.spi.DoubleOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.MethodSetter
[WARNING]   - org.kohsuke.args4j.spi.StringArrayOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.MacAddressOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.SubCommand
[WARNING]   - org.kohsuke.args4j.spi.PatternOptionHandler
[WARNING]   - org.kohsuke.args4j.ParserProperties$1
[WARNING]   - org.kohsuke.args4j.OptionHandlerFilter$2
[WARNING]   - org.kohsuke.args4j.spi.MultiFileOptionHandler
[WARNING]   - org.kohsuke.args4j.Localizable
[WARNING]   - 61 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jets3t-0.9.4.jar define 616 overlapping classes: 
[WARNING]   - org.jets3t.service.acl.GroupGrantee
[WARNING]   - org.jets3t.service.multithread.CreateObjectsEvent
[WARNING]   - org.jets3t.service.model.S3BucketLoggingStatus
[WARNING]   - contribs.com.centerkey.utils.BareBonesBrowserLaunch
[WARNING]   - org.jets3t.service.impl.rest.CloudFrontXmlResponsesSaxParser$CacheBehaviorHandler
[WARNING]   - org.jets3t.apps.uploader.XmlGenerator$ObjectAndSignatureRequestDetails
[WARNING]   - org.jets3t.service.MultipartUploadChunk
[WARNING]   - org.jets3t.apps.cockpit.Cockpit$27
[WARNING]   - org.jets3t.service.model.S3DeleteMarker
[WARNING]   - org.jets3t.gui.TableSorter$Row
[WARNING]   - 606 more...
[WARNING] javax.inject-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar, javax.inject-1.jar define 6 overlapping classes: 
[WARNING]   - javax.inject.Inject
[WARNING]   - javax.inject.Singleton
[WARNING]   - javax.inject.Named
[WARNING]   - javax.inject.Scope
[WARNING]   - javax.inject.Provider
[WARNING]   - javax.inject.Qualifier
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, parquet-scala_2.10-1.8.3.jar define 19 overlapping classes: 
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$SupportsEqNotEq
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$FloatColumn$
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$Column$class
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$FloatColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$LongColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$BinaryColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$IntColumn$
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn$
[WARNING]   - 9 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-net-2.2.jar define 137 overlapping classes: 
[WARNING]   - org.apache.commons.net.telnet.SimpleOptionHandler
[WARNING]   - org.apache.commons.net.ftp.parser.FTPFileEntryParserFactory
[WARNING]   - org.apache.commons.net.DefaultDatagramSocketFactory
[WARNING]   - org.apache.commons.net.ftp.parser.ConfigurableFTPFileEntryParserImpl
[WARNING]   - org.apache.commons.net.ntp.NTPUDPClient
[WARNING]   - org.apache.commons.net.util.SubnetUtils$1
[WARNING]   - org.apache.commons.net.tftp.TFTP
[WARNING]   - org.apache.commons.net.ftp.FTPClient
[WARNING]   - org.apache.commons.net.echo.EchoTCPClient
[WARNING]   - org.apache.commons.net.telnet.Telnet
[WARNING]   - 127 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, ivy-2.4.0.jar define 744 overlapping classes: 
[WARNING]   - org.apache.ivy.ant.IvyDeliver
[WARNING]   - org.apache.ivy.plugins.resolver.util.ApacheHttpURLLister
[WARNING]   - org.apache.ivy.ant.BuildOBRTask
[WARNING]   - org.apache.ivy.osgi.p2.P2MetadataParser$UnitsHandler$1
[WARNING]   - org.apache.ivy.core.cache.ResolutionCacheManager
[WARNING]   - org.apache.ivy.osgi.repo.EditableRepoDescriptor
[WARNING]   - org.apache.ivy.plugins.parser.AbstractModuleDescriptorParser$AbstractParser
[WARNING]   - org.apache.ivy.plugins.latest.LatestLexicographicStrategy$1
[WARNING]   - org.apache.ivy.osgi.repo.FSManifestIterable$3
[WARNING]   - org.apache.ivy.util.url.HttpClientHandler
[WARNING]   - 734 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, javax.ws.rs-api-2.0.1.jar define 125 overlapping classes: 
[WARNING]   - javax.ws.rs.ext.RuntimeDelegate$HeaderDelegate
[WARNING]   - javax.ws.rs.DefaultValue
[WARNING]   - javax.ws.rs.core.StreamingOutput
[WARNING]   - javax.ws.rs.HEAD
[WARNING]   - javax.ws.rs.ext.WriterInterceptor
[WARNING]   - javax.ws.rs.core.Request
[WARNING]   - javax.ws.rs.ext.Providers
[WARNING]   - javax.ws.rs.container.Suspended
[WARNING]   - javax.ws.rs.container.ConnectionCallback
[WARNING]   - javax.ws.rs.client.FactoryFinder
[WARNING]   - 115 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-network-common_2.11-2.3.3.jar define 1697 overlapping classes: 
[WARNING]   - org.spark_project.guava.annotations.Beta
[WARNING]   - org.spark_project.guava.util.concurrent.UncaughtExceptionHandlers$Exiter
[WARNING]   - org.spark_project.guava.eventbus.Subscribe
[WARNING]   - org.spark_project.guava.collect.TreeRangeMap
[WARNING]   - org.spark_project.guava.collect.ImmutableList$SubList
[WARNING]   - org.spark_project.guava.cache.RemovalCause$1
[WARNING]   - org.spark_project.guava.collect.ForwardingMultimap
[WARNING]   - org.spark_project.guava.io.LimitInputStream
[WARNING]   - org.spark_project.guava.math.BigIntegerMath
[WARNING]   - org.spark_project.guava.collect.Tables
[WARNING]   - 1687 more...
[WARNING] error_prone_annotations-2.2.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 22 overlapping classes: 
[WARNING]   - com.google.errorprone.annotations.NoAllocation
[WARNING]   - com.google.errorprone.annotations.Var
[WARNING]   - com.google.errorprone.annotations.IncompatibleModifiers
[WARNING]   - com.google.errorprone.annotations.CompatibleWith
[WARNING]   - com.google.errorprone.annotations.concurrent.LockMethod
[WARNING]   - com.google.errorprone.annotations.FormatString
[WARNING]   - com.google.errorprone.annotations.DoNotCall
[WARNING]   - com.google.errorprone.annotations.Immutable
[WARNING]   - com.google.errorprone.annotations.RestrictedApi
[WARNING]   - com.google.errorprone.annotations.CompileTimeConstant
[WARNING]   - 12 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-server-2.22.2.jar define 665 overlapping classes: 
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParamConverters$TypeFromString
[WARNING]   - org.glassfish.jersey.server.internal.inject.QueryParamValueFactoryProvider
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParamInjectionResolver
[WARNING]   - org.glassfish.jersey.server.internal.InternalServerProperties
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParameterInjectionBinder$5
[WARNING]   - jersey.repackaged.org.objectweb.asm.FieldWriter
[WARNING]   - org.glassfish.jersey.server.internal.RuntimeDelegateImpl
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParamConverterFactory
[WARNING]   - org.glassfish.jersey.server.internal.monitoring.RequestEventImpl$Builder
[WARNING]   - org.glassfish.jersey.server.ContainerRequest
[WARNING]   - 655 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jsr305-1.3.9.jar define 35 overlapping classes: 
[WARNING]   - javax.annotation.RegEx
[WARNING]   - javax.annotation.concurrent.Immutable
[WARNING]   - javax.annotation.meta.TypeQualifierDefault
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.CheckReturnValue
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Nonnull
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - javax.annotation.MatchesPattern
[WARNING]   - 25 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, gson-2.2.4.jar define 153 overlapping classes: 
[WARNING]   - com.google.gson.internal.bind.JsonTreeWriter
[WARNING]   - com.google.gson.internal.Excluder
[WARNING]   - com.google.gson.JsonDeserializationContext
[WARNING]   - com.google.gson.FieldNamingPolicy$5
[WARNING]   - com.google.gson.internal.LinkedTreeMap$KeySet
[WARNING]   - com.google.gson.internal.$Gson$Types
[WARNING]   - com.google.gson.internal.UnsafeAllocator$2
[WARNING]   - com.google.gson.internal.bind.SqlDateTypeAdapter$1
[WARNING]   - com.google.gson.FieldAttributes
[WARNING]   - com.google.gson.internal.$Gson$Types$ParameterizedTypeImpl
[WARNING]   - 143 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, hk2-api-2.4.0-b34.jar define 165 overlapping classes: 
[WARNING]   - org.glassfish.hk2.api.ActiveDescriptor
[WARNING]   - org.glassfish.hk2.api.Proxiable
[WARNING]   - org.glassfish.hk2.utilities.InjecteeImpl
[WARNING]   - org.glassfish.hk2.api.ProxyCtl
[WARNING]   - org.glassfish.hk2.api.DynamicConfiguration
[WARNING]   - org.glassfish.hk2.internal.ImmediateHelper$1
[WARNING]   - org.glassfish.hk2.api.InjectionResolver
[WARNING]   - org.glassfish.hk2.utilities.ServiceLocatorUtilities$3
[WARNING]   - org.glassfish.hk2.api.Validator
[WARNING]   - org.glassfish.hk2.api.PopulatorPostProcessor
[WARNING]   - 155 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jul-to-slf4j-1.7.16.jar define 1 overlapping classes: 
[WARNING]   - org.slf4j.bridge.SLF4JBridgeHandler
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-xml_2.11-1.0.2.jar define 421 overlapping classes: 
[WARNING]   - scala.xml.PrettyPrinter$Para
[WARNING]   - scala.xml.Group$
[WARNING]   - scala.xml.PrettyPrinter$$anonfun$traverse$1
[WARNING]   - scala.xml.MetaData
[WARNING]   - scala.xml.MalformedAttributeException
[WARNING]   - scala.xml.pull.EvComment
[WARNING]   - scala.xml.parsing.TokenTests$$anonfun$isSpace$1
[WARNING]   - scala.xml.Properties
[WARNING]   - scala.xml.parsing.MarkupParser$$anonfun$1
[WARNING]   - scala.xml.pull.EvEntityRef$
[WARNING]   - 411 more...
[WARNING] avro-1.8.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 1172 overlapping classes: 
[WARNING]   - org.apache.avro.message.SchemaStore
[WARNING]   - avro.shaded.com.google.common.collect.SingletonImmutableList
[WARNING]   - org.apache.avro.io.EncoderFactory$DefaultEncoderFactory
[WARNING]   - avro.shaded.com.google.common.collect.Iterables$15
[WARNING]   - org.apache.avro.GuavaClasses
[WARNING]   - avro.shaded.com.google.common.collect.Sets$PowerSet$1$1
[WARNING]   - avro.shaded.com.google.common.collect.RegularImmutableMap
[WARNING]   - org.apache.avro.generic.GenericDatumReader$2
[WARNING]   - avro.shaded.com.google.common.collect.Synchronized$SynchronizedSortedSet
[WARNING]   - org.apache.avro.file.BZip2Codec
[WARNING]   - 1162 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, aopalliance-repackaged-2.4.0-b34.jar define 17 overlapping classes: 
[WARNING]   - org.aopalliance.reflect.ClassLocator
[WARNING]   - org.aopalliance.reflect.Metadata
[WARNING]   - org.aopalliance.instrument.Instrumentation
[WARNING]   - org.aopalliance.reflect.Field
[WARNING]   - org.aopalliance.intercept.FieldInterceptor
[WARNING]   - org.aopalliance.reflect.Method
[WARNING]   - org.aopalliance.reflect.CodeLocator
[WARNING]   - org.aopalliance.intercept.FieldAccess
[WARNING]   - org.aopalliance.reflect.ProgramUnit
[WARNING]   - org.aopalliance.instrument.UndoNotSupportedException
[WARNING]   - 7 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, convert-0.6.0.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.convert.bdgenomics.SliceToRead
[WARNING]   - org.bdgenomics.convert.bdgenomics.SliceToSequence
[WARNING]   - org.bdgenomics.convert.bdgenomics.BdgenomicsModule
[WARNING]   - org.bdgenomics.convert.ConversionException
[WARNING]   - org.bdgenomics.convert.bdgenomics.OntologyTermToString
[WARNING]   - org.bdgenomics.convert.bdgenomics.StringToVariantAnnotationMessage
[WARNING]   - org.bdgenomics.convert.ConversionStringency
[WARNING]   - org.bdgenomics.convert.bdgenomics.ReadToSlice
[WARNING]   - org.bdgenomics.convert.Converter
[WARNING]   - org.bdgenomics.convert.bdgenomics.ReadToSequence
[WARNING]   - 13 more...
[WARNING] spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 18 overlapping classes: 
[WARNING]   - org.apache.spark.unsafe.types.UTF8String
[WARNING]   - org.apache.spark.unsafe.memory.HeapMemoryAllocator
[WARNING]   - org.apache.spark.unsafe.array.LongArray
[WARNING]   - org.apache.spark.unsafe.types.UTF8String$LongWrapper
[WARNING]   - org.apache.spark.unsafe.bitset.BitSetMethods
[WARNING]   - org.apache.spark.unsafe.memory.UnsafeMemoryAllocator
[WARNING]   - org.apache.spark.sql.catalyst.expressions.HiveHasher
[WARNING]   - org.apache.spark.unsafe.KVIterator
[WARNING]   - org.apache.spark.unsafe.types.CalendarInterval
[WARNING]   - org.apache.spark.unsafe.memory.MemoryBlock
[WARNING]   - 8 more...
[WARNING] lz4-java-1.4.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 77 overlapping classes: 
[WARNING]   - net.jpountz.xxhash.AbstractStreamingXXHash32Java
[WARNING]   - net.jpountz.lz4.LZ4BlockInputStream
[WARNING]   - net.jpountz.lz4.LZ4FrameOutputStream
[WARNING]   - net.jpountz.xxhash.XXHash32JNI
[WARNING]   - net.jpountz.lz4.LZ4BlockOutputStream
[WARNING]   - net.jpountz.lz4.LZ4JNI
[WARNING]   - net.jpountz.lz4.LZ4JavaUnsafeFastDecompressor
[WARNING]   - net.jpountz.lz4.LZ4SafeUtils
[WARNING]   - net.jpountz.xxhash.StreamingXXHash32JNI$Factory
[WARNING]   - net.jpountz.util.UnsafeUtils
[WARNING]   - 67 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, curator-recipes-2.6.0.jar define 190 overlapping classes: 
[WARNING]   - org.apache.curator.framework.recipes.atomic.DistributedAtomicNumber
[WARNING]   - org.apache.curator.framework.recipes.locks.Reaper$State
[WARNING]   - org.apache.curator.framework.recipes.locks.InterProcessReadWriteLock
[WARNING]   - org.apache.curator.framework.recipes.queue.QueueBase
[WARNING]   - org.apache.curator.framework.recipes.locks.ChildReaper$1
[WARNING]   - org.apache.curator.framework.recipes.cache.Operation
[WARNING]   - org.apache.curator.framework.recipes.shared.SharedValue$1
[WARNING]   - org.apache.curator.framework.recipes.locks.Revoker
[WARNING]   - org.apache.curator.framework.recipes.queue.QueueSharderPolicies
[WARNING]   - org.apache.curator.framework.recipes.locks.StandardLockInternalsDriver
[WARNING]   - 180 more...
[WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar define 1955 overlapping classes: 
[WARNING]   - com.google.common.collect.CompactHashMap$Itr
[WARNING]   - com.google.common.collect.ImmutableMapValues$1
[WARNING]   - com.google.common.util.concurrent.AbstractService$5
[WARNING]   - com.google.common.io.LineProcessor
[WARNING]   - com.google.common.io.BaseEncoding$StandardBaseEncoding$2
[WARNING]   - com.google.common.io.ByteProcessor
[WARNING]   - com.google.common.math.package-info
[WARNING]   - com.google.common.util.concurrent.SimpleTimeLimiter
[WARNING]   - com.google.common.cache.AbstractCache$StatsCounter
[WARNING]   - com.google.common.util.concurrent.CycleDetectingLockFactory$Policies
[WARNING]   - 1945 more...
[WARNING] commons-math3-3.4.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 1215 overlapping classes: 
[WARNING]   - org.apache.commons.math3.optim.linear.LinearOptimizer
[WARNING]   - org.apache.commons.math3.linear.LUDecomposition$Solver
[WARNING]   - org.apache.commons.math3.analysis.function.Gaussian$Parametric
[WARNING]   - org.apache.commons.math3.stat.descriptive.WeightedEvaluation
[WARNING]   - org.apache.commons.math3.analysis.FunctionUtils$3
[WARNING]   - org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic
[WARNING]   - org.apache.commons.math3.ml.clustering.FuzzyKMeansClusterer
[WARNING]   - org.apache.commons.math3.analysis.FunctionUtils$3$1
[WARNING]   - org.apache.commons.math3.ode.nonstiff.MidpointStepInterpolator
[WARNING]   - org.apache.commons.math3.ode.ParameterConfiguration
[WARNING]   - 1205 more...
[WARNING] commons-compress-1.8.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 127 overlapping classes: 
[WARNING]   - org.apache.commons.compress.archivers.dump.ShortFileException
[WARNING]   - org.apache.commons.compress.utils.CountingInputStream
[WARNING]   - org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream
[WARNING]   - org.apache.commons.compress.compressors.bzip2.CRC
[WARNING]   - org.apache.commons.compress.archivers.dump.DumpArchiveEntry
[WARNING]   - org.apache.commons.compress.compressors.bzip2.BlockSort
[WARNING]   - org.apache.commons.compress.archivers.tar.TarArchiveEntry
[WARNING]   - org.apache.commons.compress.archivers.dump.UnsupportedCompressionAlgorithmException
[WARNING]   - org.apache.commons.compress.archivers.zip.AbstractUnicodeExtraField
[WARNING]   - org.apache.commons.compress.archivers.dump.InvalidFormatException
[WARNING]   - 117 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, kryo-shaded-3.0.3.jar define 14 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.VersionFieldSerializer
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Context
[WARNING]   - com.esotericsoftware.kryo.serializers.EnumNameSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.ClosureSerializer
[WARNING]   - com.esotericsoftware.kryo.pool.KryoPool
[WARNING]   - com.esotericsoftware.kryo.pool.SoftReferenceQueue
[WARNING]   - com.esotericsoftware.kryo.pool.KryoCallback
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.TypePath
[WARNING]   - com.esotericsoftware.reflectasm.PublicConstructorAccess
[WARNING]   - com.esotericsoftware.kryo.pool.KryoPoolQueueImpl
[WARNING]   - 4 more...
[WARNING] jersey-media-jaxb-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 47 overlapping classes: 
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlRootElementJaxbProvider$App
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlJaxbElementProvider$General
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider$General
[WARNING]   - org.glassfish.jersey.jaxb.internal.JaxbStringReaderProvider$1
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider
[WARNING]   - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$4
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$General
[WARNING]   - org.glassfish.jersey.jaxb.internal.JaxbMessagingBinder
[WARNING]   - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$2
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$Text
[WARNING]   - 37 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, paranamer-2.8.jar define 21 overlapping classes: 
[WARNING]   - com.thoughtworks.paranamer.PositionalParanamer
[WARNING]   - com.thoughtworks.paranamer.JavadocParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$Type
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$1
[WARNING]   - com.thoughtworks.paranamer.JavadocParanamer$DirJavadocProvider
[WARNING]   - com.thoughtworks.paranamer.AnnotationParanamer$Jsr330Helper
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$TypeCollector
[WARNING]   - com.thoughtworks.paranamer.AnnotationParanamer
[WARNING]   - com.thoughtworks.paranamer.NullParanamer
[WARNING]   - 11 more...
[WARNING] chill_2.11-0.8.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 150 overlapping classes: 
[WARNING]   - com.twitter.chill.Tuple11Serializer
[WARNING]   - com.twitter.chill.InnerClosureFinder
[WARNING]   - com.twitter.chill.Instantiators$$anonfun$reflectAsm$1
[WARNING]   - com.twitter.chill.RichKryo$$anonfun$fromInputStream$1
[WARNING]   - com.twitter.chill.package$$anon$3
[WARNING]   - com.twitter.chill.JavaIterableWrapperSerializer
[WARNING]   - com.twitter.chill.Instantiators$$anonfun$newOrElse$1
[WARNING]   - com.twitter.chill.SortedMapSerializer$$anonfun$write$1
[WARNING]   - com.twitter.chill.package$$anon$5$$anonfun$apply$2
[WARNING]   - com.twitter.chill.Tuple8Serializer
[WARNING]   - 140 more...
[WARNING] parquet-encoding-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 184 overlapping classes: 
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer14
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer24
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer10
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingBE$Packer7
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer20
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer7
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer30
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer13
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer23
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$Packer19
[WARNING]   - 174 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, objenesis-2.1.jar define 37 overlapping classes: 
[WARNING]   - org.objenesis.ObjenesisBase
[WARNING]   - org.objenesis.instantiator.gcj.GCJInstantiator
[WARNING]   - org.objenesis.strategy.SingleInstantiatorStrategy
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactoryHelper
[WARNING]   - org.objenesis.ObjenesisHelper
[WARNING]   - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactoryInstantiator
[WARNING]   - org.objenesis.instantiator.basic.NullInstantiator
[WARNING]   - org.objenesis.instantiator.android.Android17Instantiator
[WARNING]   - org.objenesis.instantiator.ObjectInstantiator
[WARNING]   - 27 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, ga4gh-schemas-0.6.0a10.jar define 541 overlapping classes: 
[WARNING]   - ga4gh.AlleleAnnotations$TranscriptEffectOrBuilder
[WARNING]   - ga4gh.PeerServiceOuterClass$GetInfoResponse$1
[WARNING]   - ga4gh.MetadataServiceOuterClass$GetDatasetRequestOrBuilder
[WARNING]   - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest
[WARNING]   - ga4gh.RnaQuantificationServiceOuterClass$SearchExpressionLevelsRequest$Builder
[WARNING]   - ga4gh.GenotypePhenotypeServiceOuterClass$EvidenceQuery$1
[WARNING]   - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest$1
[WARNING]   - ga4gh.ReferenceServiceOuterClass$ListReferenceBasesResponseOrBuilder
[WARNING]   - ga4gh.VariantServiceOuterClass$SearchCallSetsRequest
[WARNING]   - ga4gh.RnaQuantificationServiceOuterClass$GetExpressionLevelRequest
[WARNING]   - 531 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-io-spark2_2.11-0.2.13.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$3
[WARNING]   - org.bdgenomics.utils.io.FileLocator
[WARNING]   - org.bdgenomics.utils.io.ByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$readByteStream$1
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$1
[WARNING]   - org.bdgenomics.utils.io.ByteAccess$$anonfun$readFully$2
[WARNING]   - org.bdgenomics.utils.io.LocalFileByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$2
[WARNING]   - org.bdgenomics.utils.io.HTTPFileLocator$
[WARNING]   - 13 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, json4s-ast_2.11-3.2.11.jar define 68 overlapping classes: 
[WARNING]   - org.json4s.Merge$Mergeable
[WARNING]   - org.json4s.Merge$Mergeable$MergeSyntax
[WARNING]   - org.json4s.Merge$$anonfun$mergeRec$2$1
[WARNING]   - org.json4s.BigDecimalMode$class
[WARNING]   - org.json4s.JsonAST$JBool$
[WARNING]   - org.json4s.JsonAST$JField$
[WARNING]   - org.json4s.DoubleMode$class
[WARNING]   - org.json4s.JsonAST$JString
[WARNING]   - org.json4s.LowPriorityMergeDep$class
[WARNING]   - org.json4s.JsonAST
[WARNING]   - 58 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, slf4j-log4j12-1.7.16.jar define 6 overlapping classes: 
[WARNING]   - org.slf4j.impl.Log4jLoggerAdapter
[WARNING]   - org.slf4j.impl.Log4jMDCAdapter
[WARNING]   - org.slf4j.impl.StaticMarkerBinder
[WARNING]   - org.slf4j.impl.Log4jLoggerFactory
[WARNING]   - org.slf4j.impl.StaticLoggerBinder
[WARNING]   - org.slf4j.impl.StaticMDCBinder
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, minlog-1.3.0.jar, minlog-1.2.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, kryo-shaded-3.0.3.jar, kryo-2.24.0.jar define 193 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.BeanSerializer$1
[WARNING]   - com.esotericsoftware.kryo.Registration
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.kryo.util.IntMap$Values
[WARNING]   - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl
[WARNING]   - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField
[WARNING]   - com.esotericsoftware.kryo.serializers.JavaSerializer
[WARNING]   - 183 more...
[WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, spark-tags_2.11-2.3.3.jar, spark-launcher_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, spark-kvstore_2.11-2.3.3.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: 
[WARNING]   - org.apache.spark.unused.UnusedStubClass
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-parser-combinators_2.11-1.0.4.jar define 352 overlapping classes: 
[WARNING]   - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$whitespace$1$$anonfun$apply$20$$anonfun$apply$21
[WARNING]   - scala.util.parsing.combinator.ImplicitConversions$$anonfun$flatten5$1
[WARNING]   - scala.util.parsing.combinator.Parsers$$anonfun$rep$1
[WARNING]   - scala.util.parsing.json.Lexer$$anonfun$number$1$$anonfun$apply$16
[WARNING]   - scala.util.parsing.combinator.Parsers$NoSuccess$$anonfun$1
[WARNING]   - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$3$$anonfun$apply$3$$anonfun$apply$4
[WARNING]   - scala.util.parsing.combinator.token.StdTokens$class
[WARNING]   - scala.util.parsing.json.Lexer$$anonfun$charSeq$10
[WARNING]   - scala.util.parsing.combinator.Parsers$Parser$$anonfun$$tilde$greater$1
[WARNING]   - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$5
[WARNING]   - 342 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-common-2.22.2.jar define 474 overlapping classes: 
[WARNING]   - org.glassfish.jersey.internal.inject.ContextInjectionResolver$Binder
[WARNING]   - org.glassfish.jersey.internal.ServiceFinder$ServiceIteratorProvider
[WARNING]   - org.glassfish.jersey.message.internal.HttpHeaderReader$1
[WARNING]   - org.glassfish.jersey.internal.util.collection.KeyComparatorHashMap$1
[WARNING]   - org.glassfish.jersey.uri.UriTemplate$1ValuesFromArrayStrategy
[WARNING]   - org.glassfish.jersey.message.internal.TracingLogger$Level
[WARNING]   - org.glassfish.jersey.internal.util.PropertyAlias
[WARNING]   - org.glassfish.jersey.uri.UriTemplate$3
[WARNING]   - org.glassfish.jersey.model.internal.ComponentBag$7
[WARNING]   - org.glassfish.jersey.spi.AbstractThreadPoolProvider
[WARNING]   - 464 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, parquet-column-1.8.3.jar define 731 overlapping classes: 
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.longs.LongComparator
[WARNING]   - org.apache.parquet.filter2.recordlevel.IncrementallyUpdatedFilterPredicateBuilder$25
[WARNING]   - org.apache.parquet.column.values.dictionary.DictionaryValuesWriter$PlainIntegerDictionaryValuesWriter
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.ints.Int2IntLinkedOpenHashMap$MapEntry
[WARNING]   - org.apache.parquet.io.PrimitiveColumnIO
[WARNING]   - org.apache.parquet.io.api.Binary$ByteBufferBackedBinary
[WARNING]   - org.apache.parquet.column.statistics.BooleanStatistics
[WARNING]   - org.apache.parquet.column.values.boundedint.BoundedIntValuesReader
[WARNING]   - org.apache.parquet.schema.PrimitiveType$PrimitiveTypeName$3
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.doubles.DoubleSortedSet
[WARNING]   - 721 more...
[WARNING] log4j-1.2.17.jar, mango-core-0.0.3-SNAPSHOT.jar define 314 overlapping classes: 
[WARNING]   - org.apache.log4j.or.sax.AttributesRenderer
[WARNING]   - org.apache.log4j.pattern.MessagePatternConverter
[WARNING]   - org.apache.log4j.chainsaw.ControlPanel$3
[WARNING]   - org.apache.log4j.pattern.NameAbbreviator$DropElementAbbreviator
[WARNING]   - org.apache.log4j.jmx.MethodUnion
[WARNING]   - org.apache.log4j.lf5.viewer.LogTable
[WARNING]   - org.apache.log4j.BasicConfigurator
[WARNING]   - org.apache.log4j.rewrite.RewriteAppender
[WARNING]   - org.apache.log4j.lf5.viewer.LogBrokerMonitor$22
[WARNING]   - org.apache.log4j.pattern.LoggingEventPatternConverter
[WARNING]   - 304 more...
[WARNING] hk2-utils-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar define 80 overlapping classes: 
[WARNING]   - org.glassfish.hk2.utilities.cache.Cache$1
[WARNING]   - org.jvnet.hk2.component.MultiMap$1
[WARNING]   - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperImpl$4
[WARNING]   - org.glassfish.hk2.utilities.cache.internal.WeakCARCacheImpl$1
[WARNING]   - org.glassfish.hk2.utilities.cache.LRUHybridCache
[WARNING]   - org.glassfish.hk2.utilities.cache.LRUCache
[WARNING]   - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperUtilities
[WARNING]   - org.glassfish.hk2.utilities.reflection.ClassReflectionHelper
[WARNING]   - org.glassfish.hk2.utilities.cache.CacheEntry
[WARNING]   - org.glassfish.hk2.utilities.reflection.ReflectionHelper
[WARNING]   - 70 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, base64-2.3.8.jar define 4 overlapping classes: 
[WARNING]   - net.iharder.Base64$InputStream
[WARNING]   - net.iharder.Base64$OutputStream
[WARNING]   - net.iharder.Base64$1
[WARNING]   - net.iharder.Base64
[WARNING] adam-cli-spark2_2.11-0.26.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-misc-spark2_2.11-0.2.13.jar define 11 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.misc.MathUtils
[WARNING]   - org.bdgenomics.utils.misc.Logging$
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$scalarArrayMultiply$1
[WARNING]   - org.bdgenomics.utils.misc.Logging$class
[WARNING]   - org.bdgenomics.utils.misc.Logging$$anonfun$getContextOrClassLoader$1
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$aggregateArray$1
[WARNING]   - org.bdgenomics.utils.misc.Logging
[WARNING]   - org.bdgenomics.utils.misc.HadoopUtil$
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$softmax$1
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$
[WARNING]   - 1 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, pyrolite-4.13.jar define 54 overlapping classes: 
[WARNING]   - net.razorvine.pickle.objects.ByteArrayConstructor
[WARNING]   - net.razorvine.pyro.NameServerProxy
[WARNING]   - net.razorvine.pyro.serializer.PyroSerializer
[WARNING]   - net.razorvine.pickle.objects.DateTimeConstructor
[WARNING]   - net.razorvine.pickle.IObjectConstructor
[WARNING]   - net.razorvine.pickle.objects.ClassDictConstructor
[WARNING]   - net.razorvine.pyro.serializer.PyroUriSerpent
[WARNING]   - net.razorvine.pickle.objects.OperatorAttrGetterForCalendarTz$CalendarLocalizer
[WARNING]   - net.razorvine.pickle.objects.TimeZoneConstructor
[WARNING]   - net.razorvine.pyro.Config
[WARNING]   - 44 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-core_2.11-2.3.3.jar define 8350 overlapping classes: 
[WARNING]   - org.apache.spark.shuffle.BaseShuffleHandle
[WARNING]   - org.apache.spark.SparkContext$$anonfun$11
[WARNING]   - org.spark_project.jetty.client.util.MultiPartContentProvider$1
[WARNING]   - org.apache.spark.TaskContextImpl$$anonfun$markTaskFailed$1
[WARNING]   - org.apache.spark.util.collection.PrimitiveVector$mcI$sp
[WARNING]   - org.spark_project.jetty.servlets.PushCacheFilter
[WARNING]   - org.apache.spark.util.Utils$$anonfun$downloadFile$1
[WARNING]   - org.apache.spark.util.JsonProtocol$$anonfun$52
[WARNING]   - org.apache.spark.ExecutorAllocationManager$$anonfun$org$apache$spark$ExecutorAllocationManager$$onExecutorAdded$2
[WARNING]   - org.apache.spark.rdd.util.PeriodicRDDCheckpointer
[WARNING]   - 8340 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, adam-codegen-spark2_2.11-0.26.0.jar define 18 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$getters$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$setters$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$apply$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$fields$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$$anonfun$fields$1
[WARNING]   - 8 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, httpclient-4.5.2.jar define 463 overlapping classes: 
[WARNING]   - org.apache.http.impl.cookie.RFC2109Spec
[WARNING]   - org.apache.http.impl.execchain.MainClientExec
[WARNING]   - org.apache.http.conn.routing.RouteInfo$TunnelType
[WARNING]   - org.apache.http.client.methods.HttpGet
[WARNING]   - org.apache.http.impl.cookie.BrowserCompatSpecFactory
[WARNING]   - org.apache.http.impl.client.HttpAuthenticator
[WARNING]   - org.apache.http.conn.ManagedClientConnection
[WARNING]   - org.apache.http.client.protocol.RequestAuthCache
[WARNING]   - org.apache.http.conn.params.ConnConnectionParamBean
[WARNING]   - org.apache.http.impl.client.IdleConnectionEvictor
[WARNING]   - 453 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-kvstore_2.11-2.3.3.jar define 28 overlapping classes: 
[WARNING]   - org.apache.spark.util.kvstore.LevelDB$TypeAliases
[WARNING]   - org.apache.spark.util.kvstore.LevelDB$1
[WARNING]   - org.apache.spark.util.kvstore.LevelDB$PrefixCache
[WARNING]   - org.apache.spark.util.kvstore.LevelDBTypeInfo$Index
[WARNING]   - org.apache.spark.util.kvstore.KVStore
[WARNING]   - org.apache.spark.util.kvstore.KVTypeInfo
[WARNING]   - org.apache.spark.util.kvstore.KVIndex
[WARNING]   - org.apache.spark.util.kvstore.KVStoreIterator
[WARNING]   - org.apache.spark.util.kvstore.InMemoryStore$InMemoryView
[WARNING]   - org.apache.spark.util.kvstore.InMemoryStore$1
[WARNING]   - 18 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-metrics-spark2_2.11-0.2.13.jar define 407 overlapping classes: 
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$reduceByKey$2$$anonfun$apply$33
[WARNING]   - org.bdgenomics.utils.instrumentation.SimpleMonitorValueExtractor
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$fullOuterJoin$2
[WARNING]   - org.bdgenomics.utils.instrumentation.MetricsListener$$anonfun$onTaskEnd$2
[WARNING]   - org.bdgenomics.utils.metrics.Histogram$$anonfun$countSubset$1
[WARNING]   - org.bdgenomics.utils.instrumentation.Alignment$
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$saveAsHadoopFile$3
[WARNING]   - org.bdgenomics.utils.instrumentation.Metrics$TreeNode$$anonfun$6
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$reduce$1$$anonfun$apply$35
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$aggregate$1$$anonfun$apply$39$$anonfun$apply$40
[WARNING]   - 397 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-launcher_2.11-2.3.3.jar define 34 overlapping classes: 
[WARNING]   - org.apache.spark.launcher.AbstractAppHandle
[WARNING]   - org.apache.spark.launcher.SparkAppHandle$State
[WARNING]   - org.apache.spark.launcher.SparkAppHandle$Listener
[WARNING]   - org.apache.spark.launcher.ChildProcAppHandle
[WARNING]   - org.apache.spark.launcher.LauncherProtocol
[WARNING]   - org.apache.spark.launcher.LauncherProtocol$Stop
[WARNING]   - org.apache.spark.launcher.SparkSubmitOptionParser
[WARNING]   - org.apache.spark.launcher.LauncherProtocol$Message
[WARNING]   - org.apache.spark.launcher.CommandBuilderUtils
[WARNING]   - org.apache.spark.launcher.SparkSubmitCommandBuilder$OptionParser
[WARNING]   - 24 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, avro-mapred-1.7.7-hadoop2.jar define 126 overlapping classes: 
[WARNING]   - org.apache.avro.mapreduce.AvroMultipleOutputs
[WARNING]   - org.apache.avro.mapreduce.AvroKeyValueOutputFormat
[WARNING]   - org.apache.avro.mapred.SequenceFileReader$8
[WARNING]   - org.apache.avro.hadoop.file.HadoopCodecFactory
[WARNING]   - org.apache.avro.mapred.Pair
[WARNING]   - org.apache.avro.mapred.AvroMultipleOutputs
[WARNING]   - org.apache.avro.mapred.FsInput
[WARNING]   - org.apache.avro.mapred.tether.InputProtocol$Callback
[WARNING]   - org.apache.avro.mapred.AvroOutputFormat$1
[WARNING]   - org.apache.avro.hadoop.file.SortedKeyValueFile$Reader$Options
[WARNING]   - 116 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-logging-1.1.3.jar define 22 overlapping classes: 
[WARNING]   - org.apache.commons.logging.LogSource
[WARNING]   - org.apache.commons.logging.impl.ServletContextCleaner
[WARNING]   - org.apache.commons.logging.LogFactory$4
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable$1
[WARNING]   - org.apache.commons.logging.LogFactory$3
[WARNING]   - org.apache.commons.logging.LogFactory$2
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl$2
[WARNING]   - org.apache.commons.logging.impl.LogKitLogger
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl$3
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable$Entry
[WARNING]   - 12 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, htsjdk-2.16.1.jar define 983 overlapping classes: 
[WARNING]   - htsjdk.samtools.cram.ref.ReferenceSource
[WARNING]   - htsjdk.samtools.HighAccuracyDownsamplingIterator
[WARNING]   - htsjdk.samtools.util.zip.DeflaterFactory
[WARNING]   - htsjdk.samtools.filter.DuplicateReadFilter
[WARNING]   - htsjdk.variant.vcf.VCFEncoder
[WARNING]   - htsjdk.samtools.util.CloserUtil
[WARNING]   - htsjdk.tribble.TribbleException$FeatureFileDoesntExist
[WARNING]   - htsjdk.tribble.index.tabix.TabixIndex
[WARNING]   - htsjdk.samtools.AbstractBAMFileIndex
[WARNING]   - htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder$1
[WARNING]   - 973 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-intervalrdd-spark2_2.11-0.2.13.jar define 51 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$collect$2
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$4
[WARNING]   - org.bdgenomics.utils.interval.array.Interval$class
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$get$1
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$4
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$1
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$filter$1
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$mapValues$1
[WARNING]   - 41 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-library-2.11.11.jar define 3828 overlapping classes: 
[WARNING]   - scala.collection.mutable.SortedSet$class
[WARNING]   - scala.collection.immutable.IndexedSeq
[WARNING]   - scala.collection.SeqLike$$anonfun$reverseMap$2
[WARNING]   - scala.Function2$mcDID$sp
[WARNING]   - scala.collection.immutable.IntMapValueIterator
[WARNING]   - scala.collection.MapLike$DefaultKeySet
[WARNING]   - scala.collection.parallel.FactoryOps$Otherwise
[WARNING]   - scala.math.Ordering$String$
[WARNING]   - scala.util.Either$
[WARNING]   - scala.collection.mutable.SetProxy
[WARNING]   - 3818 more...
[WARNING] RoaringBitmap-0.5.11.jar, mango-core-0.0.3-SNAPSHOT.jar define 69 overlapping classes: 
[WARNING]   - org.roaringbitmap.ReverseRunContainerShortIterator
[WARNING]   - org.roaringbitmap.ShortIterator
[WARNING]   - org.roaringbitmap.Util
[WARNING]   - org.roaringbitmap.buffer.RawMappeableRunContainerShortIterator
[WARNING]   - org.roaringbitmap.buffer.MappeableBitmapContainer
[WARNING]   - org.roaringbitmap.buffer.BufferFastAggregation$2
[WARNING]   - org.roaringbitmap.buffer.MappeableBitmapContainerShortIterator
[WARNING]   - org.roaringbitmap.RunContainerShortIterator
[WARNING]   - org.roaringbitmap.buffer.ReverseMappeableArrayContainerShortIterator
[WARNING]   - org.roaringbitmap.buffer.MappeableContainerPointer
[WARNING]   - 59 more...
[WARNING] jackson-module-scala_2.11-2.6.7.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 403 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializer$$anonfun$2
[WARNING]   - com.fasterxml.jackson.module.scala.deser.UnsortedSetDeserializerModule
[WARNING]   - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializerModule$class
[WARNING]   - com.fasterxml.jackson.module.scala.JacksonModule$$anonfun$1
[WARNING]   - com.fasterxml.jackson.module.scala.deser.SortedSetDeserializer$$anonfun$4
[WARNING]   - com.fasterxml.jackson.module.scala.util.Options$class
[WARNING]   - com.fasterxml.jackson.module.scala.util.EnumResolver$
[WARNING]   - com.fasterxml.jackson.module.scala.ser.OptionSerializer$$anonfun$serialize$1
[WARNING]   - com.fasterxml.jackson.module.scala.ser.OptionSerializerModule
[WARNING]   - com.fasterxml.jackson.module.scala.modifiers.CollectionLikeTypeModifier$$anonfun$modifyType$3
[WARNING]   - 393 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, fastutil-6.5.7.jar define 10653 overlapping classes: 
[WARNING]   - it.unimi.dsi.fastutil.doubles.Double2IntRBTreeMap$Submap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2CharAVLTreeMap$2$1
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2ObjectLinkedOpenHashMap$EntryIterator
[WARNING]   - it.unimi.dsi.fastutil.shorts.Short2FloatOpenCustomHashMap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.ints.Int2ReferenceRBTreeMap$Submap
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2BooleanRBTreeMap$Submap$1
[WARNING]   - it.unimi.dsi.fastutil.floats.AbstractFloat2ShortSortedMap$ValuesCollection
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2ReferenceRBTreeMap$Submap$2
[WARNING]   - it.unimi.dsi.fastutil.chars.AbstractChar2LongSortedMap$ValuesIterator
[WARNING]   - it.unimi.dsi.fastutil.doubles.DoubleHeaps
[WARNING]   - 10643 more...
[WARNING] curator-client-2.7.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 56 overlapping classes: 
[WARNING]   - org.apache.curator.HandleHolder$Helper
[WARNING]   - org.apache.curator.utils.PathUtils
[WARNING]   - org.apache.curator.ensemble.exhibitor.ExhibitorEnsembleProvider$1
[WARNING]   - org.apache.curator.utils.CloseableScheduledExecutorService
[WARNING]   - org.apache.curator.utils.EnsurePath$InitialHelper$1
[WARNING]   - org.apache.curator.SessionFailRetryLoop$2
[WARNING]   - org.apache.curator.utils.ZKPaths$PathAndNode
[WARNING]   - org.apache.curator.ensemble.exhibitor.DefaultExhibitorRestClient
[WARNING]   - org.apache.curator.TimeTrace
[WARNING]   - org.apache.curator.HandleHolder$1$1
[WARNING]   - 46 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, servo-core-0.12.12.jar define 162 overlapping classes: 
[WARNING]   - com.netflix.servo.util.Objects
[WARNING]   - com.netflix.servo.util.Clock
[WARNING]   - com.netflix.servo.monitor.MaxGauge
[WARNING]   - com.netflix.servo.publish.LocalJmxConnector
[WARNING]   - com.netflix.servo.publish.MonitorRegistryMetricPoller$MonitorValueCallable
[WARNING]   - com.netflix.servo.util.ExpiringCache$Entry
[WARNING]   - com.netflix.servo.util.ThreadCpuStats$CpuUsage
[WARNING]   - com.netflix.servo.tag.SmallTagMap$Builder
[WARNING]   - com.netflix.servo.stats.StatsConfig
[WARNING]   - com.netflix.servo.monitor.Monitors$CounterFactory
[WARNING]   - 152 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-core-2.6.7.jar define 93 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer$Bucket
[WARNING]   - com.fasterxml.jackson.core.FormatSchema
[WARNING]   - com.fasterxml.jackson.core.io.InputDecorator
[WARNING]   - com.fasterxml.jackson.core.JsonGenerator$Feature
[WARNING]   - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer
[WARNING]   - com.fasterxml.jackson.core.type.ResolvedType
[WARNING]   - com.fasterxml.jackson.core.io.SegmentedStringWriter
[WARNING]   - com.fasterxml.jackson.core.TreeNode
[WARNING]   - com.fasterxml.jackson.core.sym.Name
[WARNING]   - com.fasterxml.jackson.core.util.JsonGeneratorDelegate
[WARNING]   - 83 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-io-2.6.jar define 127 overlapping classes: 
[WARNING]   - org.apache.commons.io.FileCleaningTracker
[WARNING]   - org.apache.commons.io.comparator.SizeFileComparator
[WARNING]   - org.apache.commons.io.input.CloseShieldInputStream
[WARNING]   - org.apache.commons.io.ByteOrderParser
[WARNING]   - org.apache.commons.io.filefilter.EmptyFileFilter
[WARNING]   - org.apache.commons.io.monitor.FileEntry
[WARNING]   - org.apache.commons.io.output.ThresholdingOutputStream
[WARNING]   - org.apache.commons.io.input.TailerListener
[WARNING]   - org.apache.commons.io.IOExceptionWithCause
[WARNING]   - org.apache.commons.io.filefilter.NotFileFilter
[WARNING]   - 117 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, guice-4.2.0.jar define 572 overlapping classes: 
[WARNING]   - com.google.inject.Scope
[WARNING]   - com.google.inject.Binding
[WARNING]   - com.google.inject.internal.cglib.core.$EmitUtils$3
[WARNING]   - com.google.inject.spi.TypeConverter
[WARNING]   - com.google.inject.internal.ConstructionProxy
[WARNING]   - com.google.inject.spi.InjectionPoint
[WARNING]   - com.google.inject.spi.StaticInjectionRequest
[WARNING]   - com.google.inject.internal.cglib.proxy.$FixedValueGenerator
[WARNING]   - com.google.inject.internal.cglib.proxy.$DispatcherGenerator
[WARNING]   - com.google.inject.spi.Elements$ElementsAsModule
[WARNING]   - 562 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-cli-spark2_2.11-0.2.13.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.cli.Args4j
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$4
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$3
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$class
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$2
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$run$1
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs$class
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$1
[WARNING]   - org.bdgenomics.utils.cli.SaveArgs
[WARNING]   - 13 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, activation-1.1.1.jar define 38 overlapping classes: 
[WARNING]   - javax.activation.DataContentHandlerFactory
[WARNING]   - javax.activation.ObjectDataContentHandler
[WARNING]   - javax.activation.DataContentHandler
[WARNING]   - com.sun.activation.registries.MimeTypeEntry
[WARNING]   - com.sun.activation.viewers.TextViewer
[WARNING]   - com.sun.activation.registries.LogSupport
[WARNING]   - javax.activation.CommandObject
[WARNING]   - javax.activation.SecuritySupport$2
[WARNING]   - com.sun.activation.viewers.TextEditor
[WARNING]   - com.sun.activation.viewers.ImageViewerCanvas
[WARNING]   - 28 more...
[WARNING] bcprov-jdk15on-1.52.jar, mango-core-0.0.3-SNAPSHOT.jar define 2430 overlapping classes: 
[WARNING]   - org.bouncycastle.crypto.modes.gcm.Tables8kGCMMultiplier
[WARNING]   - org.bouncycastle.crypto.tls.HeartbeatMode
[WARNING]   - org.bouncycastle.pqc.math.linearalgebra.GF2nPolynomialElement
[WARNING]   - org.bouncycastle.jcajce.provider.asymmetric.ecgost.KeyFactorySpi
[WARNING]   - org.bouncycastle.jcajce.provider.symmetric.AES$AlgParamsCCM
[WARNING]   - org.bouncycastle.asn1.tsp.TimeStampResp
[WARNING]   - org.bouncycastle.jcajce.provider.digest.SHA384$Mappings
[WARNING]   - org.bouncycastle.jcajce.provider.asymmetric.elgamal.AlgorithmParameterGeneratorSpi
[WARNING]   - org.bouncycastle.asn1.x509.CRLNumber
[WARNING]   - org.bouncycastle.jcajce.provider.digest.SM3
[WARNING]   - 2420 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-databind-2.6.7.1.jar define 563 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.databind.BeanDescription
[WARNING]   - com.fasterxml.jackson.databind.deser.impl.BeanAsArrayBuilderDeserializer
[WARNING]   - com.fasterxml.jackson.databind.SerializerProvider
[WARNING]   - com.fasterxml.jackson.databind.introspect.AnnotatedMethodMap
[WARNING]   - com.fasterxml.jackson.databind.ser.std.StaticListSerializerBase
[WARNING]   - com.fasterxml.jackson.databind.ser.std.NumberSerializers$ShortSerializer
[WARNING]   - com.fasterxml.jackson.databind.ser.BeanSerializerFactory
[WARNING]   - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonMapFormatVisitor
[WARNING]   - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatTypes
[WARNING]   - com.fasterxml.jackson.databind.deser.impl.MethodProperty
[WARNING]   - 553 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, hadoop-bam-7.9.2.jar define 115 overlapping classes: 
[WARNING]   - org.seqdoop.hadoop_bam.BAMSplitGuesser
[WARNING]   - org.seqdoop.hadoop_bam.util.SAMHeaderReader
[WARNING]   - org.seqdoop.hadoop_bam.QseqInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter
[WARNING]   - org.seqdoop.hadoop_bam.FastaInputFormat$1
[WARNING]   - org.seqdoop.hadoop_bam.util.SAMOutputPreparer$1
[WARNING]   - org.seqdoop.hadoop_bam.QseqOutputFormat$QseqRecordWriter
[WARNING]   - org.seqdoop.hadoop_bam.FastaInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.LineReader
[WARNING]   - org.seqdoop.hadoop_bam.util.BGZFCodec
[WARNING]   - 105 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, snappy-java-1.0.5.jar define 12 overlapping classes: 
[WARNING]   - org.xerial.snappy.SnappyLoader
[WARNING]   - org.xerial.snappy.SnappyOutputStream
[WARNING]   - org.xerial.snappy.SnappyErrorCode
[WARNING]   - org.xerial.snappy.SnappyBundleActivator
[WARNING]   - org.xerial.snappy.SnappyError
[WARNING]   - org.xerial.snappy.SnappyNativeAPI
[WARNING]   - org.xerial.snappy.SnappyException
[WARNING]   - org.xerial.snappy.Snappy
[WARNING]   - org.xerial.snappy.SnappyNative
[WARNING]   - org.xerial.snappy.OSInfo
[WARNING]   - 2 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar define 3 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.SLF4JLogFactory
[WARNING]   - org.apache.commons.logging.impl.SLF4JLocationAwareLog
[WARNING]   - org.apache.commons.logging.impl.SLF4JLog
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-json-3.1.5.jar define 11 overlapping classes: 
[WARNING]   - com.codahale.metrics.json.MetricsModule$MetricRegistrySerializer
[WARNING]   - com.codahale.metrics.json.HealthCheckModule$HealthCheckResultSerializer
[WARNING]   - com.codahale.metrics.json.HealthCheckModule
[WARNING]   - com.codahale.metrics.json.MetricsModule$TimerSerializer
[WARNING]   - com.codahale.metrics.json.MetricsModule$GaugeSerializer
[WARNING]   - com.codahale.metrics.json.MetricsModule$1
[WARNING]   - com.codahale.metrics.json.MetricsModule$MeterSerializer
[WARNING]   - com.codahale.metrics.json.MetricsModule
[WARNING]   - com.codahale.metrics.json.MetricsModule$HistogramSerializer
[WARNING]   - com.codahale.metrics.json.MetricsModule$CounterSerializer
[WARNING]   - 1 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, checker-qual-2.5.2.jar define 302 overlapping classes: 
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil
[WARNING]   - org.checkerframework.checker.units.qual.MixedUnits
[WARNING]   - org.checkerframework.checker.units.qual.PolyUnit
[WARNING]   - org.checkerframework.checker.regex.qual.PolyRegex
[WARNING]   - org.checkerframework.checker.units.qual.C
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil$IllegalFormatConversionCategoryException
[WARNING]   - org.checkerframework.framework.qual.Unqualified
[WARNING]   - org.checkerframework.common.reflection.qual.UnknownMethod
[WARNING]   - org.checkerframework.framework.qual.EnsuresQualifierIf
[WARNING]   - org.checkerframework.checker.signedness.SignednessUtil
[WARNING]   - 292 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-tags_2.11-2.3.3.jar define 11 overlapping classes: 
[WARNING]   - org.apache.spark.annotation.Since
[WARNING]   - org.apache.spark.annotation.InterfaceStability$Stable
[WARNING]   - org.apache.spark.annotation.package
[WARNING]   - org.apache.spark.annotation.DeveloperApi
[WARNING]   - org.apache.spark.annotation.InterfaceStability$Evolving
[WARNING]   - org.apache.spark.annotation.package$
[WARNING]   - org.apache.spark.annotation.Experimental
[WARNING]   - org.apache.spark.annotation.AlphaComponent
[WARNING]   - org.apache.spark.annotation.Private
[WARNING]   - org.apache.spark.annotation.InterfaceStability
[WARNING]   - 1 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-codec-1.10.jar define 92 overlapping classes: 
[WARNING]   - org.apache.commons.codec.language.Nysiis
[WARNING]   - org.apache.commons.codec.language.bm.Rule$1
[WARNING]   - org.apache.commons.codec.language.bm.Rule$RPattern
[WARNING]   - org.apache.commons.codec.language.ColognePhonetic$CologneInputBuffer
[WARNING]   - org.apache.commons.codec.digest.HmacUtils
[WARNING]   - org.apache.commons.codec.language.bm.BeiderMorseEncoder
[WARNING]   - org.apache.commons.codec.digest.UnixCrypt
[WARNING]   - org.apache.commons.codec.language.Soundex
[WARNING]   - org.apache.commons.codec.binary.BinaryCodec
[WARNING]   - org.apache.commons.codec.language.bm.Languages$1
[WARNING]   - 82 more...
[WARNING] jackson-core-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 121 overlapping classes: 
[WARNING]   - org.codehaus.jackson.annotate.JsonManagedReference
[WARNING]   - org.codehaus.jackson.util.DefaultPrettyPrinter$FixedSpaceIndenter
[WARNING]   - org.codehaus.jackson.JsonGenerationException
[WARNING]   - org.codehaus.jackson.util.BufferRecycler$CharBufferType
[WARNING]   - org.codehaus.jackson.io.UTF32Reader
[WARNING]   - org.codehaus.jackson.sym.Name1
[WARNING]   - org.codehaus.jackson.util.MinimalPrettyPrinter
[WARNING]   - org.codehaus.jackson.impl.JsonParserBase
[WARNING]   - org.codehaus.jackson.annotate.JsonValue
[WARNING]   - org.codehaus.jackson.sym.CharsToNameCanonicalizer$Bucket
[WARNING]   - 111 more...
[WARNING] json4s-jackson_2.11-3.2.11.jar, mango-core-0.0.3-SNAPSHOT.jar define 27 overlapping classes: 
[WARNING]   - org.json4s.jackson.JsonMethods$class
[WARNING]   - org.json4s.jackson.Json
[WARNING]   - org.json4s.jackson.Json$
[WARNING]   - org.json4s.jackson.JValueSerializerResolver$
[WARNING]   - org.json4s.jackson.Json4sModule$
[WARNING]   - org.json4s.jackson.JsonMethods$$anonfun$parseOpt$1
[WARNING]   - org.json4s.jackson.JValueDeserializerResolver$
[WARNING]   - org.json4s.jackson.package
[WARNING]   - org.json4s.jackson.package$
[WARNING]   - org.json4s.jackson.Json4sScalaModule$
[WARNING]   - 17 more...
[WARNING] parquet-common-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 32 overlapping classes: 
[WARNING]   - org.apache.parquet.SemanticVersion$SemanticVersionParseException
[WARNING]   - org.apache.parquet.glob.GlobNode$GlobNodeSequence
[WARNING]   - org.apache.parquet.Ints
[WARNING]   - org.apache.parquet.Version
[WARNING]   - org.apache.parquet.glob.GlobNode$Atom
[WARNING]   - org.apache.parquet.SemanticVersion$NumberOrString
[WARNING]   - org.apache.parquet.Files
[WARNING]   - org.apache.parquet.ParquetRuntimeException
[WARNING]   - org.apache.parquet.glob.GlobNode
[WARNING]   - org.apache.parquet.io.InputFile
[WARNING]   - 22 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar, commons-logging-1.1.3.jar define 6 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING]   - org.apache.commons.logging.Log
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, xbean-asm5-shaded-4.4.jar define 81 overlapping classes: 
[WARNING]   - org.apache.xbean.asm5.FieldWriter
[WARNING]   - org.apache.xbean.asm5.commons.GeneratorAdapter
[WARNING]   - org.apache.xbean.asm5.AnnotationWriter
[WARNING]   - org.apache.xbean.asm5.tree.IntInsnNode
[WARNING]   - org.apache.xbean.asm5.Type
[WARNING]   - org.apache.xbean.asm5.commons.RemappingClassAdapter
[WARNING]   - org.apache.xbean.asm5.tree.FieldInsnNode
[WARNING]   - org.apache.xbean.asm5.tree.MultiANewArrayInsnNode
[WARNING]   - org.apache.xbean.asm5.tree.IincInsnNode
[WARNING]   - org.apache.xbean.asm5.tree.InsnList$InsnListIterator
[WARNING]   - 71 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, lift-json_2.11-3.3.0.jar define 390 overlapping classes: 
[WARNING]   - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$deserialize$2
[WARNING]   - net.liftweb.json.TypeInfo$
[WARNING]   - net.liftweb.json.JsonAST$JString$
[WARNING]   - net.liftweb.json.JsonAST$RenderSettings$
[WARNING]   - net.liftweb.json.JsonAST$JDouble$
[WARNING]   - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$classFor$2
[WARNING]   - net.liftweb.json.JsonAST$RenderSpecialDoubleValuesAsIs$
[WARNING]   - net.liftweb.json.Meta$$anonfun$net$liftweb$json$Meta$$fieldMapping$1$4
[WARNING]   - net.liftweb.json.Meta$DeclaredConstructor
[WARNING]   - net.liftweb.json.Formats$$anonfun$customSerializer$1
[WARNING]   - 380 more...
[WARNING] httpcore-4.4.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 254 overlapping classes: 
[WARNING]   - org.apache.http.protocol.HttpRequestHandler
[WARNING]   - org.apache.http.impl.io.ChunkedOutputStream
[WARNING]   - org.apache.http.protocol.ChainBuilder
[WARNING]   - org.apache.http.impl.entity.DisallowIdentityContentLengthStrategy
[WARNING]   - org.apache.http.impl.ConnSupport
[WARNING]   - org.apache.http.impl.io.DefaultHttpResponseParserFactory
[WARNING]   - org.apache.http.HttpClientConnection
[WARNING]   - org.apache.http.NameValuePair
[WARNING]   - org.apache.http.protocol.HttpExpectationVerifier
[WARNING]   - org.apache.http.protocol.UriPatternMatcher
[WARNING]   - 244 more...
[WARNING] jackson-mapper-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 502 overlapping classes: 
[WARNING]   - org.codehaus.jackson.map.ext.DOMSerializer
[WARNING]   - org.codehaus.jackson.node.POJONode
[WARNING]   - org.codehaus.jackson.map.ext.JodaDeserializers$LocalDateDeserializer
[WARNING]   - org.codehaus.jackson.map.ser.StdSerializers$UtilDateSerializer
[WARNING]   - org.codehaus.jackson.map.deser.std.JsonNodeDeserializer$ArrayDeserializer
[WARNING]   - org.codehaus.jackson.map.deser.std.PrimitiveArrayDeserializers$StringDeser
[WARNING]   - org.codehaus.jackson.map.util.Comparators$1
[WARNING]   - org.codehaus.jackson.map.util.StdDateFormat
[WARNING]   - org.codehaus.jackson.map.KeyDeserializer
[WARNING]   - org.codehaus.jackson.map.MapperConfig$Impl
[WARNING]   - 492 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-module-paranamer-2.7.9.jar define 26 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.NullParanamer
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.ParameterNamesNotFoundException
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$1
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$MethodCollector
[WARNING]   - com.fasterxml.jackson.module.paranamer.SerializableParanamer
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.JavadocParanamer$DirJavadocProvider
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$Type
[WARNING]   - com.fasterxml.jackson.module.paranamer.ParanamerAnnotationIntrospector
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.CachingParanamer$WithoutWeakReferences
[WARNING]   - com.fasterxml.jackson.module.paranamer.ParanamerOnJacksonAnnotationIntrospector
[WARNING]   - 16 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-compiler-2.11.12.jar define 9084 overlapping classes: 
[WARNING]   - scala.tools.nsc.doc.base.CommentFactoryBase$SimpleTagKey
[WARNING]   - scala.tools.jline_embedded.Terminal
[WARNING]   - scala.tools.nsc.Global$$anonfun$scala$tools$nsc$Global$$writeICode$1
[WARNING]   - scala.tools.nsc.backend.opt.ClosureElimination$ClosureElim$$anonfun$analyzeMethod$1$$anonfun$apply$2
[WARNING]   - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$typedCase$2$$anonfun$apply$27
[WARNING]   - scala.tools.nsc.backend.icode.analysis.TypeFlowAnalysis$MTFAGrowable$$anonfun$scala$tools$nsc$backend$icode$analysis$TypeFlowAnalysis$MTFAGrowable$$putOnRadar$1$$anonfun$3
[WARNING]   - scala.tools.nsc.interpreter.ILoop$$anonfun$standardCommands$3
[WARNING]   - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$isReferencedFrom$1
[WARNING]   - scala.tools.nsc.typechecker.Typers$Typer$dyna$
[WARNING]   - scala.tools.nsc.transform.patmat.MatchAnalysis$MatchAnalyzer$NegativeExample$$anonfun$23
[WARNING]   - 9074 more...
[WARNING] scala-reflect-2.11.7.jar, mango-core-0.0.3-SNAPSHOT.jar define 2793 overlapping classes: 
[WARNING]   - scala.reflect.runtime.ReflectionUtils
[WARNING]   - scala.reflect.internal.Types$LazyType
[WARNING]   - scala.reflect.internal.Scopes$LookupInaccessible$
[WARNING]   - scala.reflect.internal.Definitions$DefinitionsClass$$anonfun$newT1NullaryMethod$1
[WARNING]   - scala.reflect.internal.SymbolPairs$Cursor
[WARNING]   - scala.reflect.internal.Types$StaticallyAnnotatedType$
[WARNING]   - scala.reflect.runtime.SynchronizedOps$SynchronizedScope$$anonfun$isEmpty$1
[WARNING]   - scala.reflect.internal.Kinds$TypeConKind$$anonfun$buildState$3
[WARNING]   - scala.reflect.api.StandardLiftables$StandardUnliftableInstances$$anonfun$unliftTuple18$1
[WARNING]   - scala.reflect.runtime.SynchronizedSymbols$SynchronizedClassSymbol
[WARNING]   - 2783 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, adam-core-spark2_2.11-0.26.0.jar define 2708 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$74$$anonfun$apply$77
[WARNING]   - org.bdgenomics.adam.rdd.feature.FeatureDataset$$anonfun$filterToTranscript$2$$anonfun$apply$9$$anonfun$apply$10
[WARNING]   - org.bdgenomics.adam.rdd.read.AlignmentRecordDataset$$typecreator9$1
[WARNING]   - org.bdgenomics.adam.sql.VariantCallingAnnotations$$anonfun$toAvro$58
[WARNING]   - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$63
[WARNING]   - org.bdgenomics.adam.rdd.feature.DatasetBoundFeatureDataset$$anonfun$filterByAttribute$1
[WARNING]   - org.bdgenomics.adam.io.InterleavedFastqInputFormat
[WARNING]   - org.bdgenomics.adam.util.FileMerger$$anonfun$mergeFilesAcrossFilesystems$4
[WARNING]   - org.bdgenomics.adam.rdd.fragment.DatasetBoundFragmentDataset
[WARNING]   - org.bdgenomics.adam.sql.VariantAnnotation$$anonfun$fromAvro$80
[WARNING]   - 2698 more...
[WARNING] commons-lang3-3.5.jar, mango-core-0.0.3-SNAPSHOT.jar define 260 overlapping classes: 
[WARNING]   - org.apache.commons.lang3.time.StopWatch$State$1
[WARNING]   - org.apache.commons.lang3.ThreadUtils$1
[WARNING]   - org.apache.commons.lang3.ThreadUtils$ThreadGroupPredicate
[WARNING]   - org.apache.commons.lang3.builder.MultilineRecursiveToStringStyle
[WARNING]   - org.apache.commons.lang3.concurrent.AbstractCircuitBreaker
[WARNING]   - org.apache.commons.lang3.SerializationUtils
[WARNING]   - org.apache.commons.lang3.time.FastDatePrinter$TwentyFourHourField
[WARNING]   - org.apache.commons.lang3.LocaleUtils
[WARNING]   - org.apache.commons.lang3.concurrent.ConcurrentException
[WARNING]   - org.apache.commons.lang3.CharRange
[WARNING]   - 250 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, animal-sniffer-annotations-1.17.jar define 1 overlapping classes: 
[WARNING]   - org.codehaus.mojo.animal_sniffer.IgnoreJRERequirement
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, leveldbjni-all-1.8.jar define 75 overlapping classes: 
[WARNING]   - org.fusesource.leveldbjni.internal.NativeObject
[WARNING]   - org.fusesource.leveldbjni.internal.NativeDB$DBJNI
[WARNING]   - org.fusesource.leveldbjni.internal.NativeCache
[WARNING]   - org.fusesource.leveldbjni.internal.NativeComparator$ComparatorJNI
[WARNING]   - org.fusesource.leveldbjni.internal.NativeIterator
[WARNING]   - org.iq80.leveldb.WriteBatch
[WARNING]   - org.fusesource.hawtjni.runtime.ClassFlag
[WARNING]   - org.fusesource.leveldbjni.internal.NativeBuffer$1
[WARNING]   - org.iq80.leveldb.DBComparator
[WARNING]   - org.fusesource.leveldbjni.internal.NativeBuffer$Pool
[WARNING]   - 65 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, py4j-0.10.7.jar define 67 overlapping classes: 
[WARNING]   - py4j.reflection.TypeConverter
[WARNING]   - py4j.Py4JJavaServer
[WARNING]   - py4j.Py4JNetworkException
[WARNING]   - py4j.reflection.PythonProxyHandler
[WARNING]   - py4j.reflection.MethodInvoker$1
[WARNING]   - py4j.commands.JVMViewCommand
[WARNING]   - py4j.Py4JClientConnection
[WARNING]   - py4j.model.Py4JClass
[WARNING]   - py4j.commands.ReflectionCommand
[WARNING]   - py4j.commands.MemoryCommand
[WARNING]   - 57 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, slf4j-api-1.7.7.jar define 24 overlapping classes: 
[WARNING]   - org.slf4j.helpers.SubstituteLogger
[WARNING]   - org.slf4j.ILoggerFactory
[WARNING]   - org.slf4j.MDC
[WARNING]   - org.slf4j.helpers.BasicMDCAdapter
[WARNING]   - org.slf4j.spi.MDCAdapter
[WARNING]   - org.slf4j.LoggerFactory
[WARNING]   - org.slf4j.helpers.Util
[WARNING]   - org.slf4j.helpers.NOPLogger
[WARNING]   - org.slf4j.helpers.NOPLoggerFactory
[WARNING]   - org.slf4j.helpers.SubstituteLoggerFactory
[WARNING]   - 14 more...
[WARNING] jsr203hadoop-1.0.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 27 overlapping classes: 
[WARNING]   - hdfs.jsr203.HadoopDirectoryStream
[WARNING]   - hdfs.jsr203.HadoopPath
[WARNING]   - hdfs.jsr203.HadoopFileSystem$1
[WARNING]   - hdfs.jsr203.HadoopFileOwnerAttributeView
[WARNING]   - hdfs.jsr203.HadoopUserPrincipal
[WARNING]   - hdfs.jsr203.IAttributeReader
[WARNING]   - hdfs.jsr203.HadoopPath$1
[WARNING]   - hdfs.jsr203.HadoopBasicFileAttributes
[WARNING]   - hdfs.jsr203.HadoopDirectoryStream$1
[WARNING]   - hdfs.jsr203.package-info
[WARNING]   - 17 more...
[WARNING] convert-ga4gh-0.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 20 overlapping classes: 
[WARNING]   - org.bdgenomics.convert.ga4gh.CigarOperatorToOperation$1
[WARNING]   - org.bdgenomics.convert.ga4gh.BdgenomicsVariantToGa4ghVariant
[WARNING]   - org.bdgenomics.convert.ga4gh.CigarToCigarUnits
[WARNING]   - org.bdgenomics.convert.ga4gh.BdgenomicsFeatureToGa4ghFeature
[WARNING]   - org.bdgenomics.convert.ga4gh.StringToOntologyTerm
[WARNING]   - org.bdgenomics.convert.ga4gh.ProgramToProcessingStep
[WARNING]   - org.bdgenomics.convert.ga4gh.Ga4ghReadGroupToBdgenomicsReadGroup
[WARNING]   - org.bdgenomics.convert.ga4gh.Ga4ghOntologyTermToBdgenomicsOntologyTerm
[WARNING]   - org.bdgenomics.convert.ga4gh.ProcessingStepToProgram
[WARNING]   - org.bdgenomics.convert.ga4gh.BdgenomicsStrandToGa4ghStrand
[WARNING]   - 10 more...
[WARNING] stream-2.7.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 78 overlapping classes: 
[WARNING]   - com.clearspring.analytics.stream.cardinality.HyperLogLog
[WARNING]   - com.clearspring.analytics.stream.membership.DataOutputBuffer
[WARNING]   - com.clearspring.analytics.stream.quantile.TDigest
[WARNING]   - com.clearspring.analytics.stream.cardinality.HyperLogLog$SerializationHolder
[WARNING]   - com.clearspring.analytics.util.ListNode2
[WARNING]   - com.clearspring.analytics.stream.frequency.CountMinSketch
[WARNING]   - com.clearspring.analytics.util.DoublyLinkedList
[WARNING]   - com.clearspring.analytics.stream.cardinality.CountThenEstimate$CountThenEstimateMergeException
[WARNING]   - com.clearspring.analytics.stream.quantile.QDigest$1
[WARNING]   - com.clearspring.analytics.stream.cardinality.HyperLogLog$HyperLogLogMergeException
[WARNING]   - 68 more...
[WARNING] bdg-formats-0.12.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 61 overlapping classes: 
[WARNING]   - org.bdgenomics.formats.avro.VariantCallingAnnotations$Builder
[WARNING]   - org.bdgenomics.formats.avro.VariantAnnotation$Builder
[WARNING]   - org.bdgenomics.formats.avro.Reference$1
[WARNING]   - org.bdgenomics.formats.avro.VariantAnnotationMessage
[WARNING]   - org.bdgenomics.formats.avro.OntologyTerm$1
[WARNING]   - org.bdgenomics.formats.avro.Feature$1
[WARNING]   - org.bdgenomics.formats.avro.AlignmentRecord
[WARNING]   - org.bdgenomics.formats.avro.Sequence$1
[WARNING]   - org.bdgenomics.formats.avro.ReadGroup$Builder
[WARNING]   - org.bdgenomics.formats.avro.ReadGroup
[WARNING]   - 51 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, osgi-resource-locator-1.0.1.jar define 12 overlapping classes: 
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$1
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoader$ProviderFactory
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoader
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$ProvidersPerBundle
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ResourceFinderImpl
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ResourceFinder
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.Activator
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$DefaultFactory
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$BundleTracker
[WARNING]   - 2 more...
[WARNING] javax.servlet-api-3.1.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 79 overlapping classes: 
[WARNING]   - javax.servlet.http.Cookie
[WARNING]   - javax.servlet.ServletContext
[WARNING]   - javax.servlet.Registration
[WARNING]   - javax.servlet.http.HttpSessionListener
[WARNING]   - javax.servlet.http.HttpSessionContext
[WARNING]   - javax.servlet.FilterChain
[WARNING]   - javax.servlet.http.WebConnection
[WARNING]   - javax.servlet.http.HttpServletRequestWrapper
[WARNING]   - javax.servlet.http.HttpSessionAttributeListener
[WARNING]   - javax.servlet.annotation.HandlesTypes
[WARNING]   - 69 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, curator-framework-2.6.0.jar define 167 overlapping classes: 
[WARNING]   - org.apache.curator.framework.imps.TempGetDataBuilderImpl
[WARNING]   - org.apache.curator.framework.imps.GetDataBuilderImpl$2
[WARNING]   - org.apache.curator.framework.imps.CuratorFrameworkImpl$4
[WARNING]   - org.apache.curator.framework.state.ConnectionState
[WARNING]   - org.apache.curator.framework.api.CreateModable
[WARNING]   - org.apache.curator.framework.imps.SetDataBuilderImpl$4
[WARNING]   - org.apache.curator.framework.imps.PathAndBytes
[WARNING]   - org.apache.curator.framework.api.ACLVersionBackgroundPathable
[WARNING]   - org.apache.curator.framework.api.ACLCreateModeBackgroundPathAndBytesable
[WARNING]   - org.apache.curator.framework.listen.ListenerContainer
[WARNING]   - 157 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, validation-api-1.1.0.Final.jar define 106 overlapping classes: 
[WARNING]   - javax.validation.ConstraintDeclarationException
[WARNING]   - javax.validation.GroupDefinitionException
[WARNING]   - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder$LeafNodeBuilderDefinedContext
[WARNING]   - javax.validation.metadata.ParameterDescriptor
[WARNING]   - javax.validation.Validator
[WARNING]   - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder
[WARNING]   - javax.validation.constraints.AssertTrue$List
[WARNING]   - javax.validation.constraints.Past
[WARNING]   - javax.validation.metadata.GroupConversionDescriptor
[WARNING]   - javax.validation.constraints.Max
[WARNING]   - 96 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, parquet-avro-1.8.1.jar define 83 overlapping classes: 
[WARNING]   - org.apache.parquet.avro.AvroRecordConverter$AvroCollectionConverter$1
[WARNING]   - org.apache.parquet.avro.AvroParquetInputFormat
[WARNING]   - org.apache.parquet.avro.AvroRecordConverter$AvroArrayConverter$7
[WARNING]   - org.apache.parquet.avro.AvroConverters$AvroPrimitiveConverter
[WARNING]   - org.apache.parquet.avro.AvroWriteSupport$TwoLevelListWriter
[WARNING]   - org.apache.parquet.avro.AvroConverters$FieldIntegerConverter
[WARNING]   - org.apache.parquet.avro.AvroCompatRecordMaterializer
[WARNING]   - org.apache.parquet.avro.AvroIndexedRecordConverter$AvroArrayConverter$1
[WARNING]   - org.apache.parquet.avro.AvroWriteSupport$ListWriter
[WARNING]   - org.apache.parquet.avro.AvroConverters$FieldByteBufferConverter
[WARNING]   - 73 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, avro-ipc-1.7.7-tests.jar define 248 overlapping classes: 
[WARNING]   - test.StringablesRecord$Builder
[WARNING]   - org.apache.avro.specific.TestSpecificRecordBuilder
[WARNING]   - org.apache.avro.test.TestRecordWithUnion$Builder
[WARNING]   - org.apache.avro.test.TestError
[WARNING]   - org.apache.avro.test.Kind
[WARNING]   - org.apache.avro.io.Perf$IntTest
[WARNING]   - org.apache.avro.Interop$1
[WARNING]   - org.apache.avro.test.TestError$Builder
[WARNING]   - org.apache.avro.TestProtocolReflect$1
[WARNING]   - org.apache.avro.ipc.trace.TestFileSpanStorage
[WARNING]   - 238 more...
[WARNING] javax.annotation-api-1.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 15 overlapping classes: 
[WARNING]   - javax.annotation.ManagedBean
[WARNING]   - javax.annotation.PreDestroy
[WARNING]   - javax.annotation.Generated
[WARNING]   - javax.annotation.Resource$AuthenticationType
[WARNING]   - javax.annotation.security.DeclareRoles
[WARNING]   - javax.annotation.Priority
[WARNING]   - javax.annotation.Resource
[WARNING]   - javax.annotation.security.DenyAll
[WARNING]   - javax.annotation.security.RunAs
[WARNING]   - javax.annotation.sql.DataSourceDefinitions
[WARNING]   - 5 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, javassist-3.18.1-GA.jar define 390 overlapping classes: 
[WARNING]   - javassist.util.proxy.ProxyFactory$3
[WARNING]   - javassist.bytecode.FieldInfo
[WARNING]   - javassist.DirClassPath
[WARNING]   - javassist.ClassPool$1
[WARNING]   - javassist.expr.Cast$ProceedForCast
[WARNING]   - javassist.URLClassPath
[WARNING]   - javassist.CtMethod$LongConstParameter
[WARNING]   - javassist.compiler.Javac$2
[WARNING]   - javassist.bytecode.annotation.ClassMemberValue
[WARNING]   - javassist.bytecode.stackmap.TypeData$ClassName
[WARNING]   - 380 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, convert-htsjdk-0.6.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.convert.htsjdk.HtsjdkModule
[WARNING]   - org.bdgenomics.convert.htsjdk.ConversionStringencyToValidationStringency
[WARNING]   - org.bdgenomics.convert.htsjdk.ValidationStringencyToConversionStringency
[WARNING] commons-crypto-1.0.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 46 overlapping classes: 
[WARNING]   - org.apache.commons.crypto.stream.PositionedCryptoInputStream
[WARNING]   - org.apache.commons.crypto.cipher.OpenSsl
[WARNING]   - org.apache.commons.crypto.random.CryptoRandomFactory$RandomProvider
[WARNING]   - org.apache.commons.crypto.cipher.OpenSsl$AlgorithmMode
[WARNING]   - org.apache.commons.crypto.utils.Utils$DefaultPropertiesHolder
[WARNING]   - org.apache.commons.crypto.Crypto
[WARNING]   - org.apache.commons.crypto.cipher.OpenSsl$Transform
[WARNING]   - org.apache.commons.crypto.OpenSslInfoNative
[WARNING]   - org.apache.commons.crypto.stream.CtrCryptoOutputStream
[WARNING]   - org.apache.commons.crypto.jna.OpenSslNativeJna
[WARNING]   - 36 more...
[WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.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-core-0.0.3-SNAPSHOT.jar, jersey-guava-2.22.2.jar define 753 overlapping classes: 
[WARNING]   - jersey.repackaged.com.google.common.collect.AbstractNavigableMap$DescendingMap
[WARNING]   - jersey.repackaged.com.google.common.collect.AbstractMultiset$ElementSet
[WARNING]   - jersey.repackaged.com.google.common.collect.Collections2$OrderedPermutationCollection
[WARNING]   - jersey.repackaged.com.google.common.collect.StandardTable$TableSet
[WARNING]   - jersey.repackaged.com.google.common.base.Splitter
[WARNING]   - jersey.repackaged.com.google.common.util.concurrent.Futures$1$1
[WARNING]   - jersey.repackaged.com.google.common.base.CharMatcher$5
[WARNING]   - jersey.repackaged.com.google.common.collect.SortedMapDifference
[WARNING]   - jersey.repackaged.com.google.common.collect.ImmutableListMultimap
[WARNING]   - jersey.repackaged.com.google.common.cache.LocalCache$AbstractReferenceEntry
[WARNING]   - 743 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, scalap-2.11.11.jar define 581 overlapping classes: 
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ScalaSigEntryParsers$$anonfun$25$$anonfun$apply$13
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$_pmt$1$1
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ScalaSigParser$$anonfun$scalaSigFromAnnotation$2
[WARNING]   - scala.tools.scalap.scalax.rules.StateRules$$anonfun$anyOf$2
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ConstantType$
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.Symbol$class
[WARNING]   - scala.tools.scalap.scalax.rules.Rule$$anonfun$flatMap$1
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$printSymbolAttributes$1
[WARNING]   - scala.tools.scalap.scalax.rules.InRule$$anonfun$unary_$bang$1$$anonfun$apply$1
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.NoType$
[WARNING]   - 571 more...
[WARNING] jersey-container-servlet-core-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 51 overlapping classes: 
[WARNING]   - org.glassfish.jersey.servlet.WebComponent$3
[WARNING]   - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder
[WARNING]   - org.glassfish.jersey.servlet.internal.LocalizationMessages
[WARNING]   - org.glassfish.jersey.servlet.WebConfig
[WARNING]   - org.glassfish.jersey.servlet.spi.FilterUrlMappingsProvider
[WARNING]   - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder$3
[WARNING]   - org.glassfish.jersey.servlet.ServletPropertiesDelegate
[WARNING]   - org.glassfish.jersey.servlet.WebComponent$7
[WARNING]   - org.glassfish.jersey.servlet.internal.ResponseWriter
[WARNING]   - org.glassfish.jersey.servlet.WebAppResourcesScanner$1
[WARNING]   - 41 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, j2objc-annotations-1.1.jar define 12 overlapping classes: 
[WARNING]   - com.google.j2objc.annotations.Property
[WARNING]   - com.google.j2objc.annotations.RetainedWith
[WARNING]   - com.google.j2objc.annotations.RetainedLocalRef
[WARNING]   - com.google.j2objc.annotations.J2ObjCIncompatible
[WARNING]   - com.google.j2objc.annotations.AutoreleasePool
[WARNING]   - com.google.j2objc.annotations.LoopTranslation$LoopStyle
[WARNING]   - com.google.j2objc.annotations.ReflectionSupport$Level
[WARNING]   - com.google.j2objc.annotations.ReflectionSupport
[WARNING]   - com.google.j2objc.annotations.Weak
[WARNING]   - com.google.j2objc.annotations.WeakOuter
[WARNING]   - 2 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, netty-all-4.1.17.Final.jar define 2501 overlapping classes: 
[WARNING]   - io.netty.handler.codec.http.multipart.InterfaceHttpData$HttpDataType
[WARNING]   - io.netty.resolver.dns.InflightNameResolver$1
[WARNING]   - io.netty.channel.AbstractChannel$AbstractUnsafe$8
[WARNING]   - io.netty.handler.codec.smtp.DefaultSmtpRequest
[WARNING]   - io.netty.handler.codec.redis.RedisMessage
[WARNING]   - io.netty.handler.codec.memcache.binary.BinaryMemcacheResponse
[WARNING]   - io.netty.handler.timeout.IdleStateHandler
[WARNING]   - io.netty.buffer.FixedCompositeByteBuf$Component
[WARNING]   - io.netty.handler.codec.http.HttpHeaders
[WARNING]   - io.netty.handler.codec.http2.Http2ClientUpgradeCodec
[WARNING]   - 2491 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, hk2-locator-2.4.0-b34.jar define 95 overlapping classes: 
[WARNING]   - org.jvnet.hk2.internal.PerLocatorUtilities$1
[WARNING]   - org.jvnet.hk2.internal.Utilities$4
[WARNING]   - org.jvnet.hk2.internal.ProxyUtilities$2
[WARNING]   - org.jvnet.hk2.internal.ServiceLocatorImpl$12
[WARNING]   - org.jvnet.hk2.internal.MethodInterceptorInvocationHandler
[WARNING]   - org.jvnet.hk2.internal.ClazzCreator
[WARNING]   - org.jvnet.hk2.internal.ValidationInformationImpl
[WARNING]   - org.jvnet.hk2.internal.ServiceLocatorImpl$6
[WARNING]   - org.jvnet.hk2.internal.ConstructorInterceptorHandler$1
[WARNING]   - org.jvnet.hk2.internal.ServiceLocatorImpl$IgdValue
[WARNING]   - 85 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, json4s-core_2.11-3.2.11.jar define 407 overlapping classes: 
[WARNING]   - org.json4s.CustomSerializer
[WARNING]   - org.json4s.reflect.Reflector$ClassDescriptorBuilder$$anonfun$constructorsAndCompanion$3$$anonfun$13$$anonfun$apply$3
[WARNING]   - org.json4s.reflect.package$$anon$2
[WARNING]   - org.json4s.DefaultReaders$JValueReader$
[WARNING]   - org.json4s.StreamingJsonWriter$$anonfun$addJValue$1
[WARNING]   - org.json4s.ParserUtil$RecycledSegment
[WARNING]   - org.json4s.package
[WARNING]   - org.json4s.DefaultReaders$
[WARNING]   - org.json4s.Xml$$anonfun$directChildren$1$1
[WARNING]   - org.json4s.JDoubleJObjectJsonWriter
[WARNING]   - 397 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, aopalliance-1.0.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: 
[WARNING]   - org.aopalliance.intercept.ConstructorInterceptor
[WARNING]   - org.aopalliance.intercept.MethodInvocation
[WARNING]   - org.aopalliance.intercept.MethodInterceptor
[WARNING]   - org.aopalliance.intercept.Invocation
[WARNING]   - org.aopalliance.aop.AspectException
[WARNING]   - org.aopalliance.intercept.Interceptor
[WARNING]   - org.aopalliance.intercept.Joinpoint
[WARNING]   - org.aopalliance.aop.Advice
[WARNING]   - org.aopalliance.intercept.ConstructorInvocation
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, oro-2.0.8.jar define 62 overlapping classes: 
[WARNING]   - org.apache.oro.text.perl.MalformedPerl5PatternException
[WARNING]   - org.apache.oro.text.regex.Perl5Pattern
[WARNING]   - org.apache.oro.io.RegexFilenameFilter
[WARNING]   - org.apache.oro.util.Cache
[WARNING]   - org.apache.oro.text.GenericPatternCache
[WARNING]   - org.apache.oro.text.awk.DFAState
[WARNING]   - org.apache.oro.text.regex.StringSubstitution
[WARNING]   - org.apache.oro.text.awk.AwkCompiler
[WARNING]   - org.apache.oro.text.PatternCacheLRU
[WARNING]   - org.apache.oro.text.regex.Substitution
[WARNING]   - 52 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, netty-3.9.9.Final.jar define 879 overlapping classes: 
[WARNING]   - org.jboss.netty.handler.traffic.TrafficCounter$TrafficMonitoringTask
[WARNING]   - org.jboss.netty.handler.codec.spdy.SpdyGoAwayFrame
[WARNING]   - org.jboss.netty.util.internal.jzlib.Deflate
[WARNING]   - org.jboss.netty.channel.socket.ServerSocketChannelConfig
[WARNING]   - org.jboss.netty.util.internal.ConcurrentHashMap$HashIterator
[WARNING]   - org.jboss.netty.handler.codec.serialization.ObjectDecoder
[WARNING]   - org.jboss.netty.util.internal.jzlib.Tree
[WARNING]   - org.jboss.netty.util.internal.ConcurrentIdentityWeakKeyHashMap$Segment
[WARNING]   - org.jboss.netty.util.internal.ConcurrentIdentityHashMap$ValueIterator
[WARNING]   - org.jboss.netty.handler.codec.http.multipart.HttpPostRequestEncoder
[WARNING]   - 869 more...
[WARNING] jersey-container-servlet-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 6 overlapping classes: 
[WARNING]   - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl
[WARNING]   - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$ExtensionImpl
[WARNING]   - org.glassfish.jersey.servlet.init.JerseyServletContainerInitializer
[WARNING]   - org.glassfish.jersey.servlet.init.FilterUrlMappingsProviderImpl
[WARNING]   - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$1
[WARNING]   - org.glassfish.jersey.servlet.init.internal.LocalizationMessages
[WARNING] avro-ipc-1.7.7.jar, mango-core-0.0.3-SNAPSHOT.jar define 114 overlapping classes: 
[WARNING]   - org.apache.avro.ipc.HandshakeRequest$1
[WARNING]   - org.apache.avro.ipc.stats.Histogram
[WARNING]   - org.apache.avro.ipc.stats.Histogram$Entry
[WARNING]   - org.apache.avro.ipc.trace.Span$Builder
[WARNING]   - org.apache.avro.ipc.trace.TraceNode
[WARNING]   - org.apache.avro.ipc.specific.SpecificRequestor
[WARNING]   - org.apache.avro.ipc.stats.Histogram$SegmenterException
[WARNING]   - org.apache.avro.ipc.SaslSocketServer$AnonymousServer
[WARNING]   - org.apache.avro.ipc.stats.Histogram$Segmenter
[WARNING]   - org.apache.avro.ipc.SaslSocketServer$2
[WARNING]   - 104 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, zookeeper-3.4.6.jar define 440 overlapping classes: 
[WARNING]   - org.apache.zookeeper.server.NettyServerCnxn$DumpCommand
[WARNING]   - org.apache.zookeeper.proto.GetMaxChildrenRequest
[WARNING]   - org.apache.jute.XmlInputArchive$XMLParser
[WARNING]   - org.apache.zookeeper.server.NettyServerCnxn$SendBufferWriter
[WARNING]   - org.apache.jute.CsvInputArchive$1
[WARNING]   - org.apache.zookeeper.KeeperException$CodeDeprecated
[WARNING]   - org.apache.zookeeper.server.ZooKeeperServerMXBean
[WARNING]   - org.apache.zookeeper.server.NettyServerCnxn$EnvCommand
[WARNING]   - org.apache.zookeeper.server.quorum.Learner$PacketInFlight
[WARNING]   - org.apache.zookeeper.Op$Check
[WARNING]   - 430 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-jvm-3.1.5.jar define 38 overlapping classes: 
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$15
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$3
[WARNING]   - com.codahale.metrics.jvm.CachedThreadStatesGaugeSet
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$8
[WARNING]   - com.codahale.metrics.jvm.ClassLoadingGaugeSet$1
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$5
[WARNING]   - com.codahale.metrics.jvm.BufferPoolMetricSet
[WARNING]   - com.codahale.metrics.jvm.ThreadStatesGaugeSet
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$10
[WARNING]   - 28 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-core-3.1.5.jar define 115 overlapping classes: 
[WARNING]   - com.codahale.metrics.JmxReporter$JmxGaugeMBean
[WARNING]   - com.codahale.metrics.ThreadLocalRandomProxy$InternalProvider
[WARNING]   - com.codahale.metrics.JmxReporter
[WARNING]   - com.codahale.metrics.EWMA
[WARNING]   - com.codahale.metrics.Gauge
[WARNING]   - com.codahale.metrics.MetricRegistry$MetricBuilder$1
[WARNING]   - com.codahale.metrics.MetricFilter$1
[WARNING]   - com.codahale.metrics.JmxReporter$JmxCounterMBean
[WARNING]   - com.codahale.metrics.InstrumentedExecutorService$InstrumentedRunnable
[WARNING]   - com.codahale.metrics.RatioGauge$Ratio
[WARNING]   - 105 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, zstd-jni-1.3.2-2.jar define 8 overlapping classes: 
[WARNING]   - com.github.luben.zstd.ZstdDirectBufferDecompressingStream
[WARNING]   - com.github.luben.zstd.ZstdOutputStream
[WARNING]   - com.github.luben.zstd.ZstdDictCompress
[WARNING]   - com.github.luben.zstd.ZstdDictDecompress
[WARNING]   - com.github.luben.zstd.ZstdInputStream
[WARNING]   - com.github.luben.zstd.Zstd
[WARNING]   - com.github.luben.zstd.util.Native
[WARNING]   - com.github.luben.zstd.ZstdDirectBufferCompressingStream
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, xz-1.5.jar define 105 overlapping classes: 
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder$LengthDecoder
[WARNING]   - org.tukaani.xz.index.IndexDecoder
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoderFast
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoder$LengthEncoder
[WARNING]   - org.tukaani.xz.BlockOutputStream
[WARNING]   - org.tukaani.xz.simple.SimpleFilter
[WARNING]   - org.tukaani.xz.rangecoder.RangeCoder
[WARNING]   - org.tukaani.xz.XZOutputStream
[WARNING]   - org.tukaani.xz.UncompressedLZMA2OutputStream
[WARNING]   - 95 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-graphite-3.1.5.jar define 10 overlapping classes: 
[WARNING]   - com.codahale.metrics.graphite.PickledGraphite$MetricTuple
[WARNING]   - com.codahale.metrics.graphite.GraphiteReporter$Builder
[WARNING]   - com.codahale.metrics.graphite.Graphite
[WARNING]   - com.codahale.metrics.graphite.GraphiteRabbitMQ$1
[WARNING]   - com.codahale.metrics.graphite.GraphiteSender
[WARNING]   - com.codahale.metrics.graphite.PickledGraphite
[WARNING]   - com.codahale.metrics.graphite.GraphiteUDP
[WARNING]   - com.codahale.metrics.graphite.GraphiteReporter
[WARNING]   - com.codahale.metrics.graphite.GraphiteReporter$1
[WARNING]   - com.codahale.metrics.graphite.GraphiteRabbitMQ
[WARNING] jersey-client-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 111 overlapping classes: 
[WARNING]   - org.glassfish.jersey.client.ChunkParser
[WARNING]   - org.glassfish.jersey.client.HttpUrlConnectorProvider
[WARNING]   - org.glassfish.jersey.client.JerseyInvocation$EntityPresence
[WARNING]   - org.glassfish.jersey.client.ResponseCallback
[WARNING]   - org.glassfish.jersey.client.authentication.RequestAuthenticationException
[WARNING]   - org.glassfish.jersey.client.JerseyInvocation$5
[WARNING]   - org.glassfish.jersey.client.ClientConfig$State$4
[WARNING]   - org.glassfish.jersey.client.ClientResponse$1
[WARNING]   - org.glassfish.jersey.client.InboundJaxrsResponse$2
[WARNING]   - org.glassfish.jersey.client.internal.HttpUrlConnector$5
[WARNING]   - 101 more...
[WARNING] spark-network-shuffle_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 41 overlapping classes: 
[WARNING]   - org.apache.spark.network.shuffle.RetryingBlockFetcher$1
[WARNING]   - org.apache.spark.network.shuffle.protocol.BlockTransferMessage$Type
[WARNING]   - org.apache.spark.network.shuffle.ShuffleIndexRecord
[WARNING]   - org.apache.spark.network.sasl.ShuffleSecretManager
[WARNING]   - org.apache.spark.network.shuffle.SimpleDownloadFile
[WARNING]   - org.apache.spark.network.shuffle.OneForOneBlockFetcher
[WARNING]   - org.apache.spark.network.shuffle.ExternalShuffleBlockResolver$2
[WARNING]   - org.apache.spark.network.shuffle.ExternalShuffleBlockHandler$ManagedBufferIterator
[WARNING]   - org.apache.spark.network.shuffle.DownloadFileManager
[WARNING]   - org.apache.spark.network.shuffle.protocol.RegisterExecutor
[WARNING]   - 31 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, chill-java-0.8.4.jar define 54 overlapping classes: 
[WARNING]   - com.twitter.chill.java.ClosureSerializer
[WARNING]   - com.twitter.chill.config.JavaMapConfig
[WARNING]   - com.twitter.chill.java.IterableRegistrar
[WARNING]   - com.twitter.chill.java.SqlTimeSerializer
[WARNING]   - com.twitter.chill.KryoInstantiator
[WARNING]   - com.twitter.chill.java.PackageRegistrar
[WARNING]   - com.twitter.chill.config.ConfiguredInstantiator
[WARNING]   - com.twitter.chill.java.SimpleDateFormatSerializer
[WARNING]   - com.twitter.chill.KryoInstantiator$4
[WARNING]   - com.twitter.chill.java.UnmodifiableSetSerializer
[WARNING]   - 44 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-jexl-2.1.1.jar define 178 overlapping classes: 
[WARNING]   - org.apache.commons.jexl2.internal.AbstractExecutor$Get
[WARNING]   - org.apache.commons.jexl2.introspection.JexlPropertyGet
[WARNING]   - org.apache.commons.jexl2.parser.StringParser
[WARNING]   - org.apache.commons.jexl2.parser.ASTBitwiseOrNode
[WARNING]   - org.apache.commons.jexl2.internal.introspection.MethodKey$1
[WARNING]   - org.apache.commons.jexl2.Main
[WARNING]   - org.apache.commons.jexl2.parser.ASTForeachStatement
[WARNING]   - org.apache.commons.jexl2.introspection.Sandbox
[WARNING]   - org.apache.commons.jexl2.internal.introspection.ClassMap
[WARNING]   - org.apache.commons.jexl2.parser.ASTFunctionNode
[WARNING]   - 168 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-annotations-2.6.0.jar define 58 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.annotation.JsonAutoDetect
[WARNING]   - com.fasterxml.jackson.annotation.JsonInclude
[WARNING]   - com.fasterxml.jackson.annotation.ObjectIdGenerators
[WARNING]   - com.fasterxml.jackson.annotation.JsonFormat$Features
[WARNING]   - com.fasterxml.jackson.annotation.JsonFormat$Feature
[WARNING]   - com.fasterxml.jackson.annotation.JsonIgnore
[WARNING]   - com.fasterxml.jackson.annotation.JsonSetter
[WARNING]   - com.fasterxml.jackson.annotation.JsonTypeInfo$None
[WARNING]   - com.fasterxml.jackson.annotation.JsonSubTypes
[WARNING]   - com.fasterxml.jackson.annotation.JsonFormat$Shape
[WARNING]   - 48 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, compress-lzf-1.0.3.jar define 42 overlapping classes: 
[WARNING]   - com.ning.compress.lzf.LZFUncompressor
[WARNING]   - com.ning.compress.BufferRecycler
[WARNING]   - com.ning.compress.lzf.LZFEncoder
[WARNING]   - com.ning.compress.lzf.impl.UnsafeChunkEncoderBE
[WARNING]   - com.ning.compress.lzf.impl.UnsafeChunkEncoderLE
[WARNING]   - com.ning.compress.gzip.OptimizedGZIPInputStream
[WARNING]   - com.ning.compress.lzf.util.LZFFileOutputStream$Wrapper
[WARNING]   - com.ning.compress.lzf.util.LZFFileInputStream$1
[WARNING]   - com.ning.compress.lzf.ChunkEncoder
[WARNING]   - com.ning.compress.lzf.impl.UnsafeChunkDecoder
[WARNING]   - 32 more...
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT.jar with /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT-shaded.jar
[INFO] Dependency-reduced POM written at: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/dependency-reduced-pom.xml
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-cli ---
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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 ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/curator/curator-client/2.7.1/curator-client-2.7.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/curator/curator-client/2.7.1/curator-client-2.7.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/zookeeper/zookeeper/3.4.6/zookeeper-3.4.6.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/zookeeper/zookeeper/3.4.6/zookeeper-3.4.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/fusesource/leveldbjni/leveldbjni-all/1.8/leveldbjni-all-1.8.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/fusesource/leveldbjni/leveldbjni-all/1.8/leveldbjni-all-1.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/it/unimi/dsi/fastutil/6.5.7/fastutil-6.5.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.5.7/fastutil-6.5.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-codec/commons-codec/1.10/commons-codec-1.10.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/commons-codec/commons-codec/1.10/commons-codec-1.10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-tags_2.11/2.3.3/spark-tags_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-tags_2.11/2.3.3/spark-tags_2.11-2.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo-shaded/3.0.3/kryo-shaded-3.0.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/kryo-shaded/3.0.3/kryo-shaded-3.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/minlog/1.3.0/minlog-1.3.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/minlog/1.3.0/minlog-1.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-column/1.8.3/parquet-column-1.8.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.8.3/parquet-column-1.8.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-common/1.8.3/parquet-common-1.8.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.8.3/parquet-common-1.8.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-encoding/1.8.3/parquet-encoding-1.8.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.8.3/parquet-encoding-1.8.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-databind/2.6.7.1/jackson-databind-2.6.7.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-databind/2.6.7.1/jackson-databind-2.6.7.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-annotations/2.6.0/jackson-annotations-2.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-annotations/2.6.0/jackson-annotations-2.6.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-core/2.6.7/jackson-core-2.6.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-core/2.6.7/jackson-core-2.6.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/xbean/xbean-asm5-shaded/4.4/xbean-asm5-shaded-4.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/xbean/xbean-asm5-shaded/4.4/xbean-asm5-shaded-4.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/spark-project/spark/unused/1.0.0/unused-1.0.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/spark-project/spark/unused/1.0.0/unused-1.0.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-scala_2.10/1.8.3/parquet-scala_2.10-1.8.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.8.3/parquet-scala_2.10-1.8.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-core_2.11/2.3.3/spark-core_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-core_2.11/2.3.3/spark-core_2.11-2.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro-mapred/1.7.7/avro-mapred-1.7.7-hadoop2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro-mapred/1.7.7/avro-mapred-1.7.7-hadoop2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro-ipc/1.7.7/avro-ipc-1.7.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro-ipc/1.7.7/avro-ipc-1.7.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro-ipc/1.7.7/avro-ipc-1.7.7-tests.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro-ipc/1.7.7/avro-ipc-1.7.7-tests.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/chill_2.11/0.8.4/chill_2.11-0.8.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/twitter/chill_2.11/0.8.4/chill_2.11-0.8.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/chill-java/0.8.4/chill-java-0.8.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/twitter/chill-java/0.8.4/chill-java-0.8.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-launcher_2.11/2.3.3/spark-launcher_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-launcher_2.11/2.3.3/spark-launcher_2.11-2.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-kvstore_2.11/2.3.3/spark-kvstore_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-kvstore_2.11/2.3.3/spark-kvstore_2.11-2.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-network-common_2.11/2.3.3/spark-network-common_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-network-common_2.11/2.3.3/spark-network-common_2.11-2.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-network-shuffle_2.11/2.3.3/spark-network-shuffle_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-network-shuffle_2.11/2.3.3/spark-network-shuffle_2.11-2.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-unsafe_2.11/2.3.3/spark-unsafe_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-unsafe_2.11/2.3.3/spark-unsafe_2.11-2.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/net/java/dev/jets3t/jets3t/0.9.4/jets3t-0.9.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/java/dev/jets3t/jets3t/0.9.4/jets3t-0.9.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/activation/activation/1.1.1/activation-1.1.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/activation/activation/1.1.1/activation-1.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bouncycastle/bcprov-jdk15on/1.52/bcprov-jdk15on-1.52.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bouncycastle/bcprov-jdk15on/1.52/bcprov-jdk15on-1.52.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/jamesmurty/utils/java-xmlbuilder/1.1/java-xmlbuilder-1.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/jamesmurty/utils/java-xmlbuilder/1.1/java-xmlbuilder-1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/net/iharder/base64/2.3.8/base64-2.3.8.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/iharder/base64/2.3.8/base64-2.3.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/curator/curator-recipes/2.6.0/curator-recipes-2.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/curator/curator-recipes/2.6.0/curator-recipes-2.6.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/curator/curator-framework/2.6.0/curator-framework-2.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/curator/curator-framework/2.6.0/curator-framework-2.6.0.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/org/apache/commons/commons-math3/3.4.1/commons-math3-3.4.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-math3/3.4.1/commons-math3-3.4.1.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/slf4j/jul-to-slf4j/1.7.16/jul-to-slf4j-1.7.16.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/jul-to-slf4j/1.7.16/jul-to-slf4j-1.7.16.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/jcl-over-slf4j/1.7.16/jcl-over-slf4j-1.7.16.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/jcl-over-slf4j/1.7.16/jcl-over-slf4j-1.7.16.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/log4j/log4j/1.2.17/log4j-1.2.17.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-log4j12/1.7.16/slf4j-log4j12-1.7.16.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.16/slf4j-log4j12-1.7.16.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/ning/compress-lzf/1.0.3/compress-lzf-1.0.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/ning/compress-lzf/1.0.3/compress-lzf-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/lz4/lz4-java/1.4.0/lz4-java-1.4.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/lz4/lz4-java/1.4.0/lz4-java-1.4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/luben/zstd-jni/1.3.2-2/zstd-jni-1.3.2-2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/github/luben/zstd-jni/1.3.2-2/zstd-jni-1.3.2-2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/roaringbitmap/RoaringBitmap/0.5.11/RoaringBitmap-0.5.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/roaringbitmap/RoaringBitmap/0.5.11/RoaringBitmap-0.5.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-net/commons-net/2.2/commons-net-2.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/commons-net/commons-net/2.2/commons-net-2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/json4s/json4s-jackson_2.11/3.2.11/json4s-jackson_2.11-3.2.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/json4s/json4s-jackson_2.11/3.2.11/json4s-jackson_2.11-3.2.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/json4s/json4s-core_2.11/3.2.11/json4s-core_2.11-3.2.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/json4s/json4s-core_2.11/3.2.11/json4s-core_2.11-3.2.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/json4s/json4s-ast_2.11/3.2.11/json4s-ast_2.11-3.2.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/json4s/json4s-ast_2.11/3.2.11/json4s-ast_2.11-3.2.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/core/jersey-client/2.22.2/jersey-client-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/core/jersey-client/2.22.2/jersey-client-2.22.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/ws/rs/javax.ws.rs-api/2.0.1/javax.ws.rs-api-2.0.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/ws/rs/javax.ws.rs-api/2.0.1/javax.ws.rs-api-2.0.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/hk2-api/2.4.0-b34/hk2-api-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/hk2-api/2.4.0-b34/hk2-api-2.4.0-b34.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/hk2-utils/2.4.0-b34/hk2-utils-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/hk2-utils/2.4.0-b34/hk2-utils-2.4.0-b34.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/external/aopalliance-repackaged/2.4.0-b34/aopalliance-repackaged-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/external/aopalliance-repackaged/2.4.0-b34/aopalliance-repackaged-2.4.0-b34.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/external/javax.inject/2.4.0-b34/javax.inject-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/external/javax.inject/2.4.0-b34/javax.inject-2.4.0-b34.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/hk2-locator/2.4.0-b34/hk2-locator-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/hk2-locator/2.4.0-b34/hk2-locator-2.4.0-b34.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/javassist/javassist/3.18.1-GA/javassist-3.18.1-GA.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/javassist/javassist/3.18.1-GA/javassist-3.18.1-GA.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/core/jersey-common/2.22.2/jersey-common-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/core/jersey-common/2.22.2/jersey-common-2.22.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/annotation/javax.annotation-api/1.2/javax.annotation-api-1.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/annotation/javax.annotation-api/1.2/javax.annotation-api-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/bundles/repackaged/jersey-guava/2.22.2/jersey-guava-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/bundles/repackaged/jersey-guava/2.22.2/jersey-guava-2.22.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/osgi-resource-locator/1.0.1/osgi-resource-locator-1.0.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/osgi-resource-locator/1.0.1/osgi-resource-locator-1.0.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/core/jersey-server/2.22.2/jersey-server-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/core/jersey-server/2.22.2/jersey-server-2.22.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/media/jersey-media-jaxb/2.22.2/jersey-media-jaxb-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/media/jersey-media-jaxb/2.22.2/jersey-media-jaxb-2.22.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/validation/validation-api/1.1.0.Final/validation-api-1.1.0.Final.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/validation/validation-api/1.1.0.Final/validation-api-1.1.0.Final.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/containers/jersey-container-servlet/2.22.2/jersey-container-servlet-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/containers/jersey-container-servlet/2.22.2/jersey-container-servlet-2.22.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/containers/jersey-container-servlet-core/2.22.2/jersey-container-servlet-core-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/containers/jersey-container-servlet-core/2.22.2/jersey-container-servlet-core-2.22.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/io/netty/netty-all/4.1.17.Final/netty-all-4.1.17.Final.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/netty/netty-all/4.1.17.Final/netty-all-4.1.17.Final.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/io/netty/netty/3.9.9.Final/netty-3.9.9.Final.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/netty/netty/3.9.9.Final/netty-3.9.9.Final.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/clearspring/analytics/stream/2.7.0/stream-2.7.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/clearspring/analytics/stream/2.7.0/stream-2.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/io/dropwizard/metrics/metrics-core/3.1.5/metrics-core-3.1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/dropwizard/metrics/metrics-core/3.1.5/metrics-core-3.1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/io/dropwizard/metrics/metrics-jvm/3.1.5/metrics-jvm-3.1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/dropwizard/metrics/metrics-jvm/3.1.5/metrics-jvm-3.1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/io/dropwizard/metrics/metrics-json/3.1.5/metrics-json-3.1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/dropwizard/metrics/metrics-json/3.1.5/metrics-json-3.1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/io/dropwizard/metrics/metrics-graphite/3.1.5/metrics-graphite-3.1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/dropwizard/metrics/metrics-graphite/3.1.5/metrics-graphite-3.1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/module/jackson-module-scala_2.11/2.6.7.1/jackson-module-scala_2.11-2.6.7.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/module/jackson-module-scala_2.11/2.6.7.1/jackson-module-scala_2.11-2.6.7.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/module/jackson-module-paranamer/2.7.9/jackson-module-paranamer-2.7.9.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/module/jackson-module-paranamer/2.7.9/jackson-module-paranamer-2.7.9.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/ivy/ivy/2.4.0/ivy-2.4.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/ivy/ivy/2.4.0/ivy-2.4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/oro/oro/2.0.8/oro-2.0.8.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/oro/oro/2.0.8/oro-2.0.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/net/razorvine/pyrolite/4.13/pyrolite-4.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/razorvine/pyrolite/4.13/pyrolite-4.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/net/sf/py4j/py4j/0.10.7/py4j-0.10.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/sf/py4j/py4j/0.10.7/py4j-0.10.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-crypto/1.0.0/commons-crypto-1.0.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-crypto/1.0.0/commons-crypto-1.0.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli-spark2_2.11/0.26.0/adam-cli-spark2_2.11-0.26.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli-spark2_2.11/0.26.0/adam-cli-spark2_2.11-0.26.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-apis-spark2_2.11/0.26.0/adam-apis-spark2_2.11-0.26.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis-spark2_2.11/0.26.0/adam-apis-spark2_2.11-0.26.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/args4j/args4j/2.0.31/args4j-2.0.31.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/args4j/args4j/2.0.31/args4j-2.0.31.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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_2.11/0.26.0/adam-core-spark2_2.11-0.26.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core-spark2_2.11/0.26.0/adam-core-spark2_2.11-0.26.0.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/2.16.1/htsjdk-2.16.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/github/samtools/htsjdk/2.16.1/htsjdk-2.16.1.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/4.5.2/httpclient-4.5.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.5.2/httpclient-4.5.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpcore/4.4.4/httpcore-4.4.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.4.4/httpcore-4.4.4.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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_2.11/0.26.0/adam-codegen-spark2_2.11-0.26.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.26.0/adam-codegen-spark2_2.11-0.26.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.12.0/bdg-formats-0.12.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.12.0/bdg-formats-0.12.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.13/utils-cli-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.13/utils-cli-spark2_2.11-0.2.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.13/utils-misc-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.13/utils-misc-spark2_2.11-0.2.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.13/utils-intervalrdd-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.13/utils-intervalrdd-spark2_2.11-0.2.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.13/utils-metrics-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.13/utils-metrics-spark2_2.11-0.2.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/servo/servo-core/0.12.12/servo-core-0.12.12.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.12.12/servo-core-0.12.12.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-server/9.4.15.v20190215/jetty-server-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-server/9.4.15.v20190215/jetty-server-9.4.15.v20190215.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-http/9.4.15.v20190215/jetty-http-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-http/9.4.15.v20190215/jetty-http-9.4.15.v20190215.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-util/9.4.15.v20190215/jetty-util-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util/9.4.15.v20190215/jetty-util-9.4.15.v20190215.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-io/9.4.15.v20190215/jetty-io-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-io/9.4.15.v20190215/jetty-io-9.4.15.v20190215.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.15.v20190215/jetty-webapp-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-webapp/9.4.15.v20190215/jetty-webapp-9.4.15.v20190215.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.15.v20190215/jetty-xml-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-xml/9.4.15.v20190215/jetty-xml-9.4.15.v20190215.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.15.v20190215/jetty-servlet-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-servlet/9.4.15.v20190215/jetty-servlet-9.4.15.v20190215.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-security/9.4.15.v20190215/jetty-security-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-security/9.4.15.v20190215/jetty-security-9.4.15.v20190215.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-reflect/2.11.7/scala-reflect-2.11.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-reflect/2.11.7/scala-reflect-2.11.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/clapper/grizzled-slf4j_2.11/1.0.2/grizzled-slf4j_2.11-1.0.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/clapper/grizzled-slf4j_2.11/1.0.2/grizzled-slf4j_2.11-1.0.2.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core/0.0.3-SNAPSHOT/mango-core-0.0.3-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.13/utils-io-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.13/utils-io-spark2_2.11-0.2.13.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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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/0.6.0/convert-ga4gh-0.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.6.0/convert-ga4gh-0.6.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.6.0/convert-htsjdk-0.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.6.0/convert-htsjdk-0.6.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.6.0/convert-0.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.6.0/convert-0.6.0.jar
[INFO] Installing artifact /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli/0.0.3-SNAPSHOT/mango-cli-0.0.3-SNAPSHOT.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Assembly 0.0.3-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:2.2.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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:3.0.1:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-assembly ---
[INFO] Including org.bdgenomics.mango:mango-cli:jar:0.0.3-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:1.8.1 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar.
[INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar.
[INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar.
[INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar.
[INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar.
[INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar.
[INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.7 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.12 in the shaded jar.
[INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar.
[INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar.
[INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar.
[INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar.
[INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-client:jar:2.6.0 in the shaded jar.
[INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar.
[INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar.
[INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar.
[INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar.
[INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar.
[INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar.
[INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar.
[INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar.
[INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar.
[INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar.
[INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar.
[INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar.
[INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.8 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar.
[INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar.
[INFO] Including oro:oro:jar:2.0.8 in the shaded jar.
[INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar.
[INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar.
[INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar.
[INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.26.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.26.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 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.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 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.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:2.16.1 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:4.5.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 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:0.26.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.15.v20190215 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.clapper:grizzled-slf4j_2.11:jar:1.0.2 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:0.0.3-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 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:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar.
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, validation-api-1.1.0.Final.jar, mango-cli-0.0.3-SNAPSHOT.jar define 106 overlapping classes: 
[WARNING]   - javax.validation.ConstraintDeclarationException
[WARNING]   - javax.validation.GroupDefinitionException
[WARNING]   - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder$LeafNodeBuilderDefinedContext
[WARNING]   - javax.validation.metadata.ParameterDescriptor
[WARNING]   - javax.validation.Validator
[WARNING]   - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder
[WARNING]   - javax.validation.constraints.AssertTrue$List
[WARNING]   - javax.validation.constraints.Past
[WARNING]   - javax.validation.metadata.GroupConversionDescriptor
[WARNING]   - javax.validation.constraints.Max
[WARNING]   - 96 more...
[WARNING] javax.servlet-api-3.1.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 79 overlapping classes: 
[WARNING]   - javax.servlet.http.Cookie
[WARNING]   - javax.servlet.ServletContext
[WARNING]   - javax.servlet.Registration
[WARNING]   - javax.servlet.http.HttpSessionListener
[WARNING]   - javax.servlet.http.HttpSessionContext
[WARNING]   - javax.servlet.FilterChain
[WARNING]   - javax.servlet.http.WebConnection
[WARNING]   - javax.servlet.http.HttpServletRequestWrapper
[WARNING]   - javax.servlet.http.HttpSessionAttributeListener
[WARNING]   - javax.servlet.annotation.HandlesTypes
[WARNING]   - 69 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, avro-ipc-1.7.7-tests.jar define 248 overlapping classes: 
[WARNING]   - test.StringablesRecord$Builder
[WARNING]   - org.apache.avro.specific.TestSpecificRecordBuilder
[WARNING]   - org.apache.avro.test.TestRecordWithUnion$Builder
[WARNING]   - org.apache.avro.test.TestError
[WARNING]   - org.apache.avro.test.Kind
[WARNING]   - org.apache.avro.io.Perf$IntTest
[WARNING]   - org.apache.avro.Interop$1
[WARNING]   - org.apache.avro.test.TestError$Builder
[WARNING]   - org.apache.avro.TestProtocolReflect$1
[WARNING]   - org.apache.avro.ipc.trace.TestFileSpanStorage
[WARNING]   - 238 more...
[WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.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-0.0.3-SNAPSHOT.jar, jetty-servlet-9.4.15.v20190215.jar define 48 overlapping classes: 
[WARNING]   - org.eclipse.jetty.servlet.ServletHandler$Default404Servlet
[WARNING]   - org.eclipse.jetty.servlet.FilterMapping
[WARNING]   - org.eclipse.jetty.servlet.ErrorPageErrorHandler$PageLookupTechnique
[WARNING]   - org.eclipse.jetty.servlet.ServletContextHandler
[WARNING]   - org.eclipse.jetty.servlet.Holder$1
[WARNING]   - org.eclipse.jetty.servlet.FilterMapping$1
[WARNING]   - org.eclipse.jetty.servlet.ServletContextHandler$ServletContainerInitializerCaller
[WARNING]   - org.eclipse.jetty.servlet.FilterHolder
[WARNING]   - org.eclipse.jetty.servlet.Invoker
[WARNING]   - org.eclipse.jetty.servlet.Holder
[WARNING]   - 38 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 760 overlapping classes: 
[WARNING]   - shaded.com.google.protobuf.FieldMaskProto
[WARNING]   - org.bdgenomics.mango.filters.Discovery$$anonfun$4
[WARNING]   - shaded.com.google.protobuf.DescriptorProtos$EnumValueDescriptorProto
[WARNING]   - shaded.com.google.protobuf.NioByteString$1
[WARNING]   - scala.tools.nsc.plugins.Plugins$$anonfun$computePluginPhases$1$$anonfun$apply$6
[WARNING]   - shaded.com.google.protobuf.GeneratedMessage$BuilderParent
[WARNING]   - org.bdgenomics.mango.models.LazyMaterialization$$anonfun$put$1$$anonfun$2
[WARNING]   - org.bdgenomics.mango.io.BedReader$$anonfun$10$$anonfun$apply$1$$anonfun$apply$2
[WARNING]   - shaded.com.google.protobuf.GeneratedMessage$4
[WARNING]   - shaded.com.google.protobuf.TextFormat$UnknownFieldParseException
[WARNING]   - 750 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, htsjdk-2.16.1.jar define 983 overlapping classes: 
[WARNING]   - htsjdk.samtools.cram.ref.ReferenceSource
[WARNING]   - htsjdk.samtools.HighAccuracyDownsamplingIterator
[WARNING]   - htsjdk.samtools.util.zip.DeflaterFactory
[WARNING]   - htsjdk.samtools.filter.DuplicateReadFilter
[WARNING]   - htsjdk.variant.vcf.VCFEncoder
[WARNING]   - htsjdk.samtools.util.CloserUtil
[WARNING]   - htsjdk.tribble.TribbleException$FeatureFileDoesntExist
[WARNING]   - htsjdk.tribble.index.tabix.TabixIndex
[WARNING]   - htsjdk.samtools.AbstractBAMFileIndex
[WARNING]   - htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder$1
[WARNING]   - 973 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-io-spark2_2.11-0.2.13.jar, mango-cli-0.0.3-SNAPSHOT.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$3
[WARNING]   - org.bdgenomics.utils.io.FileLocator
[WARNING]   - org.bdgenomics.utils.io.ByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$readByteStream$1
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$1
[WARNING]   - org.bdgenomics.utils.io.ByteAccess$$anonfun$readFully$2
[WARNING]   - org.bdgenomics.utils.io.LocalFileByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$2
[WARNING]   - org.bdgenomics.utils.io.HTTPFileLocator$
[WARNING]   - 13 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, javassist-3.18.1-GA.jar define 390 overlapping classes: 
[WARNING]   - javassist.util.proxy.ProxyFactory$3
[WARNING]   - javassist.bytecode.FieldInfo
[WARNING]   - javassist.DirClassPath
[WARNING]   - javassist.ClassPool$1
[WARNING]   - javassist.expr.Cast$ProceedForCast
[WARNING]   - javassist.URLClassPath
[WARNING]   - javassist.CtMethod$LongConstParameter
[WARNING]   - javassist.compiler.Javac$2
[WARNING]   - javassist.bytecode.annotation.ClassMemberValue
[WARNING]   - javassist.bytecode.stackmap.TypeData$ClassName
[WARNING]   - 380 more...
[WARNING] log4j-1.2.17.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 314 overlapping classes: 
[WARNING]   - org.apache.log4j.or.sax.AttributesRenderer
[WARNING]   - org.apache.log4j.pattern.MessagePatternConverter
[WARNING]   - org.apache.log4j.chainsaw.ControlPanel$3
[WARNING]   - org.apache.log4j.pattern.NameAbbreviator$DropElementAbbreviator
[WARNING]   - org.apache.log4j.jmx.MethodUnion
[WARNING]   - org.apache.log4j.lf5.viewer.LogTable
[WARNING]   - org.apache.log4j.BasicConfigurator
[WARNING]   - org.apache.log4j.rewrite.RewriteAppender
[WARNING]   - org.apache.log4j.lf5.viewer.LogBrokerMonitor$22
[WARNING]   - org.apache.log4j.pattern.LoggingEventPatternConverter
[WARNING]   - 304 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, compress-lzf-1.0.3.jar define 42 overlapping classes: 
[WARNING]   - com.ning.compress.lzf.LZFUncompressor
[WARNING]   - com.ning.compress.BufferRecycler
[WARNING]   - com.ning.compress.lzf.LZFEncoder
[WARNING]   - com.ning.compress.lzf.impl.UnsafeChunkEncoderBE
[WARNING]   - com.ning.compress.lzf.impl.UnsafeChunkEncoderLE
[WARNING]   - com.ning.compress.gzip.OptimizedGZIPInputStream
[WARNING]   - com.ning.compress.lzf.util.LZFFileOutputStream$Wrapper
[WARNING]   - com.ning.compress.lzf.util.LZFFileInputStream$1
[WARNING]   - com.ning.compress.lzf.ChunkEncoder
[WARNING]   - com.ning.compress.lzf.impl.UnsafeChunkDecoder
[WARNING]   - 32 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, pyrolite-4.13.jar define 54 overlapping classes: 
[WARNING]   - net.razorvine.pickle.objects.ByteArrayConstructor
[WARNING]   - net.razorvine.pyro.NameServerProxy
[WARNING]   - net.razorvine.pyro.serializer.PyroSerializer
[WARNING]   - net.razorvine.pickle.objects.DateTimeConstructor
[WARNING]   - net.razorvine.pickle.IObjectConstructor
[WARNING]   - net.razorvine.pickle.objects.ClassDictConstructor
[WARNING]   - net.razorvine.pyro.serializer.PyroUriSerpent
[WARNING]   - net.razorvine.pickle.objects.OperatorAttrGetterForCalendarTz$CalendarLocalizer
[WARNING]   - net.razorvine.pickle.objects.TimeZoneConstructor
[WARNING]   - net.razorvine.pyro.Config
[WARNING]   - 44 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, netty-all-4.1.17.Final.jar define 2501 overlapping classes: 
[WARNING]   - io.netty.handler.codec.http.multipart.InterfaceHttpData$HttpDataType
[WARNING]   - io.netty.resolver.dns.InflightNameResolver$1
[WARNING]   - io.netty.channel.AbstractChannel$AbstractUnsafe$8
[WARNING]   - io.netty.handler.codec.smtp.DefaultSmtpRequest
[WARNING]   - io.netty.handler.codec.redis.RedisMessage
[WARNING]   - io.netty.handler.codec.memcache.binary.BinaryMemcacheResponse
[WARNING]   - io.netty.handler.timeout.IdleStateHandler
[WARNING]   - io.netty.buffer.FixedCompositeByteBuf$Component
[WARNING]   - io.netty.handler.codec.http.HttpHeaders
[WARNING]   - io.netty.handler.codec.http2.Http2ClientUpgradeCodec
[WARNING]   - 2491 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-metrics-spark2_2.11-0.2.13.jar, mango-cli-0.0.3-SNAPSHOT.jar define 407 overlapping classes: 
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$reduceByKey$2$$anonfun$apply$33
[WARNING]   - org.bdgenomics.utils.instrumentation.SimpleMonitorValueExtractor
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$fullOuterJoin$2
[WARNING]   - org.bdgenomics.utils.instrumentation.MetricsListener$$anonfun$onTaskEnd$2
[WARNING]   - org.bdgenomics.utils.metrics.Histogram$$anonfun$countSubset$1
[WARNING]   - org.bdgenomics.utils.instrumentation.Alignment$
[WARNING]   - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$saveAsHadoopFile$3
[WARNING]   - org.bdgenomics.utils.instrumentation.Metrics$TreeNode$$anonfun$6
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$reduce$1$$anonfun$apply$35
[WARNING]   - org.apache.spark.rdd.InstrumentedRDD$$anonfun$aggregate$1$$anonfun$apply$39$$anonfun$apply$40
[WARNING]   - 397 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, parquet-column-1.8.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 731 overlapping classes: 
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.longs.LongComparator
[WARNING]   - org.apache.parquet.filter2.recordlevel.IncrementallyUpdatedFilterPredicateBuilder$25
[WARNING]   - org.apache.parquet.column.values.dictionary.DictionaryValuesWriter$PlainIntegerDictionaryValuesWriter
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.ints.Int2IntLinkedOpenHashMap$MapEntry
[WARNING]   - org.apache.parquet.io.PrimitiveColumnIO
[WARNING]   - org.apache.parquet.io.api.Binary$ByteBufferBackedBinary
[WARNING]   - org.apache.parquet.column.statistics.BooleanStatistics
[WARNING]   - org.apache.parquet.column.values.boundedint.BoundedIntValuesReader
[WARNING]   - org.apache.parquet.schema.PrimitiveType$PrimitiveTypeName$3
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.doubles.DoubleSortedSet
[WARNING]   - 721 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, leveldbjni-all-1.8.jar define 75 overlapping classes: 
[WARNING]   - org.fusesource.leveldbjni.internal.NativeObject
[WARNING]   - org.fusesource.leveldbjni.internal.NativeDB$DBJNI
[WARNING]   - org.fusesource.leveldbjni.internal.NativeCache
[WARNING]   - org.fusesource.leveldbjni.internal.NativeComparator$ComparatorJNI
[WARNING]   - org.fusesource.leveldbjni.internal.NativeIterator
[WARNING]   - org.iq80.leveldb.WriteBatch
[WARNING]   - org.fusesource.hawtjni.runtime.ClassFlag
[WARNING]   - org.fusesource.leveldbjni.internal.NativeBuffer$1
[WARNING]   - org.iq80.leveldb.DBComparator
[WARNING]   - org.fusesource.leveldbjni.internal.NativeBuffer$Pool
[WARNING]   - 65 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, slf4j-api-1.7.7.jar define 24 overlapping classes: 
[WARNING]   - org.slf4j.helpers.SubstituteLogger
[WARNING]   - org.slf4j.ILoggerFactory
[WARNING]   - org.slf4j.MDC
[WARNING]   - org.slf4j.helpers.BasicMDCAdapter
[WARNING]   - org.slf4j.spi.MDCAdapter
[WARNING]   - org.slf4j.LoggerFactory
[WARNING]   - org.slf4j.helpers.Util
[WARNING]   - org.slf4j.helpers.NOPLogger
[WARNING]   - org.slf4j.helpers.NOPLoggerFactory
[WARNING]   - org.slf4j.helpers.SubstituteLoggerFactory
[WARNING]   - 14 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, convert-htsjdk-0.6.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.convert.htsjdk.HtsjdkModule
[WARNING]   - org.bdgenomics.convert.htsjdk.ConversionStringencyToValidationStringency
[WARNING]   - org.bdgenomics.convert.htsjdk.ValidationStringencyToConversionStringency
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, scala-library-2.11.11.jar define 3828 overlapping classes: 
[WARNING]   - scala.collection.mutable.SortedSet$class
[WARNING]   - scala.collection.immutable.IndexedSeq
[WARNING]   - scala.collection.SeqLike$$anonfun$reverseMap$2
[WARNING]   - scala.Function2$mcDID$sp
[WARNING]   - scala.collection.immutable.IntMapValueIterator
[WARNING]   - scala.collection.MapLike$DefaultKeySet
[WARNING]   - scala.collection.parallel.FactoryOps$Otherwise
[WARNING]   - scala.math.Ordering$String$
[WARNING]   - scala.util.Either$
[WARNING]   - scala.collection.mutable.SetProxy
[WARNING]   - 3818 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, objenesis-2.1.jar define 37 overlapping classes: 
[WARNING]   - org.objenesis.ObjenesisBase
[WARNING]   - org.objenesis.instantiator.gcj.GCJInstantiator
[WARNING]   - org.objenesis.strategy.SingleInstantiatorStrategy
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactoryHelper
[WARNING]   - org.objenesis.ObjenesisHelper
[WARNING]   - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactoryInstantiator
[WARNING]   - org.objenesis.instantiator.basic.NullInstantiator
[WARNING]   - org.objenesis.instantiator.android.Android17Instantiator
[WARNING]   - org.objenesis.instantiator.ObjectInstantiator
[WARNING]   - 27 more...
[WARNING] jersey-media-jaxb-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 47 overlapping classes: 
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlRootElementJaxbProvider$App
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlJaxbElementProvider$General
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider$General
[WARNING]   - org.glassfish.jersey.jaxb.internal.JaxbStringReaderProvider$1
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider
[WARNING]   - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$4
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$General
[WARNING]   - org.glassfish.jersey.jaxb.internal.JaxbMessagingBinder
[WARNING]   - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$2
[WARNING]   - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$Text
[WARNING]   - 37 more...
[WARNING] chill_2.11-0.8.4.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 150 overlapping classes: 
[WARNING]   - com.twitter.chill.Tuple11Serializer
[WARNING]   - com.twitter.chill.InnerClosureFinder
[WARNING]   - com.twitter.chill.Instantiators$$anonfun$reflectAsm$1
[WARNING]   - com.twitter.chill.RichKryo$$anonfun$fromInputStream$1
[WARNING]   - com.twitter.chill.package$$anon$3
[WARNING]   - com.twitter.chill.JavaIterableWrapperSerializer
[WARNING]   - com.twitter.chill.Instantiators$$anonfun$newOrElse$1
[WARNING]   - com.twitter.chill.SortedMapSerializer$$anonfun$write$1
[WARNING]   - com.twitter.chill.package$$anon$5$$anonfun$apply$2
[WARNING]   - com.twitter.chill.Tuple8Serializer
[WARNING]   - 140 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, animal-sniffer-annotations-1.17.jar define 1 overlapping classes: 
[WARNING]   - org.codehaus.mojo.animal_sniffer.IgnoreJRERequirement
[WARNING] mango-cli-0.0.3-SNAPSHOT.jar, jetty-server-9.4.15.v20190215.jar define 302 overlapping classes: 
[WARNING]   - org.eclipse.jetty.server.handler.ThreadLimitHandler$RFC7239
[WARNING]   - org.eclipse.jetty.server.handler.ManagedAttributeListener
[WARNING]   - org.eclipse.jetty.server.ServletRequestHttpWrapper
[WARNING]   - org.eclipse.jetty.server.DebugListener$1
[WARNING]   - org.eclipse.jetty.server.ShutdownMonitor$1
[WARNING]   - org.eclipse.jetty.server.HttpInput$1
[WARNING]   - org.eclipse.jetty.server.UserIdentity$Scope
[WARNING]   - org.eclipse.jetty.server.AcceptRateLimit$1
[WARNING]   - org.eclipse.jetty.server.session.AbstractSessionDataStoreFactory
[WARNING]   - org.eclipse.jetty.server.AsyncContextState$1
[WARNING]   - 292 more...
[WARNING] stream-2.7.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 78 overlapping classes: 
[WARNING]   - com.clearspring.analytics.stream.cardinality.HyperLogLog
[WARNING]   - com.clearspring.analytics.stream.membership.DataOutputBuffer
[WARNING]   - com.clearspring.analytics.stream.quantile.TDigest
[WARNING]   - com.clearspring.analytics.stream.cardinality.HyperLogLog$SerializationHolder
[WARNING]   - com.clearspring.analytics.util.ListNode2
[WARNING]   - com.clearspring.analytics.stream.frequency.CountMinSketch
[WARNING]   - com.clearspring.analytics.util.DoublyLinkedList
[WARNING]   - com.clearspring.analytics.stream.cardinality.CountThenEstimate$CountThenEstimateMergeException
[WARNING]   - com.clearspring.analytics.stream.quantile.QDigest$1
[WARNING]   - com.clearspring.analytics.stream.cardinality.HyperLogLog$HyperLogLogMergeException
[WARNING]   - 68 more...
[WARNING] mango-cli-0.0.3-SNAPSHOT.jar, jetty-webapp-9.4.15.v20190215.jar define 51 overlapping classes: 
[WARNING]   - org.eclipse.jetty.webapp.FragmentDescriptor
[WARNING]   - org.eclipse.jetty.webapp.CachingWebAppClassLoader
[WARNING]   - org.eclipse.jetty.webapp.ClasspathPattern$ClassEntry
[WARNING]   - org.eclipse.jetty.webapp.WebAppContext
[WARNING]   - org.eclipse.jetty.webapp.ClasspathPattern$ByClass
[WARNING]   - org.eclipse.jetty.webapp.CloneConfiguration
[WARNING]   - org.eclipse.jetty.webapp.RelativeOrdering$1
[WARNING]   - org.eclipse.jetty.webapp.Configuration$ClassList
[WARNING]   - org.eclipse.jetty.webapp.ClasspathPattern$ByModule
[WARNING]   - org.eclipse.jetty.webapp.StandardDescriptorProcessor$1
[WARNING]   - 41 more...
[WARNING] jersey-container-servlet-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 6 overlapping classes: 
[WARNING]   - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl
[WARNING]   - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$ExtensionImpl
[WARNING]   - org.glassfish.jersey.servlet.init.JerseyServletContainerInitializer
[WARNING]   - org.glassfish.jersey.servlet.init.FilterUrlMappingsProviderImpl
[WARNING]   - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$1
[WARNING]   - org.glassfish.jersey.servlet.init.internal.LocalizationMessages
[WARNING] mango-cli-0.0.3-SNAPSHOT.jar, joda-convert-1.8.1.jar define 94 overlapping classes: 
[WARNING]   - org.joda.convert.JDKStringConverter$18
[WARNING]   - org.joda.convert.JDKStringConverter$28
[WARNING]   - org.joda.convert.factory.NumericArrayStringConverterFactory$FloatArrayStringConverter
[WARNING]   - org.joda.convert.JDKStringConverter$1
[WARNING]   - org.joda.convert.factory.BooleanArrayStringConverterFactory
[WARNING]   - org.joda.convert.factory.NumericObjectArrayStringConverterFactory
[WARNING]   - org.joda.convert.FromString
[WARNING]   - org.joda.convert.StringConverter
[WARNING]   - org.joda.convert.StringConvert$1
[WARNING]   - org.joda.convert.factory.CharObjectArrayStringConverterFactory$CharecterArrayStringConverter
[WARNING]   - 84 more...
[WARNING] mango-cli-0.0.3-SNAPSHOT.jar, guice-4.2.0.jar define 1 overlapping classes: 
[WARNING]   - com.google.inject.internal.asm.$Item
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-network-common_2.11-2.3.3.jar define 1697 overlapping classes: 
[WARNING]   - org.spark_project.guava.annotations.Beta
[WARNING]   - org.spark_project.guava.util.concurrent.UncaughtExceptionHandlers$Exiter
[WARNING]   - org.spark_project.guava.eventbus.Subscribe
[WARNING]   - org.spark_project.guava.collect.TreeRangeMap
[WARNING]   - org.spark_project.guava.collect.ImmutableList$SubList
[WARNING]   - org.spark_project.guava.cache.RemovalCause$1
[WARNING]   - org.spark_project.guava.collect.ForwardingMultimap
[WARNING]   - org.spark_project.guava.io.LimitInputStream
[WARNING]   - org.spark_project.guava.math.BigIntegerMath
[WARNING]   - org.spark_project.guava.collect.Tables
[WARNING]   - 1687 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, json4s-core_2.11-3.2.11.jar, mango-cli-0.0.3-SNAPSHOT.jar define 407 overlapping classes: 
[WARNING]   - org.json4s.CustomSerializer
[WARNING]   - org.json4s.reflect.Reflector$ClassDescriptorBuilder$$anonfun$constructorsAndCompanion$3$$anonfun$13$$anonfun$apply$3
[WARNING]   - org.json4s.reflect.package$$anon$2
[WARNING]   - org.json4s.DefaultReaders$JValueReader$
[WARNING]   - org.json4s.StreamingJsonWriter$$anonfun$addJValue$1
[WARNING]   - org.json4s.ParserUtil$RecycledSegment
[WARNING]   - org.json4s.package
[WARNING]   - org.json4s.DefaultReaders$
[WARNING]   - org.json4s.Xml$$anonfun$directChildren$1$1
[WARNING]   - org.json4s.JDoubleJObjectJsonWriter
[WARNING]   - 397 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, avro-mapred-1.7.7-hadoop2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 126 overlapping classes: 
[WARNING]   - org.apache.avro.mapreduce.AvroMultipleOutputs
[WARNING]   - org.apache.avro.mapreduce.AvroKeyValueOutputFormat
[WARNING]   - org.apache.avro.mapred.SequenceFileReader$8
[WARNING]   - org.apache.avro.hadoop.file.HadoopCodecFactory
[WARNING]   - org.apache.avro.mapred.Pair
[WARNING]   - org.apache.avro.mapred.AvroMultipleOutputs
[WARNING]   - org.apache.avro.mapred.FsInput
[WARNING]   - org.apache.avro.mapred.tether.InputProtocol$Callback
[WARNING]   - org.apache.avro.mapred.AvroOutputFormat$1
[WARNING]   - org.apache.avro.hadoop.file.SortedKeyValueFile$Reader$Options
[WARNING]   - 116 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-core_2.11-2.3.3.jar define 8350 overlapping classes: 
[WARNING]   - org.apache.spark.shuffle.BaseShuffleHandle
[WARNING]   - org.apache.spark.SparkContext$$anonfun$11
[WARNING]   - org.spark_project.jetty.client.util.MultiPartContentProvider$1
[WARNING]   - org.apache.spark.TaskContextImpl$$anonfun$markTaskFailed$1
[WARNING]   - org.apache.spark.util.collection.PrimitiveVector$mcI$sp
[WARNING]   - org.spark_project.jetty.servlets.PushCacheFilter
[WARNING]   - org.apache.spark.util.Utils$$anonfun$downloadFile$1
[WARNING]   - org.apache.spark.util.JsonProtocol$$anonfun$52
[WARNING]   - org.apache.spark.ExecutorAllocationManager$$anonfun$org$apache$spark$ExecutorAllocationManager$$onExecutorAdded$2
[WARNING]   - org.apache.spark.rdd.util.PeriodicRDDCheckpointer
[WARNING]   - 8340 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, ga4gh-schemas-0.6.0a10.jar define 541 overlapping classes: 
[WARNING]   - ga4gh.AlleleAnnotations$TranscriptEffectOrBuilder
[WARNING]   - ga4gh.PeerServiceOuterClass$GetInfoResponse$1
[WARNING]   - ga4gh.MetadataServiceOuterClass$GetDatasetRequestOrBuilder
[WARNING]   - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest
[WARNING]   - ga4gh.RnaQuantificationServiceOuterClass$SearchExpressionLevelsRequest$Builder
[WARNING]   - ga4gh.GenotypePhenotypeServiceOuterClass$EvidenceQuery$1
[WARNING]   - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest$1
[WARNING]   - ga4gh.ReferenceServiceOuterClass$ListReferenceBasesResponseOrBuilder
[WARNING]   - ga4gh.VariantServiceOuterClass$SearchCallSetsRequest
[WARNING]   - ga4gh.RnaQuantificationServiceOuterClass$GetExpressionLevelRequest
[WARNING]   - 531 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-graphite-3.1.5.jar, mango-cli-0.0.3-SNAPSHOT.jar define 10 overlapping classes: 
[WARNING]   - com.codahale.metrics.graphite.PickledGraphite$MetricTuple
[WARNING]   - com.codahale.metrics.graphite.GraphiteReporter$Builder
[WARNING]   - com.codahale.metrics.graphite.Graphite
[WARNING]   - com.codahale.metrics.graphite.GraphiteRabbitMQ$1
[WARNING]   - com.codahale.metrics.graphite.GraphiteSender
[WARNING]   - com.codahale.metrics.graphite.PickledGraphite
[WARNING]   - com.codahale.metrics.graphite.GraphiteUDP
[WARNING]   - com.codahale.metrics.graphite.GraphiteReporter
[WARNING]   - com.codahale.metrics.graphite.GraphiteReporter$1
[WARNING]   - com.codahale.metrics.graphite.GraphiteRabbitMQ
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-logging-1.1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar define 6 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING]   - org.apache.commons.logging.Log
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-jexl-2.1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 178 overlapping classes: 
[WARNING]   - org.apache.commons.jexl2.internal.AbstractExecutor$Get
[WARNING]   - org.apache.commons.jexl2.introspection.JexlPropertyGet
[WARNING]   - org.apache.commons.jexl2.parser.StringParser
[WARNING]   - org.apache.commons.jexl2.parser.ASTBitwiseOrNode
[WARNING]   - org.apache.commons.jexl2.internal.introspection.MethodKey$1
[WARNING]   - org.apache.commons.jexl2.Main
[WARNING]   - org.apache.commons.jexl2.parser.ASTForeachStatement
[WARNING]   - org.apache.commons.jexl2.introspection.Sandbox
[WARNING]   - org.apache.commons.jexl2.internal.introspection.ClassMap
[WARNING]   - org.apache.commons.jexl2.parser.ASTFunctionNode
[WARNING]   - 168 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, metrics-core-3.1.5.jar define 115 overlapping classes: 
[WARNING]   - com.codahale.metrics.JmxReporter$JmxGaugeMBean
[WARNING]   - com.codahale.metrics.ThreadLocalRandomProxy$InternalProvider
[WARNING]   - com.codahale.metrics.JmxReporter
[WARNING]   - com.codahale.metrics.EWMA
[WARNING]   - com.codahale.metrics.Gauge
[WARNING]   - com.codahale.metrics.MetricRegistry$MetricBuilder$1
[WARNING]   - com.codahale.metrics.MetricFilter$1
[WARNING]   - com.codahale.metrics.JmxReporter$JmxCounterMBean
[WARNING]   - com.codahale.metrics.InstrumentedExecutorService$InstrumentedRunnable
[WARNING]   - com.codahale.metrics.RatioGauge$Ratio
[WARNING]   - 105 more...
[WARNING] jersey-client-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 111 overlapping classes: 
[WARNING]   - org.glassfish.jersey.client.ChunkParser
[WARNING]   - org.glassfish.jersey.client.HttpUrlConnectorProvider
[WARNING]   - org.glassfish.jersey.client.JerseyInvocation$EntityPresence
[WARNING]   - org.glassfish.jersey.client.ResponseCallback
[WARNING]   - org.glassfish.jersey.client.authentication.RequestAuthenticationException
[WARNING]   - org.glassfish.jersey.client.JerseyInvocation$5
[WARNING]   - org.glassfish.jersey.client.ClientConfig$State$4
[WARNING]   - org.glassfish.jersey.client.ClientResponse$1
[WARNING]   - org.glassfish.jersey.client.InboundJaxrsResponse$2
[WARNING]   - org.glassfish.jersey.client.internal.HttpUrlConnector$5
[WARNING]   - 101 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar define 3 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.SLF4JLogFactory
[WARNING]   - org.apache.commons.logging.impl.SLF4JLocationAwareLog
[WARNING]   - org.apache.commons.logging.impl.SLF4JLog
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, xz-1.5.jar, mango-cli-0.0.3-SNAPSHOT.jar define 105 overlapping classes: 
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder$LengthDecoder
[WARNING]   - org.tukaani.xz.index.IndexDecoder
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoderFast
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoder$LengthEncoder
[WARNING]   - org.tukaani.xz.BlockOutputStream
[WARNING]   - org.tukaani.xz.simple.SimpleFilter
[WARNING]   - org.tukaani.xz.rangecoder.RangeCoder
[WARNING]   - org.tukaani.xz.XZOutputStream
[WARNING]   - org.tukaani.xz.UncompressedLZMA2OutputStream
[WARNING]   - 95 more...
[WARNING] mime-util-2.1.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 26 overlapping classes: 
[WARNING]   - eu.medsea.mimeutil.detector.MagicMimeMimeDetector
[WARNING]   - eu.medsea.mimeutil.detector.OpendesktopMimeDetector$1
[WARNING]   - eu.medsea.mimeutil.MimeDetectorRegistry
[WARNING]   - eu.medsea.mimeutil.detector.OpendesktopMimeDetector
[WARNING]   - eu.medsea.mimeutil.detector.InvalidMagicMimeEntryException
[WARNING]   - eu.medsea.mimeutil.TextMimeDetector
[WARNING]   - eu.medsea.util.ZipJarUtil
[WARNING]   - eu.medsea.mimeutil.detector.MagicMimeEntry
[WARNING]   - eu.medsea.mimeutil.detector.FileWatcher
[WARNING]   - eu.medsea.mimeutil.detector.WindowsRegistryMimeDetector$StreamReader
[WARNING]   - 16 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, oro-2.0.8.jar, mango-cli-0.0.3-SNAPSHOT.jar define 62 overlapping classes: 
[WARNING]   - org.apache.oro.text.perl.MalformedPerl5PatternException
[WARNING]   - org.apache.oro.text.regex.Perl5Pattern
[WARNING]   - org.apache.oro.io.RegexFilenameFilter
[WARNING]   - org.apache.oro.util.Cache
[WARNING]   - org.apache.oro.text.GenericPatternCache
[WARNING]   - org.apache.oro.text.awk.DFAState
[WARNING]   - org.apache.oro.text.regex.StringSubstitution
[WARNING]   - org.apache.oro.text.awk.AwkCompiler
[WARNING]   - org.apache.oro.text.PatternCacheLRU
[WARNING]   - org.apache.oro.text.regex.Substitution
[WARNING]   - 52 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-kvstore_2.11-2.3.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 28 overlapping classes: 
[WARNING]   - org.apache.spark.util.kvstore.LevelDB$TypeAliases
[WARNING]   - org.apache.spark.util.kvstore.LevelDB$1
[WARNING]   - org.apache.spark.util.kvstore.LevelDB$PrefixCache
[WARNING]   - org.apache.spark.util.kvstore.LevelDBTypeInfo$Index
[WARNING]   - org.apache.spark.util.kvstore.KVStore
[WARNING]   - org.apache.spark.util.kvstore.KVTypeInfo
[WARNING]   - org.apache.spark.util.kvstore.KVIndex
[WARNING]   - org.apache.spark.util.kvstore.KVStoreIterator
[WARNING]   - org.apache.spark.util.kvstore.InMemoryStore$InMemoryView
[WARNING]   - org.apache.spark.util.kvstore.InMemoryStore$1
[WARNING]   - 18 more...
[WARNING] jetty-io-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 96 overlapping classes: 
[WARNING]   - org.eclipse.jetty.io.ssl.ALPNProcessor
[WARNING]   - org.eclipse.jetty.io.CyclicTimeout$Wakeup
[WARNING]   - org.eclipse.jetty.io.AbstractEndPoint$2
[WARNING]   - org.eclipse.jetty.io.CyclicTimeout$Timeout
[WARNING]   - org.eclipse.jetty.io.ChannelEndPoint$1
[WARNING]   - org.eclipse.jetty.io.WriteFlusher$FailedState
[WARNING]   - org.eclipse.jetty.io.CyclicTimeout$1
[WARNING]   - org.eclipse.jetty.io.ManagedSelector$Acceptor
[WARNING]   - org.eclipse.jetty.io.ssl.SslClientConnectionFactory$1
[WARNING]   - org.eclipse.jetty.io.ByteBufferPool$Lease
[WARNING]   - 86 more...
[WARNING] jetty-http-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 93 overlapping classes: 
[WARNING]   - org.eclipse.jetty.http.pathmap.PathSpec
[WARNING]   - org.eclipse.jetty.http.MultiPartFormInputStream
[WARNING]   - org.eclipse.jetty.http.HttpParser$HttpHandler
[WARNING]   - org.eclipse.jetty.http.MultiPartFormInputStream$MultiPart
[WARNING]   - org.eclipse.jetty.http.BadMessageException
[WARNING]   - org.eclipse.jetty.http.HttpGenerator$PreparedResponse
[WARNING]   - org.eclipse.jetty.http.HttpComplianceSection
[WARNING]   - org.eclipse.jetty.http.HttpParser$IllegalCharacterException
[WARNING]   - org.eclipse.jetty.http.HttpParser$1
[WARNING]   - org.eclipse.jetty.http.PathMap$PathSet
[WARNING]   - 83 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, args4j-2.0.31.jar define 71 overlapping classes: 
[WARNING]   - org.kohsuke.args4j.spi.DoubleOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.MethodSetter
[WARNING]   - org.kohsuke.args4j.spi.StringArrayOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.MacAddressOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.SubCommand
[WARNING]   - org.kohsuke.args4j.spi.PatternOptionHandler
[WARNING]   - org.kohsuke.args4j.ParserProperties$1
[WARNING]   - org.kohsuke.args4j.OptionHandlerFilter$2
[WARNING]   - org.kohsuke.args4j.spi.MultiFileOptionHandler
[WARNING]   - org.kohsuke.args4j.Localizable
[WARNING]   - 61 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-net-2.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 137 overlapping classes: 
[WARNING]   - org.apache.commons.net.telnet.SimpleOptionHandler
[WARNING]   - org.apache.commons.net.ftp.parser.FTPFileEntryParserFactory
[WARNING]   - org.apache.commons.net.DefaultDatagramSocketFactory
[WARNING]   - org.apache.commons.net.ftp.parser.ConfigurableFTPFileEntryParserImpl
[WARNING]   - org.apache.commons.net.ntp.NTPUDPClient
[WARNING]   - org.apache.commons.net.util.SubnetUtils$1
[WARNING]   - org.apache.commons.net.tftp.TFTP
[WARNING]   - org.apache.commons.net.ftp.FTPClient
[WARNING]   - org.apache.commons.net.echo.EchoTCPClient
[WARNING]   - org.apache.commons.net.telnet.Telnet
[WARNING]   - 127 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, utils-misc-spark2_2.11-0.2.13.jar define 11 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.misc.MathUtils
[WARNING]   - org.bdgenomics.utils.misc.Logging$
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$scalarArrayMultiply$1
[WARNING]   - org.bdgenomics.utils.misc.Logging$class
[WARNING]   - org.bdgenomics.utils.misc.Logging$$anonfun$getContextOrClassLoader$1
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$aggregateArray$1
[WARNING]   - org.bdgenomics.utils.misc.Logging
[WARNING]   - org.bdgenomics.utils.misc.HadoopUtil$
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$softmax$1
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$
[WARNING]   - 1 more...
[WARNING] jetty-util-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 285 overlapping classes: 
[WARNING]   - org.eclipse.jetty.util.MemoryUtils$1
[WARNING]   - org.eclipse.jetty.util.resource.URLResource
[WARNING]   - org.eclipse.jetty.util.Scanner$DiscreteListener
[WARNING]   - org.eclipse.jetty.util.MultiReleaseJarFile$VersionedJarEntry
[WARNING]   - org.eclipse.jetty.util.log.StacklessLogging
[WARNING]   - org.eclipse.jetty.util.component.Dumpable
[WARNING]   - org.eclipse.jetty.util.preventers.Java2DLeakPreventer
[WARNING]   - org.eclipse.jetty.util.InetAddressSet$LegacyInetRange
[WARNING]   - org.eclipse.jetty.util.resource.JarFileResource
[WARNING]   - org.eclipse.jetty.util.IncludeExcludeSet$SetContainsPredicate
[WARNING]   - 275 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, parquet-scala_2.10-1.8.3.jar define 19 overlapping classes: 
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$SupportsEqNotEq
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$FloatColumn$
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$Column$class
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$FloatColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$LongColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$BinaryColumn
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$IntColumn$
[WARNING]   - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn$
[WARNING]   - 9 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, metrics-jvm-3.1.5.jar define 38 overlapping classes: 
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$15
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$3
[WARNING]   - com.codahale.metrics.jvm.CachedThreadStatesGaugeSet
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$8
[WARNING]   - com.codahale.metrics.jvm.ClassLoadingGaugeSet$1
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$5
[WARNING]   - com.codahale.metrics.jvm.BufferPoolMetricSet
[WARNING]   - com.codahale.metrics.jvm.ThreadStatesGaugeSet
[WARNING]   - com.codahale.metrics.jvm.MemoryUsageGaugeSet$10
[WARNING]   - 28 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, chill-java-0.8.4.jar, mango-cli-0.0.3-SNAPSHOT.jar define 54 overlapping classes: 
[WARNING]   - com.twitter.chill.java.ClosureSerializer
[WARNING]   - com.twitter.chill.config.JavaMapConfig
[WARNING]   - com.twitter.chill.java.IterableRegistrar
[WARNING]   - com.twitter.chill.java.SqlTimeSerializer
[WARNING]   - com.twitter.chill.KryoInstantiator
[WARNING]   - com.twitter.chill.java.PackageRegistrar
[WARNING]   - com.twitter.chill.config.ConfiguredInstantiator
[WARNING]   - com.twitter.chill.java.SimpleDateFormatSerializer
[WARNING]   - com.twitter.chill.KryoInstantiator$4
[WARNING]   - com.twitter.chill.java.UnmodifiableSetSerializer
[WARNING]   - 44 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-logging-1.1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 22 overlapping classes: 
[WARNING]   - org.apache.commons.logging.LogSource
[WARNING]   - org.apache.commons.logging.impl.ServletContextCleaner
[WARNING]   - org.apache.commons.logging.LogFactory$4
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable$1
[WARNING]   - org.apache.commons.logging.LogFactory$3
[WARNING]   - org.apache.commons.logging.LogFactory$2
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl$2
[WARNING]   - org.apache.commons.logging.impl.LogKitLogger
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl$3
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable$Entry
[WARNING]   - 12 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, zstd-jni-1.3.2-2.jar define 8 overlapping classes: 
[WARNING]   - com.github.luben.zstd.ZstdDirectBufferDecompressingStream
[WARNING]   - com.github.luben.zstd.ZstdOutputStream
[WARNING]   - com.github.luben.zstd.ZstdDictCompress
[WARNING]   - com.github.luben.zstd.ZstdDictDecompress
[WARNING]   - com.github.luben.zstd.ZstdInputStream
[WARNING]   - com.github.luben.zstd.Zstd
[WARNING]   - com.github.luben.zstd.util.Native
[WARNING]   - com.github.luben.zstd.ZstdDirectBufferCompressingStream
[WARNING] jackson-mapper-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 502 overlapping classes: 
[WARNING]   - org.codehaus.jackson.map.ext.DOMSerializer
[WARNING]   - org.codehaus.jackson.node.POJONode
[WARNING]   - org.codehaus.jackson.map.ext.JodaDeserializers$LocalDateDeserializer
[WARNING]   - org.codehaus.jackson.map.ser.StdSerializers$UtilDateSerializer
[WARNING]   - org.codehaus.jackson.map.deser.std.JsonNodeDeserializer$ArrayDeserializer
[WARNING]   - org.codehaus.jackson.map.deser.std.PrimitiveArrayDeserializers$StringDeser
[WARNING]   - org.codehaus.jackson.map.util.Comparators$1
[WARNING]   - org.codehaus.jackson.map.util.StdDateFormat
[WARNING]   - org.codehaus.jackson.map.KeyDeserializer
[WARNING]   - org.codehaus.jackson.map.MapperConfig$Impl
[WARNING]   - 492 more...
[WARNING] spark-network-shuffle_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 41 overlapping classes: 
[WARNING]   - org.apache.spark.network.shuffle.RetryingBlockFetcher$1
[WARNING]   - org.apache.spark.network.shuffle.protocol.BlockTransferMessage$Type
[WARNING]   - org.apache.spark.network.shuffle.ShuffleIndexRecord
[WARNING]   - org.apache.spark.network.sasl.ShuffleSecretManager
[WARNING]   - org.apache.spark.network.shuffle.SimpleDownloadFile
[WARNING]   - org.apache.spark.network.shuffle.OneForOneBlockFetcher
[WARNING]   - org.apache.spark.network.shuffle.ExternalShuffleBlockResolver$2
[WARNING]   - org.apache.spark.network.shuffle.ExternalShuffleBlockHandler$ManagedBufferIterator
[WARNING]   - org.apache.spark.network.shuffle.DownloadFileManager
[WARNING]   - org.apache.spark.network.shuffle.protocol.RegisterExecutor
[WARNING]   - 31 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, javax.ws.rs-api-2.0.1.jar define 125 overlapping classes: 
[WARNING]   - javax.ws.rs.ext.RuntimeDelegate$HeaderDelegate
[WARNING]   - javax.ws.rs.DefaultValue
[WARNING]   - javax.ws.rs.core.StreamingOutput
[WARNING]   - javax.ws.rs.HEAD
[WARNING]   - javax.ws.rs.ext.WriterInterceptor
[WARNING]   - javax.ws.rs.core.Request
[WARNING]   - javax.ws.rs.ext.Providers
[WARNING]   - javax.ws.rs.container.Suspended
[WARNING]   - javax.ws.rs.container.ConnectionCallback
[WARNING]   - javax.ws.rs.client.FactoryFinder
[WARNING]   - 115 more...
[WARNING] joda-time-2.9.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 246 overlapping classes: 
[WARNING]   - org.joda.time.field.RemainderDateTimeField
[WARNING]   - org.joda.time.convert.ReadableDurationConverter
[WARNING]   - org.joda.time.convert.ReadableIntervalConverter
[WARNING]   - org.joda.time.field.SkipUndoDateTimeField
[WARNING]   - org.joda.time.format.DateTimeFormatterBuilder$TimeZoneName
[WARNING]   - org.joda.time.tz.DateTimeZoneBuilder$RuleSet
[WARNING]   - org.joda.time.chrono.BasicDayOfMonthDateTimeField
[WARNING]   - org.joda.time.Duration
[WARNING]   - org.joda.time.field.OffsetDateTimeField
[WARNING]   - org.joda.time.format.ISODateTimeFormat
[WARNING]   - 236 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, j2objc-annotations-1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 12 overlapping classes: 
[WARNING]   - com.google.j2objc.annotations.Property
[WARNING]   - com.google.j2objc.annotations.RetainedWith
[WARNING]   - com.google.j2objc.annotations.RetainedLocalRef
[WARNING]   - com.google.j2objc.annotations.J2ObjCIncompatible
[WARNING]   - com.google.j2objc.annotations.AutoreleasePool
[WARNING]   - com.google.j2objc.annotations.LoopTranslation$LoopStyle
[WARNING]   - com.google.j2objc.annotations.ReflectionSupport$Level
[WARNING]   - com.google.j2objc.annotations.ReflectionSupport
[WARNING]   - com.google.j2objc.annotations.Weak
[WARNING]   - com.google.j2objc.annotations.WeakOuter
[WARNING]   - 2 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jackson-databind-2.6.7.1.jar define 563 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.databind.BeanDescription
[WARNING]   - com.fasterxml.jackson.databind.deser.impl.BeanAsArrayBuilderDeserializer
[WARNING]   - com.fasterxml.jackson.databind.SerializerProvider
[WARNING]   - com.fasterxml.jackson.databind.introspect.AnnotatedMethodMap
[WARNING]   - com.fasterxml.jackson.databind.ser.std.StaticListSerializerBase
[WARNING]   - com.fasterxml.jackson.databind.ser.std.NumberSerializers$ShortSerializer
[WARNING]   - com.fasterxml.jackson.databind.ser.BeanSerializerFactory
[WARNING]   - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonMapFormatVisitor
[WARNING]   - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatTypes
[WARNING]   - com.fasterxml.jackson.databind.deser.impl.MethodProperty
[WARNING]   - 553 more...
[WARNING] juniversalchardet-1.0.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 62 overlapping classes: 
[WARNING]   - org.mozilla.universalchardet.prober.distributionanalysis.EUCJPDistributionAnalysis
[WARNING]   - org.mozilla.universalchardet.prober.SJISProber
[WARNING]   - org.mozilla.universalchardet.prober.statemachine.ISO2022KRSMModel
[WARNING]   - org.mozilla.universalchardet.prober.sequence.Latin7Model
[WARNING]   - org.mozilla.universalchardet.prober.CharsetProber$ProbingState
[WARNING]   - org.mozilla.universalchardet.prober.distributionanalysis.JISDistributionAnalysis
[WARNING]   - org.mozilla.universalchardet.prober.UTF8Prober
[WARNING]   - org.mozilla.universalchardet.prober.sequence.Koi8rModel
[WARNING]   - org.mozilla.universalchardet.prober.contextanalysis.JapaneseContextAnalysis
[WARNING]   - org.mozilla.universalchardet.prober.sequence.MacCyrillicModel
[WARNING]   - 52 more...
[WARNING] javax.inject-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, javax.inject-1.jar define 6 overlapping classes: 
[WARNING]   - javax.inject.Inject
[WARNING]   - javax.inject.Singleton
[WARNING]   - javax.inject.Named
[WARNING]   - javax.inject.Scope
[WARNING]   - javax.inject.Provider
[WARNING]   - javax.inject.Qualifier
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, hk2-locator-2.4.0-b34.jar define 95 overlapping classes: 
[WARNING]   - org.jvnet.hk2.internal.PerLocatorUtilities$1
[WARNING]   - org.jvnet.hk2.internal.Utilities$4
[WARNING]   - org.jvnet.hk2.internal.ProxyUtilities$2
[WARNING]   - org.jvnet.hk2.internal.ServiceLocatorImpl$12
[WARNING]   - org.jvnet.hk2.internal.MethodInterceptorInvocationHandler
[WARNING]   - org.jvnet.hk2.internal.ClazzCreator
[WARNING]   - org.jvnet.hk2.internal.ValidationInformationImpl
[WARNING]   - org.jvnet.hk2.internal.ServiceLocatorImpl$6
[WARNING]   - org.jvnet.hk2.internal.ConstructorInterceptorHandler$1
[WARNING]   - org.jvnet.hk2.internal.ServiceLocatorImpl$IgdValue
[WARNING]   - 85 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jackson-core-2.6.7.jar define 93 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer$Bucket
[WARNING]   - com.fasterxml.jackson.core.FormatSchema
[WARNING]   - com.fasterxml.jackson.core.io.InputDecorator
[WARNING]   - com.fasterxml.jackson.core.JsonGenerator$Feature
[WARNING]   - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer
[WARNING]   - com.fasterxml.jackson.core.type.ResolvedType
[WARNING]   - com.fasterxml.jackson.core.io.SegmentedStringWriter
[WARNING]   - com.fasterxml.jackson.core.TreeNode
[WARNING]   - com.fasterxml.jackson.core.sym.Name
[WARNING]   - com.fasterxml.jackson.core.util.JsonGeneratorDelegate
[WARNING]   - 83 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, aopalliance-1.0.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: 
[WARNING]   - org.aopalliance.intercept.ConstructorInterceptor
[WARNING]   - org.aopalliance.intercept.MethodInvocation
[WARNING]   - org.aopalliance.intercept.MethodInterceptor
[WARNING]   - org.aopalliance.intercept.Invocation
[WARNING]   - org.aopalliance.aop.AspectException
[WARNING]   - org.aopalliance.intercept.Interceptor
[WARNING]   - org.aopalliance.intercept.Joinpoint
[WARNING]   - org.aopalliance.aop.Advice
[WARNING]   - org.aopalliance.intercept.ConstructorInvocation
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, curator-framework-2.6.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 167 overlapping classes: 
[WARNING]   - org.apache.curator.framework.imps.TempGetDataBuilderImpl
[WARNING]   - org.apache.curator.framework.imps.GetDataBuilderImpl$2
[WARNING]   - org.apache.curator.framework.imps.CuratorFrameworkImpl$4
[WARNING]   - org.apache.curator.framework.state.ConnectionState
[WARNING]   - org.apache.curator.framework.api.CreateModable
[WARNING]   - org.apache.curator.framework.imps.SetDataBuilderImpl$4
[WARNING]   - org.apache.curator.framework.imps.PathAndBytes
[WARNING]   - org.apache.curator.framework.api.ACLVersionBackgroundPathable
[WARNING]   - org.apache.curator.framework.api.ACLCreateModeBackgroundPathAndBytesable
[WARNING]   - org.apache.curator.framework.listen.ListenerContainer
[WARNING]   - 157 more...
[WARNING] jersey-container-servlet-core-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 51 overlapping classes: 
[WARNING]   - org.glassfish.jersey.servlet.WebComponent$3
[WARNING]   - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder
[WARNING]   - org.glassfish.jersey.servlet.internal.LocalizationMessages
[WARNING]   - org.glassfish.jersey.servlet.WebConfig
[WARNING]   - org.glassfish.jersey.servlet.spi.FilterUrlMappingsProvider
[WARNING]   - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder$3
[WARNING]   - org.glassfish.jersey.servlet.ServletPropertiesDelegate
[WARNING]   - org.glassfish.jersey.servlet.WebComponent$7
[WARNING]   - org.glassfish.jersey.servlet.internal.ResponseWriter
[WARNING]   - org.glassfish.jersey.servlet.WebAppResourcesScanner$1
[WARNING]   - 41 more...
[WARNING] lz4-java-1.4.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 77 overlapping classes: 
[WARNING]   - net.jpountz.xxhash.AbstractStreamingXXHash32Java
[WARNING]   - net.jpountz.lz4.LZ4BlockInputStream
[WARNING]   - net.jpountz.lz4.LZ4FrameOutputStream
[WARNING]   - net.jpountz.xxhash.XXHash32JNI
[WARNING]   - net.jpountz.lz4.LZ4BlockOutputStream
[WARNING]   - net.jpountz.lz4.LZ4JNI
[WARNING]   - net.jpountz.lz4.LZ4JavaUnsafeFastDecompressor
[WARNING]   - net.jpountz.lz4.LZ4SafeUtils
[WARNING]   - net.jpountz.xxhash.StreamingXXHash32JNI$Factory
[WARNING]   - net.jpountz.util.UnsafeUtils
[WARNING]   - 67 more...
[WARNING] adam-cli-spark2_2.11-0.26.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 130 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.PrintADAMArgs
[WARNING]   - org.bdgenomics.adam.cli.Reads2Coverage$$anonfun$1$$anonfun$apply$1
[WARNING]   - org.bdgenomics.adam.cli.TransformVariants$$anonfun$maybeCoalesce$2
[WARNING]   - org.bdgenomics.adam.cli.FlagStat$
[WARNING]   - org.bdgenomics.adam.cli.TransformAlignments$$anonfun$7
[WARNING]   - org.bdgenomics.adam.cli.TransformVariants$
[WARNING]   - org.bdgenomics.adam.cli.View$$anonfun$getFilter$1$1
[WARNING]   - org.bdgenomics.adam.cli.TransformAlignments$$anonfun$maybeCoalesce$2
[WARNING]   - org.bdgenomics.adam.cli.TransformAlignments$$anonfun$4
[WARNING]   - org.bdgenomics.adam.cli.ADAMMain$$anonfun$1
[WARNING]   - 120 more...
[WARNING] parquet-common-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 32 overlapping classes: 
[WARNING]   - org.apache.parquet.SemanticVersion$SemanticVersionParseException
[WARNING]   - org.apache.parquet.glob.GlobNode$GlobNodeSequence
[WARNING]   - org.apache.parquet.Ints
[WARNING]   - org.apache.parquet.Version
[WARNING]   - org.apache.parquet.glob.GlobNode$Atom
[WARNING]   - org.apache.parquet.SemanticVersion$NumberOrString
[WARNING]   - org.apache.parquet.Files
[WARNING]   - org.apache.parquet.ParquetRuntimeException
[WARNING]   - org.apache.parquet.glob.GlobNode
[WARNING]   - org.apache.parquet.io.InputFile
[WARNING]   - 22 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-xml_2.11-1.0.5.jar, mango-cli-0.0.3-SNAPSHOT.jar define 421 overlapping classes: 
[WARNING]   - scala.xml.PrettyPrinter$Para
[WARNING]   - scala.xml.Group$
[WARNING]   - scala.xml.PrettyPrinter$$anonfun$traverse$1
[WARNING]   - scala.xml.MetaData
[WARNING]   - scala.xml.MalformedAttributeException
[WARNING]   - scala.xml.pull.EvComment
[WARNING]   - scala.xml.parsing.TokenTests$$anonfun$isSpace$1
[WARNING]   - scala.xml.Properties
[WARNING]   - scala.xml.parsing.MarkupParser$$anonfun$1
[WARNING]   - scala.xml.pull.EvEntityRef$
[WARNING]   - 411 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, lift-json_2.11-3.3.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 390 overlapping classes: 
[WARNING]   - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$deserialize$2
[WARNING]   - net.liftweb.json.TypeInfo$
[WARNING]   - net.liftweb.json.JsonAST$JString$
[WARNING]   - net.liftweb.json.JsonAST$RenderSettings$
[WARNING]   - net.liftweb.json.JsonAST$JDouble$
[WARNING]   - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$classFor$2
[WARNING]   - net.liftweb.json.JsonAST$RenderSpecialDoubleValuesAsIs$
[WARNING]   - net.liftweb.json.Meta$$anonfun$net$liftweb$json$Meta$$fieldMapping$1$4
[WARNING]   - net.liftweb.json.Meta$DeclaredConstructor
[WARNING]   - net.liftweb.json.Formats$$anonfun$customSerializer$1
[WARNING]   - 380 more...
[WARNING] httpcore-4.4.4.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 254 overlapping classes: 
[WARNING]   - org.apache.http.protocol.HttpRequestHandler
[WARNING]   - org.apache.http.impl.io.ChunkedOutputStream
[WARNING]   - org.apache.http.protocol.ChainBuilder
[WARNING]   - org.apache.http.impl.entity.DisallowIdentityContentLengthStrategy
[WARNING]   - org.apache.http.impl.ConnSupport
[WARNING]   - org.apache.http.impl.io.DefaultHttpResponseParserFactory
[WARNING]   - org.apache.http.HttpClientConnection
[WARNING]   - org.apache.http.NameValuePair
[WARNING]   - org.apache.http.protocol.HttpExpectationVerifier
[WARNING]   - org.apache.http.protocol.UriPatternMatcher
[WARNING]   - 244 more...
[WARNING] javax.annotation-api-1.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 15 overlapping classes: 
[WARNING]   - javax.annotation.ManagedBean
[WARNING]   - javax.annotation.PreDestroy
[WARNING]   - javax.annotation.Generated
[WARNING]   - javax.annotation.Resource$AuthenticationType
[WARNING]   - javax.annotation.security.DeclareRoles
[WARNING]   - javax.annotation.Priority
[WARNING]   - javax.annotation.Resource
[WARNING]   - javax.annotation.security.DenyAll
[WARNING]   - javax.annotation.security.RunAs
[WARNING]   - javax.annotation.sql.DataSourceDefinitions
[WARNING]   - 5 more...
[WARNING] mango-cli-0.0.3-SNAPSHOT.jar, scalatra-common_2.11-2.4.1.jar define 21 overlapping classes: 
[WARNING]   - org.scalatra.servlet.HasMultipartConfig$$anonfun$org$scalatra$servlet$HasMultipartConfig$$multipartConfigFromContext$1$$anonfun$apply$3
[WARNING]   - org.scalatra.servlet.HasMultipartConfig$$anonfun$org$scalatra$servlet$HasMultipartConfig$$multipartConfigFromContext$1$$anonfun$apply$2
[WARNING]   - org.scalatra.servlet.ScalatraAsyncSupport
[WARNING]   - org.scalatra.servlet.HasMultipartConfig
[WARNING]   - org.scalatra.servlet.MountConfig
[WARNING]   - org.scalatra.servlet.HasMultipartConfig$
[WARNING]   - org.scalatra.servlet.MultipartConfig$
[WARNING]   - org.scalatra.servlet.HasMultipartConfig$$anonfun$org$scalatra$servlet$HasMultipartConfig$$multipartConfigFromContext$1$$anonfun$apply$1
[WARNING]   - org.scalatra.servlet.MultipartConfig$$anonfun$toMultipartConfigElement$2
[WARNING]   - org.scalatra.servlet.HasMultipartConfig$$anonfun$initialize$1
[WARNING]   - 11 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, scalap-2.11.11.jar define 581 overlapping classes: 
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ScalaSigEntryParsers$$anonfun$25$$anonfun$apply$13
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$_pmt$1$1
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ScalaSigParser$$anonfun$scalaSigFromAnnotation$2
[WARNING]   - scala.tools.scalap.scalax.rules.StateRules$$anonfun$anyOf$2
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ConstantType$
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.Symbol$class
[WARNING]   - scala.tools.scalap.scalax.rules.Rule$$anonfun$flatMap$1
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$printSymbolAttributes$1
[WARNING]   - scala.tools.scalap.scalax.rules.InRule$$anonfun$unary_$bang$1$$anonfun$apply$1
[WARNING]   - scala.tools.scalap.scalax.rules.scalasig.NoType$
[WARNING]   - 571 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, py4j-0.10.7.jar define 67 overlapping classes: 
[WARNING]   - py4j.reflection.TypeConverter
[WARNING]   - py4j.Py4JJavaServer
[WARNING]   - py4j.Py4JNetworkException
[WARNING]   - py4j.reflection.PythonProxyHandler
[WARNING]   - py4j.reflection.MethodInvoker$1
[WARNING]   - py4j.commands.JVMViewCommand
[WARNING]   - py4j.Py4JClientConnection
[WARNING]   - py4j.model.Py4JClass
[WARNING]   - py4j.commands.ReflectionCommand
[WARNING]   - py4j.commands.MemoryCommand
[WARNING]   - 57 more...
[WARNING] ngs-java-2.9.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 73 overlapping classes: 
[WARNING]   - ngs.itf.ReadItf
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.cause.JvmErrorCause
[WARNING]   - ngs.ReferenceIterator
[WARNING]   - gov.nih.nlm.ncbi.ngs.Manager$1
[WARNING]   - gov.nih.nlm.ncbi.ngs.LMProperties
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.LibraryLoadError
[WARNING]   - gov.nih.nlm.ncbi.ngs.LibDependencies
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.cause.ConnectionProblemCause
[WARNING]   - ngs.itf.PileupEventItf
[WARNING]   - gov.nih.nlm.ncbi.ngs.LibManager$Location
[WARNING]   - 63 more...
[WARNING] scalatra_2.11-2.4.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 936 overlapping classes: 
[WARNING]   - org.scalatra.util.FileCharset$
[WARNING]   - org.scalatra.ApiFormats$$anonfun$requestFormat$1
[WARNING]   - org.scalatra.ScalatraBase$$anonfun$11
[WARNING]   - org.scalatra.SinatraRouteMatcher$BuilderGeneratorParser$$anonfun$org$scalatra$SinatraRouteMatcher$BuilderGeneratorParser$$prefixedOptional$5
[WARNING]   - org.scalatra.util.conversion.Conversions$SeqConversion
[WARNING]   - org.scalatra.Route$$anonfun$appendMatcher$1
[WARNING]   - org.scalatra.Route
[WARNING]   - org.scalatra.FutureSupport$$anonfun$renderFutureResult$1$1$$anonfun$apply$2
[WARNING]   - org.scalatra.PreconditionFailed$
[WARNING]   - org.scalatra.util.conversion.DefaultImplicitConversions$$anonfun$17
[WARNING]   - 926 more...
[WARNING] mango-cli-0.0.3-SNAPSHOT.jar, adam-apis-spark2_2.11-0.26.0.jar define 133 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.api.java.FeaturesToFragmentsConverter
[WARNING]   - org.bdgenomics.adam.api.java.GenotypesToCoverageConverter
[WARNING]   - org.bdgenomics.adam.api.java.GenotypesToFragmentsConverter
[WARNING]   - org.bdgenomics.adam.api.java.ToVariantDatasetConversion$class
[WARNING]   - org.bdgenomics.adam.api.java.ToCoverageDatasetConversion$class
[WARNING]   - org.bdgenomics.adam.api.java.FeaturesToVariantsDatasetConverter
[WARNING]   - org.bdgenomics.adam.api.java.ToVariantDatasetConversion$$typecreator7$1
[WARNING]   - org.bdgenomics.adam.api.java.VariantContextsToContigsConverter
[WARNING]   - org.bdgenomics.adam.api.java.VariantsToContigsDatasetConverter
[WARNING]   - org.bdgenomics.adam.api.java.VariantsToVariantsConverter
[WARNING]   - 123 more...
[WARNING] convert-ga4gh-0.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 20 overlapping classes: 
[WARNING]   - org.bdgenomics.convert.ga4gh.CigarOperatorToOperation$1
[WARNING]   - org.bdgenomics.convert.ga4gh.BdgenomicsVariantToGa4ghVariant
[WARNING]   - org.bdgenomics.convert.ga4gh.CigarToCigarUnits
[WARNING]   - org.bdgenomics.convert.ga4gh.BdgenomicsFeatureToGa4ghFeature
[WARNING]   - org.bdgenomics.convert.ga4gh.StringToOntologyTerm
[WARNING]   - org.bdgenomics.convert.ga4gh.ProgramToProcessingStep
[WARNING]   - org.bdgenomics.convert.ga4gh.Ga4ghReadGroupToBdgenomicsReadGroup
[WARNING]   - org.bdgenomics.convert.ga4gh.Ga4ghOntologyTermToBdgenomicsOntologyTerm
[WARNING]   - org.bdgenomics.convert.ga4gh.ProcessingStepToProgram
[WARNING]   - org.bdgenomics.convert.ga4gh.BdgenomicsStrandToGa4ghStrand
[WARNING]   - 10 more...
[WARNING] avro-1.8.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1172 overlapping classes: 
[WARNING]   - org.apache.avro.message.SchemaStore
[WARNING]   - avro.shaded.com.google.common.collect.SingletonImmutableList
[WARNING]   - org.apache.avro.io.EncoderFactory$DefaultEncoderFactory
[WARNING]   - avro.shaded.com.google.common.collect.Iterables$15
[WARNING]   - org.apache.avro.GuavaClasses
[WARNING]   - avro.shaded.com.google.common.collect.Sets$PowerSet$1$1
[WARNING]   - avro.shaded.com.google.common.collect.RegularImmutableMap
[WARNING]   - org.apache.avro.generic.GenericDatumReader$2
[WARNING]   - avro.shaded.com.google.common.collect.Synchronized$SynchronizedSortedSet
[WARNING]   - org.apache.avro.file.BZip2Codec
[WARNING]   - 1162 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jackson-annotations-2.6.7.jar define 58 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.annotation.JsonAutoDetect
[WARNING]   - com.fasterxml.jackson.annotation.JsonInclude
[WARNING]   - com.fasterxml.jackson.annotation.ObjectIdGenerators
[WARNING]   - com.fasterxml.jackson.annotation.JsonFormat$Features
[WARNING]   - com.fasterxml.jackson.annotation.JsonFormat$Feature
[WARNING]   - com.fasterxml.jackson.annotation.JsonIgnore
[WARNING]   - com.fasterxml.jackson.annotation.JsonSetter
[WARNING]   - com.fasterxml.jackson.annotation.JsonTypeInfo$None
[WARNING]   - com.fasterxml.jackson.annotation.JsonSubTypes
[WARNING]   - com.fasterxml.jackson.annotation.JsonFormat$Shape
[WARNING]   - 48 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-tags_2.11-2.3.3.jar define 11 overlapping classes: 
[WARNING]   - org.apache.spark.annotation.Since
[WARNING]   - org.apache.spark.annotation.InterfaceStability$Stable
[WARNING]   - org.apache.spark.annotation.package
[WARNING]   - org.apache.spark.annotation.DeveloperApi
[WARNING]   - org.apache.spark.annotation.InterfaceStability$Evolving
[WARNING]   - org.apache.spark.annotation.package$
[WARNING]   - org.apache.spark.annotation.Experimental
[WARNING]   - org.apache.spark.annotation.AlphaComponent
[WARNING]   - org.apache.spark.annotation.Private
[WARNING]   - org.apache.spark.annotation.InterfaceStability
[WARNING]   - 1 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, osgi-resource-locator-1.0.1.jar define 12 overlapping classes: 
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$1
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoader$ProviderFactory
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoader
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$ProvidersPerBundle
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ResourceFinderImpl
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ResourceFinder
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.Activator
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$DefaultFactory
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl
[WARNING]   - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$BundleTracker
[WARNING]   - 2 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-common-2.22.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 474 overlapping classes: 
[WARNING]   - org.glassfish.jersey.internal.inject.ContextInjectionResolver$Binder
[WARNING]   - org.glassfish.jersey.internal.ServiceFinder$ServiceIteratorProvider
[WARNING]   - org.glassfish.jersey.message.internal.HttpHeaderReader$1
[WARNING]   - org.glassfish.jersey.internal.util.collection.KeyComparatorHashMap$1
[WARNING]   - org.glassfish.jersey.uri.UriTemplate$1ValuesFromArrayStrategy
[WARNING]   - org.glassfish.jersey.message.internal.TracingLogger$Level
[WARNING]   - org.glassfish.jersey.internal.util.PropertyAlias
[WARNING]   - org.glassfish.jersey.uri.UriTemplate$3
[WARNING]   - org.glassfish.jersey.model.internal.ComponentBag$7
[WARNING]   - org.glassfish.jersey.spi.AbstractThreadPoolProvider
[WARNING]   - 464 more...
[WARNING] json4s-jackson_2.11-3.2.11.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 27 overlapping classes: 
[WARNING]   - org.json4s.jackson.JsonMethods$class
[WARNING]   - org.json4s.jackson.Json
[WARNING]   - org.json4s.jackson.Json$
[WARNING]   - org.json4s.jackson.JValueSerializerResolver$
[WARNING]   - org.json4s.jackson.Json4sModule$
[WARNING]   - org.json4s.jackson.JsonMethods$$anonfun$parseOpt$1
[WARNING]   - org.json4s.jackson.JValueDeserializerResolver$
[WARNING]   - org.json4s.jackson.package
[WARNING]   - org.json4s.jackson.package$
[WARNING]   - org.json4s.jackson.Json4sScalaModule$
[WARNING]   - 17 more...
[WARNING] avro-ipc-1.7.7.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 114 overlapping classes: 
[WARNING]   - org.apache.avro.ipc.HandshakeRequest$1
[WARNING]   - org.apache.avro.ipc.stats.Histogram
[WARNING]   - org.apache.avro.ipc.stats.Histogram$Entry
[WARNING]   - org.apache.avro.ipc.trace.Span$Builder
[WARNING]   - org.apache.avro.ipc.trace.TraceNode
[WARNING]   - org.apache.avro.ipc.specific.SpecificRequestor
[WARNING]   - org.apache.avro.ipc.stats.Histogram$SegmenterException
[WARNING]   - org.apache.avro.ipc.SaslSocketServer$AnonymousServer
[WARNING]   - org.apache.avro.ipc.stats.Histogram$Segmenter
[WARNING]   - org.apache.avro.ipc.SaslSocketServer$2
[WARNING]   - 104 more...
[WARNING] scala-reflect-2.11.8.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 2792 overlapping classes: 
[WARNING]   - scala.reflect.runtime.ReflectionUtils
[WARNING]   - scala.reflect.internal.Types$LazyType
[WARNING]   - scala.reflect.internal.Scopes$LookupInaccessible$
[WARNING]   - scala.reflect.internal.Definitions$DefinitionsClass$$anonfun$newT1NullaryMethod$1
[WARNING]   - scala.reflect.internal.SymbolPairs$Cursor
[WARNING]   - scala.reflect.internal.Types$StaticallyAnnotatedType$
[WARNING]   - scala.reflect.runtime.SynchronizedOps$SynchronizedScope$$anonfun$isEmpty$1
[WARNING]   - scala.reflect.internal.Kinds$TypeConKind$$anonfun$buildState$3
[WARNING]   - scala.reflect.api.StandardLiftables$StandardUnliftableInstances$$anonfun$unliftTuple18$1
[WARNING]   - scala.reflect.runtime.SynchronizedSymbols$SynchronizedClassSymbol
[WARNING]   - 2782 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, parquet-avro-1.8.1.jar define 83 overlapping classes: 
[WARNING]   - org.apache.parquet.avro.AvroRecordConverter$AvroCollectionConverter$1
[WARNING]   - org.apache.parquet.avro.AvroParquetInputFormat
[WARNING]   - org.apache.parquet.avro.AvroRecordConverter$AvroArrayConverter$7
[WARNING]   - org.apache.parquet.avro.AvroConverters$AvroPrimitiveConverter
[WARNING]   - org.apache.parquet.avro.AvroWriteSupport$TwoLevelListWriter
[WARNING]   - org.apache.parquet.avro.AvroConverters$FieldIntegerConverter
[WARNING]   - org.apache.parquet.avro.AvroCompatRecordMaterializer
[WARNING]   - org.apache.parquet.avro.AvroIndexedRecordConverter$AvroArrayConverter$1
[WARNING]   - org.apache.parquet.avro.AvroWriteSupport$ListWriter
[WARNING]   - org.apache.parquet.avro.AvroConverters$FieldByteBufferConverter
[WARNING]   - 73 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, gson-2.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 165 overlapping classes: 
[WARNING]   - com.google.gson.internal.bind.JsonTreeWriter
[WARNING]   - com.google.gson.internal.Excluder
[WARNING]   - com.google.gson.JsonDeserializationContext
[WARNING]   - com.google.gson.FieldNamingPolicy$5
[WARNING]   - com.google.gson.internal.LinkedTreeMap$KeySet
[WARNING]   - com.google.gson.internal.$Gson$Types
[WARNING]   - com.google.gson.internal.UnsafeAllocator$2
[WARNING]   - com.google.gson.internal.bind.SqlDateTypeAdapter$1
[WARNING]   - com.google.gson.FieldAttributes
[WARNING]   - com.google.gson.internal.$Gson$Types$ParameterizedTypeImpl
[WARNING]   - 155 more...
[WARNING] jsr203hadoop-1.0.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 27 overlapping classes: 
[WARNING]   - hdfs.jsr203.HadoopDirectoryStream
[WARNING]   - hdfs.jsr203.HadoopPath
[WARNING]   - hdfs.jsr203.HadoopFileSystem$1
[WARNING]   - hdfs.jsr203.HadoopFileOwnerAttributeView
[WARNING]   - hdfs.jsr203.HadoopUserPrincipal
[WARNING]   - hdfs.jsr203.IAttributeReader
[WARNING]   - hdfs.jsr203.HadoopPath$1
[WARNING]   - hdfs.jsr203.HadoopBasicFileAttributes
[WARNING]   - hdfs.jsr203.HadoopDirectoryStream$1
[WARNING]   - hdfs.jsr203.package-info
[WARNING]   - 17 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, adam-core-spark2_2.11-0.26.0.jar define 2708 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$74$$anonfun$apply$77
[WARNING]   - org.bdgenomics.adam.rdd.feature.FeatureDataset$$anonfun$filterToTranscript$2$$anonfun$apply$9$$anonfun$apply$10
[WARNING]   - org.bdgenomics.adam.rdd.read.AlignmentRecordDataset$$typecreator9$1
[WARNING]   - org.bdgenomics.adam.sql.VariantCallingAnnotations$$anonfun$toAvro$58
[WARNING]   - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$63
[WARNING]   - org.bdgenomics.adam.rdd.feature.DatasetBoundFeatureDataset$$anonfun$filterByAttribute$1
[WARNING]   - org.bdgenomics.adam.io.InterleavedFastqInputFormat
[WARNING]   - org.bdgenomics.adam.util.FileMerger$$anonfun$mergeFilesAcrossFilesystems$4
[WARNING]   - org.bdgenomics.adam.rdd.fragment.DatasetBoundFragmentDataset
[WARNING]   - org.bdgenomics.adam.sql.VariantAnnotation$$anonfun$fromAvro$80
[WARNING]   - 2698 more...
[WARNING] commons-crypto-1.0.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 46 overlapping classes: 
[WARNING]   - org.apache.commons.crypto.stream.PositionedCryptoInputStream
[WARNING]   - org.apache.commons.crypto.cipher.OpenSsl
[WARNING]   - org.apache.commons.crypto.random.CryptoRandomFactory$RandomProvider
[WARNING]   - org.apache.commons.crypto.cipher.OpenSsl$AlgorithmMode
[WARNING]   - org.apache.commons.crypto.utils.Utils$DefaultPropertiesHolder
[WARNING]   - org.apache.commons.crypto.Crypto
[WARNING]   - org.apache.commons.crypto.cipher.OpenSsl$Transform
[WARNING]   - org.apache.commons.crypto.OpenSslInfoNative
[WARNING]   - org.apache.commons.crypto.stream.CtrCryptoOutputStream
[WARNING]   - org.apache.commons.crypto.jna.OpenSslNativeJna
[WARNING]   - 36 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, kryo-shaded-3.0.3.jar define 14 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.VersionFieldSerializer
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Context
[WARNING]   - com.esotericsoftware.kryo.serializers.EnumNameSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.ClosureSerializer
[WARNING]   - com.esotericsoftware.kryo.pool.KryoPool
[WARNING]   - com.esotericsoftware.kryo.pool.SoftReferenceQueue
[WARNING]   - com.esotericsoftware.kryo.pool.KryoCallback
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.TypePath
[WARNING]   - com.esotericsoftware.reflectasm.PublicConstructorAccess
[WARNING]   - com.esotericsoftware.kryo.pool.KryoPoolQueueImpl
[WARNING]   - 4 more...
[WARNING] hk2-utils-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 80 overlapping classes: 
[WARNING]   - org.glassfish.hk2.utilities.cache.Cache$1
[WARNING]   - org.jvnet.hk2.component.MultiMap$1
[WARNING]   - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperImpl$4
[WARNING]   - org.glassfish.hk2.utilities.cache.internal.WeakCARCacheImpl$1
[WARNING]   - org.glassfish.hk2.utilities.cache.LRUHybridCache
[WARNING]   - org.glassfish.hk2.utilities.cache.LRUCache
[WARNING]   - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperUtilities
[WARNING]   - org.glassfish.hk2.utilities.reflection.ClassReflectionHelper
[WARNING]   - org.glassfish.hk2.utilities.cache.CacheEntry
[WARNING]   - org.glassfish.hk2.utilities.reflection.ReflectionHelper
[WARNING]   - 70 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, httpclient-4.5.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 463 overlapping classes: 
[WARNING]   - org.apache.http.impl.cookie.RFC2109Spec
[WARNING]   - org.apache.http.impl.execchain.MainClientExec
[WARNING]   - org.apache.http.conn.routing.RouteInfo$TunnelType
[WARNING]   - org.apache.http.client.methods.HttpGet
[WARNING]   - org.apache.http.impl.cookie.BrowserCompatSpecFactory
[WARNING]   - org.apache.http.impl.client.HttpAuthenticator
[WARNING]   - org.apache.http.conn.ManagedClientConnection
[WARNING]   - org.apache.http.client.protocol.RequestAuthCache
[WARNING]   - org.apache.http.conn.params.ConnConnectionParamBean
[WARNING]   - org.apache.http.impl.client.IdleConnectionEvictor
[WARNING]   - 453 more...
[WARNING] commons-lang3-3.5.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 260 overlapping classes: 
[WARNING]   - org.apache.commons.lang3.time.StopWatch$State$1
[WARNING]   - org.apache.commons.lang3.ThreadUtils$1
[WARNING]   - org.apache.commons.lang3.ThreadUtils$ThreadGroupPredicate
[WARNING]   - org.apache.commons.lang3.builder.MultilineRecursiveToStringStyle
[WARNING]   - org.apache.commons.lang3.concurrent.AbstractCircuitBreaker
[WARNING]   - org.apache.commons.lang3.SerializationUtils
[WARNING]   - org.apache.commons.lang3.time.FastDatePrinter$TwentyFourHourField
[WARNING]   - org.apache.commons.lang3.LocaleUtils
[WARNING]   - org.apache.commons.lang3.concurrent.ConcurrentException
[WARNING]   - org.apache.commons.lang3.CharRange
[WARNING]   - 250 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, slf4j-log4j12-1.7.16.jar, mango-cli-0.0.3-SNAPSHOT.jar define 6 overlapping classes: 
[WARNING]   - org.slf4j.impl.Log4jLoggerAdapter
[WARNING]   - org.slf4j.impl.Log4jMDCAdapter
[WARNING]   - org.slf4j.impl.StaticMarkerBinder
[WARNING]   - org.slf4j.impl.Log4jLoggerFactory
[WARNING]   - org.slf4j.impl.StaticLoggerBinder
[WARNING]   - org.slf4j.impl.StaticMDCBinder
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, metrics-json-3.1.5.jar define 11 overlapping classes: 
[WARNING]   - com.codahale.metrics.json.MetricsModule$MetricRegistrySerializer
[WARNING]   - com.codahale.metrics.json.HealthCheckModule$HealthCheckResultSerializer
[WARNING]   - com.codahale.metrics.json.HealthCheckModule
[WARNING]   - com.codahale.metrics.json.MetricsModule$TimerSerializer
[WARNING]   - com.codahale.metrics.json.MetricsModule$GaugeSerializer
[WARNING]   - com.codahale.metrics.json.MetricsModule$1
[WARNING]   - com.codahale.metrics.json.MetricsModule$MeterSerializer
[WARNING]   - com.codahale.metrics.json.MetricsModule
[WARNING]   - com.codahale.metrics.json.MetricsModule$HistogramSerializer
[WARNING]   - com.codahale.metrics.json.MetricsModule$CounterSerializer
[WARNING]   - 1 more...
[WARNING] scala-guice_2.11-4.2.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 95 overlapping classes: 
[WARNING]   - net.codingwell.scalaguice.ScalaModule$
[WARNING]   - net.codingwell.scalaguice.ScalaModule$ScalaScopedBindingBuilder
[WARNING]   - net.codingwell.scalaguice.InternalModule$BindingBuilder$$typecreator1$2
[WARNING]   - net.codingwell.scalaguice.InjectorExtensions$ScalaInjector$$typecreator2$1
[WARNING]   - net.codingwell.scalaguice.ScalaModule$ScalaLinkedBindingBuilder$$anon$2$$typecreator1$1
[WARNING]   - net.codingwell.scalaguice.binder.ScopedBindingBuilderProxy
[WARNING]   - net.codingwell.scalaguice.ScalaModule$$anonfun$filterTrace$2
[WARNING]   - net.codingwell.scalaguice.ScalaPrivateModule$ElementBuilder
[WARNING]   - net.codingwell.scalaguice.binder.LinkedBindingBuilderProxy$class
[WARNING]   - net.codingwell.scalaguice.ScalaModule$ScalaAnnotatedBindingBuilder
[WARNING]   - 85 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, checker-qual-2.5.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 302 overlapping classes: 
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil
[WARNING]   - org.checkerframework.checker.units.qual.MixedUnits
[WARNING]   - org.checkerframework.checker.units.qual.PolyUnit
[WARNING]   - org.checkerframework.checker.regex.qual.PolyRegex
[WARNING]   - org.checkerframework.checker.units.qual.C
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil$IllegalFormatConversionCategoryException
[WARNING]   - org.checkerframework.framework.qual.Unqualified
[WARNING]   - org.checkerframework.common.reflection.qual.UnknownMethod
[WARNING]   - org.checkerframework.framework.qual.EnsuresQualifierIf
[WARNING]   - org.checkerframework.checker.signedness.SignednessUtil
[WARNING]   - 292 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, zookeeper-3.4.6.jar define 440 overlapping classes: 
[WARNING]   - org.apache.zookeeper.server.NettyServerCnxn$DumpCommand
[WARNING]   - org.apache.zookeeper.proto.GetMaxChildrenRequest
[WARNING]   - org.apache.jute.XmlInputArchive$XMLParser
[WARNING]   - org.apache.zookeeper.server.NettyServerCnxn$SendBufferWriter
[WARNING]   - org.apache.jute.CsvInputArchive$1
[WARNING]   - org.apache.zookeeper.KeeperException$CodeDeprecated
[WARNING]   - org.apache.zookeeper.server.ZooKeeperServerMXBean
[WARNING]   - org.apache.zookeeper.server.NettyServerCnxn$EnvCommand
[WARNING]   - org.apache.zookeeper.server.quorum.Learner$PacketInFlight
[WARNING]   - org.apache.zookeeper.Op$Check
[WARNING]   - 430 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, adam-codegen-spark2_2.11-0.26.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 18 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$getters$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$setters$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$apply$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$fields$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$$anonfun$fields$1
[WARNING]   - 8 more...
[WARNING] bcprov-jdk15on-1.52.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 2430 overlapping classes: 
[WARNING]   - org.bouncycastle.crypto.modes.gcm.Tables8kGCMMultiplier
[WARNING]   - org.bouncycastle.crypto.tls.HeartbeatMode
[WARNING]   - org.bouncycastle.pqc.math.linearalgebra.GF2nPolynomialElement
[WARNING]   - org.bouncycastle.jcajce.provider.asymmetric.ecgost.KeyFactorySpi
[WARNING]   - org.bouncycastle.jcajce.provider.symmetric.AES$AlgParamsCCM
[WARNING]   - org.bouncycastle.asn1.tsp.TimeStampResp
[WARNING]   - org.bouncycastle.jcajce.provider.digest.SHA384$Mappings
[WARNING]   - org.bouncycastle.jcajce.provider.asymmetric.elgamal.AlgorithmParameterGeneratorSpi
[WARNING]   - org.bouncycastle.asn1.x509.CRLNumber
[WARNING]   - org.bouncycastle.jcajce.provider.digest.SM3
[WARNING]   - 2420 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jersey-guava-2.22.2.jar define 753 overlapping classes: 
[WARNING]   - jersey.repackaged.com.google.common.collect.AbstractNavigableMap$DescendingMap
[WARNING]   - jersey.repackaged.com.google.common.collect.AbstractMultiset$ElementSet
[WARNING]   - jersey.repackaged.com.google.common.collect.Collections2$OrderedPermutationCollection
[WARNING]   - jersey.repackaged.com.google.common.collect.StandardTable$TableSet
[WARNING]   - jersey.repackaged.com.google.common.base.Splitter
[WARNING]   - jersey.repackaged.com.google.common.util.concurrent.Futures$1$1
[WARNING]   - jersey.repackaged.com.google.common.base.CharMatcher$5
[WARNING]   - jersey.repackaged.com.google.common.collect.SortedMapDifference
[WARNING]   - jersey.repackaged.com.google.common.collect.ImmutableListMultimap
[WARNING]   - jersey.repackaged.com.google.common.cache.LocalCache$AbstractReferenceEntry
[WARNING]   - 743 more...
[WARNING] RoaringBitmap-0.5.11.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 69 overlapping classes: 
[WARNING]   - org.roaringbitmap.ReverseRunContainerShortIterator
[WARNING]   - org.roaringbitmap.ShortIterator
[WARNING]   - org.roaringbitmap.Util
[WARNING]   - org.roaringbitmap.buffer.RawMappeableRunContainerShortIterator
[WARNING]   - org.roaringbitmap.buffer.MappeableBitmapContainer
[WARNING]   - org.roaringbitmap.buffer.BufferFastAggregation$2
[WARNING]   - org.roaringbitmap.buffer.MappeableBitmapContainerShortIterator
[WARNING]   - org.roaringbitmap.RunContainerShortIterator
[WARNING]   - org.roaringbitmap.buffer.ReverseMappeableArrayContainerShortIterator
[WARNING]   - org.roaringbitmap.buffer.MappeableContainerPointer
[WARNING]   - 59 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, base64-2.3.8.jar, mango-cli-0.0.3-SNAPSHOT.jar define 4 overlapping classes: 
[WARNING]   - net.iharder.Base64$InputStream
[WARNING]   - net.iharder.Base64$OutputStream
[WARNING]   - net.iharder.Base64$1
[WARNING]   - net.iharder.Base64
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, hadoop-bam-7.9.2.jar define 115 overlapping classes: 
[WARNING]   - org.seqdoop.hadoop_bam.BAMSplitGuesser
[WARNING]   - org.seqdoop.hadoop_bam.util.SAMHeaderReader
[WARNING]   - org.seqdoop.hadoop_bam.QseqInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter
[WARNING]   - org.seqdoop.hadoop_bam.FastaInputFormat$1
[WARNING]   - org.seqdoop.hadoop_bam.util.SAMOutputPreparer$1
[WARNING]   - org.seqdoop.hadoop_bam.QseqOutputFormat$QseqRecordWriter
[WARNING]   - org.seqdoop.hadoop_bam.FastaInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.LineReader
[WARNING]   - org.seqdoop.hadoop_bam.util.BGZFCodec
[WARNING]   - 105 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, fastutil-6.5.7.jar, mango-cli-0.0.3-SNAPSHOT.jar define 10653 overlapping classes: 
[WARNING]   - it.unimi.dsi.fastutil.doubles.Double2IntRBTreeMap$Submap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2CharAVLTreeMap$2$1
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2ObjectLinkedOpenHashMap$EntryIterator
[WARNING]   - it.unimi.dsi.fastutil.shorts.Short2FloatOpenCustomHashMap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.ints.Int2ReferenceRBTreeMap$Submap
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2BooleanRBTreeMap$Submap$1
[WARNING]   - it.unimi.dsi.fastutil.floats.AbstractFloat2ShortSortedMap$ValuesCollection
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2ReferenceRBTreeMap$Submap$2
[WARNING]   - it.unimi.dsi.fastutil.chars.AbstractChar2LongSortedMap$ValuesIterator
[WARNING]   - it.unimi.dsi.fastutil.doubles.DoubleHeaps
[WARNING]   - 10643 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, paranamer-2.8.jar define 21 overlapping classes: 
[WARNING]   - com.thoughtworks.paranamer.PositionalParanamer
[WARNING]   - com.thoughtworks.paranamer.JavadocParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$Type
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$1
[WARNING]   - com.thoughtworks.paranamer.JavadocParanamer$DirJavadocProvider
[WARNING]   - com.thoughtworks.paranamer.AnnotationParanamer$Jsr330Helper
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$TypeCollector
[WARNING]   - com.thoughtworks.paranamer.AnnotationParanamer
[WARNING]   - com.thoughtworks.paranamer.NullParanamer
[WARNING]   - 11 more...
[WARNING] mango-cli-0.0.3-SNAPSHOT.jar, scalate-core_2.11-1.9.1.jar define 1372 overlapping classes: 
[WARNING]   - org.fusesource.scalate.mustache.MustacheParser$$anonfun$open$1
[WARNING]   - org.fusesource.scalate.scuery.support.CssParser$$anonfun$attrib$3$$anonfun$apply$26
[WARNING]   - org.fusesource.scalate.support.TemplateFinder$$anonfun$org$fusesource$scalate$support$TemplateFinder$$findTemplateAlias$1$1$$anonfun$apply$3
[WARNING]   - org.fusesource.scalate.ssp.SspParser$$anonfun$scalaExpression$3
[WARNING]   - org.fusesource.scalate.scuery.support.InvalidCssSelectorException
[WARNING]   - org.fusesource.scalate.support.ScalaParseSupport$$anonfun$octalEscapeSeq$3
[WARNING]   - org.fusesource.scalate.scuery.support.CssParser$$anonfun$functional_nth_pseudo$4
[WARNING]   - org.fusesource.scalate.scaml.ScamlParser$$anonfun$expression$6$$anonfun$apply$30$$anonfun$apply$33
[WARNING]   - org.fusesource.scalate.scaml.ScamlParser$$anonfun$haml_comment_statement$4
[WARNING]   - org.fusesource.scalate.support.ScalaParseSupport$$anonfun$someUpto$3$$anonfun$apply$17
[WARNING]   - 1362 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, minlog-1.3.0.jar, minlog-1.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-intervalrdd-spark2_2.11-0.2.13.jar, mango-cli-0.0.3-SNAPSHOT.jar define 51 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$collect$2
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$4
[WARNING]   - org.bdgenomics.utils.interval.array.Interval$class
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$get$1
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$4
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$1
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$filter$1
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$mapValues$1
[WARNING]   - 41 more...
[WARNING] parquet-encoding-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 184 overlapping classes: 
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer14
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer24
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer10
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingBE$Packer7
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer20
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer7
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer30
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer13
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer23
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$Packer19
[WARNING]   - 174 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, netty-3.9.9.Final.jar define 879 overlapping classes: 
[WARNING]   - org.jboss.netty.handler.traffic.TrafficCounter$TrafficMonitoringTask
[WARNING]   - org.jboss.netty.handler.codec.spdy.SpdyGoAwayFrame
[WARNING]   - org.jboss.netty.util.internal.jzlib.Deflate
[WARNING]   - org.jboss.netty.channel.socket.ServerSocketChannelConfig
[WARNING]   - org.jboss.netty.util.internal.ConcurrentHashMap$HashIterator
[WARNING]   - org.jboss.netty.handler.codec.serialization.ObjectDecoder
[WARNING]   - org.jboss.netty.util.internal.jzlib.Tree
[WARNING]   - org.jboss.netty.util.internal.ConcurrentIdentityWeakKeyHashMap$Segment
[WARNING]   - org.jboss.netty.util.internal.ConcurrentIdentityHashMap$ValueIterator
[WARNING]   - org.jboss.netty.handler.codec.http.multipart.HttpPostRequestEncoder
[WARNING]   - 869 more...
[WARNING] bdg-formats-0.12.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 61 overlapping classes: 
[WARNING]   - org.bdgenomics.formats.avro.VariantCallingAnnotations$Builder
[WARNING]   - org.bdgenomics.formats.avro.VariantAnnotation$Builder
[WARNING]   - org.bdgenomics.formats.avro.Reference$1
[WARNING]   - org.bdgenomics.formats.avro.VariantAnnotationMessage
[WARNING]   - org.bdgenomics.formats.avro.OntologyTerm$1
[WARNING]   - org.bdgenomics.formats.avro.Feature$1
[WARNING]   - org.bdgenomics.formats.avro.AlignmentRecord
[WARNING]   - org.bdgenomics.formats.avro.Sequence$1
[WARNING]   - org.bdgenomics.formats.avro.ReadGroup$Builder
[WARNING]   - org.bdgenomics.formats.avro.ReadGroup
[WARNING]   - 51 more...
[WARNING] jackson-core-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 121 overlapping classes: 
[WARNING]   - org.codehaus.jackson.annotate.JsonManagedReference
[WARNING]   - org.codehaus.jackson.util.DefaultPrettyPrinter$FixedSpaceIndenter
[WARNING]   - org.codehaus.jackson.JsonGenerationException
[WARNING]   - org.codehaus.jackson.util.BufferRecycler$CharBufferType
[WARNING]   - org.codehaus.jackson.io.UTF32Reader
[WARNING]   - org.codehaus.jackson.sym.Name1
[WARNING]   - org.codehaus.jackson.util.MinimalPrettyPrinter
[WARNING]   - org.codehaus.jackson.impl.JsonParserBase
[WARNING]   - org.codehaus.jackson.annotate.JsonValue
[WARNING]   - org.codehaus.jackson.sym.CharsToNameCanonicalizer$Bucket
[WARNING]   - 111 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, servo-core-0.12.12.jar, mango-cli-0.0.3-SNAPSHOT.jar define 162 overlapping classes: 
[WARNING]   - com.netflix.servo.util.Objects
[WARNING]   - com.netflix.servo.util.Clock
[WARNING]   - com.netflix.servo.monitor.MaxGauge
[WARNING]   - com.netflix.servo.publish.LocalJmxConnector
[WARNING]   - com.netflix.servo.publish.MonitorRegistryMetricPoller$MonitorValueCallable
[WARNING]   - com.netflix.servo.util.ExpiringCache$Entry
[WARNING]   - com.netflix.servo.util.ThreadCpuStats$CpuUsage
[WARNING]   - com.netflix.servo.tag.SmallTagMap$Builder
[WARNING]   - com.netflix.servo.stats.StatsConfig
[WARNING]   - com.netflix.servo.monitor.Monitors$CounterFactory
[WARNING]   - 152 more...
[WARNING] spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 18 overlapping classes: 
[WARNING]   - org.apache.spark.unsafe.types.UTF8String
[WARNING]   - org.apache.spark.unsafe.memory.HeapMemoryAllocator
[WARNING]   - org.apache.spark.unsafe.array.LongArray
[WARNING]   - org.apache.spark.unsafe.types.UTF8String$LongWrapper
[WARNING]   - org.apache.spark.unsafe.bitset.BitSetMethods
[WARNING]   - org.apache.spark.unsafe.memory.UnsafeMemoryAllocator
[WARNING]   - org.apache.spark.sql.catalyst.expressions.HiveHasher
[WARNING]   - org.apache.spark.unsafe.KVIterator
[WARNING]   - org.apache.spark.unsafe.types.CalendarInterval
[WARNING]   - org.apache.spark.unsafe.memory.MemoryBlock
[WARNING]   - 8 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jsr305-1.3.9.jar, mango-cli-0.0.3-SNAPSHOT.jar define 35 overlapping classes: 
[WARNING]   - javax.annotation.RegEx
[WARNING]   - javax.annotation.concurrent.Immutable
[WARNING]   - javax.annotation.meta.TypeQualifierDefault
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.CheckReturnValue
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Nonnull
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - javax.annotation.MatchesPattern
[WARNING]   - 25 more...
[WARNING] error_prone_annotations-2.2.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 22 overlapping classes: 
[WARNING]   - com.google.errorprone.annotations.NoAllocation
[WARNING]   - com.google.errorprone.annotations.Var
[WARNING]   - com.google.errorprone.annotations.IncompatibleModifiers
[WARNING]   - com.google.errorprone.annotations.CompatibleWith
[WARNING]   - com.google.errorprone.annotations.concurrent.LockMethod
[WARNING]   - com.google.errorprone.annotations.FormatString
[WARNING]   - com.google.errorprone.annotations.DoNotCall
[WARNING]   - com.google.errorprone.annotations.Immutable
[WARNING]   - com.google.errorprone.annotations.RestrictedApi
[WARNING]   - com.google.errorprone.annotations.CompileTimeConstant
[WARNING]   - 12 more...
[WARNING] jetty-xml-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 14 overlapping classes: 
[WARNING]   - org.eclipse.jetty.xml.ConfigurationProcessorFactory
[WARNING]   - org.eclipse.jetty.xml.XmlParser$Node
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration$AttrOrElementNode
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration
[WARNING]   - org.eclipse.jetty.xml.ConfigurationProcessor
[WARNING]   - org.eclipse.jetty.xml.XmlParser$Handler
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration$1
[WARNING]   - org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration$1
[WARNING]   - org.eclipse.jetty.xml.XmlParser
[WARNING]   - 4 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-server-2.22.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 665 overlapping classes: 
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParamConverters$TypeFromString
[WARNING]   - org.glassfish.jersey.server.internal.inject.QueryParamValueFactoryProvider
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParamInjectionResolver
[WARNING]   - org.glassfish.jersey.server.internal.InternalServerProperties
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParameterInjectionBinder$5
[WARNING]   - jersey.repackaged.org.objectweb.asm.FieldWriter
[WARNING]   - org.glassfish.jersey.server.internal.RuntimeDelegateImpl
[WARNING]   - org.glassfish.jersey.server.internal.inject.ParamConverterFactory
[WARNING]   - org.glassfish.jersey.server.internal.monitoring.RequestEventImpl$Builder
[WARNING]   - org.glassfish.jersey.server.ContainerRequest
[WARNING]   - 655 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, scala-compiler-2.11.12.jar define 9084 overlapping classes: 
[WARNING]   - scala.tools.nsc.doc.base.CommentFactoryBase$SimpleTagKey
[WARNING]   - scala.tools.jline_embedded.Terminal
[WARNING]   - scala.tools.nsc.Global$$anonfun$scala$tools$nsc$Global$$writeICode$1
[WARNING]   - scala.tools.nsc.backend.opt.ClosureElimination$ClosureElim$$anonfun$analyzeMethod$1$$anonfun$apply$2
[WARNING]   - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$typedCase$2$$anonfun$apply$27
[WARNING]   - scala.tools.nsc.backend.icode.analysis.TypeFlowAnalysis$MTFAGrowable$$anonfun$scala$tools$nsc$backend$icode$analysis$TypeFlowAnalysis$MTFAGrowable$$putOnRadar$1$$anonfun$3
[WARNING]   - scala.tools.nsc.interpreter.ILoop$$anonfun$standardCommands$3
[WARNING]   - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$isReferencedFrom$1
[WARNING]   - scala.tools.nsc.typechecker.Typers$Typer$dyna$
[WARNING]   - scala.tools.nsc.transform.patmat.MatchAnalysis$MatchAnalyzer$NegativeExample$$anonfun$23
[WARNING]   - 9074 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-launcher_2.11-2.3.3.jar define 34 overlapping classes: 
[WARNING]   - org.apache.spark.launcher.AbstractAppHandle
[WARNING]   - org.apache.spark.launcher.SparkAppHandle$State
[WARNING]   - org.apache.spark.launcher.SparkAppHandle$Listener
[WARNING]   - org.apache.spark.launcher.ChildProcAppHandle
[WARNING]   - org.apache.spark.launcher.LauncherProtocol
[WARNING]   - org.apache.spark.launcher.LauncherProtocol$Stop
[WARNING]   - org.apache.spark.launcher.SparkSubmitOptionParser
[WARNING]   - org.apache.spark.launcher.LauncherProtocol$Message
[WARNING]   - org.apache.spark.launcher.CommandBuilderUtils
[WARNING]   - org.apache.spark.launcher.SparkSubmitCommandBuilder$OptionParser
[WARNING]   - 24 more...
[WARNING] jetty-security-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 61 overlapping classes: 
[WARNING]   - org.eclipse.jetty.security.SpnegoUserPrincipal
[WARNING]   - org.eclipse.jetty.security.authentication.DigestAuthenticator
[WARNING]   - org.eclipse.jetty.security.UserDataConstraint
[WARNING]   - org.eclipse.jetty.security.PropertyUserStore$UserListener
[WARNING]   - org.eclipse.jetty.security.authentication.FormAuthenticator
[WARNING]   - org.eclipse.jetty.security.UserAuthentication
[WARNING]   - org.eclipse.jetty.security.DefaultAuthenticatorFactory
[WARNING]   - org.eclipse.jetty.security.SecurityHandler
[WARNING]   - org.eclipse.jetty.security.IdentityService
[WARNING]   - org.eclipse.jetty.security.authentication.ConfigurableSpnegoAuthenticator$UserIdentityHolder
[WARNING]   - 51 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, java-xmlbuilder-1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 5 overlapping classes: 
[WARNING]   - com.jamesmurty.utils.NamespaceContextImpl
[WARNING]   - com.jamesmurty.utils.BaseXMLBuilder
[WARNING]   - com.jamesmurty.utils.XMLBuilder
[WARNING]   - com.jamesmurty.utils.XMLBuilder2
[WARNING]   - com.jamesmurty.utils.XMLBuilderRuntimeException
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, snappy-java-1.0.5.jar, mango-cli-0.0.3-SNAPSHOT.jar define 12 overlapping classes: 
[WARNING]   - org.xerial.snappy.SnappyLoader
[WARNING]   - org.xerial.snappy.SnappyOutputStream
[WARNING]   - org.xerial.snappy.SnappyErrorCode
[WARNING]   - org.xerial.snappy.SnappyBundleActivator
[WARNING]   - org.xerial.snappy.SnappyError
[WARNING]   - org.xerial.snappy.SnappyNativeAPI
[WARNING]   - org.xerial.snappy.SnappyException
[WARNING]   - org.xerial.snappy.Snappy
[WARNING]   - org.xerial.snappy.SnappyNative
[WARNING]   - org.xerial.snappy.OSInfo
[WARNING]   - 2 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, ivy-2.4.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 744 overlapping classes: 
[WARNING]   - org.apache.ivy.ant.IvyDeliver
[WARNING]   - org.apache.ivy.plugins.resolver.util.ApacheHttpURLLister
[WARNING]   - org.apache.ivy.ant.BuildOBRTask
[WARNING]   - org.apache.ivy.osgi.p2.P2MetadataParser$UnitsHandler$1
[WARNING]   - org.apache.ivy.core.cache.ResolutionCacheManager
[WARNING]   - org.apache.ivy.osgi.repo.EditableRepoDescriptor
[WARNING]   - org.apache.ivy.plugins.parser.AbstractModuleDescriptorParser$AbstractParser
[WARNING]   - org.apache.ivy.plugins.latest.LatestLexicographicStrategy$1
[WARNING]   - org.apache.ivy.osgi.repo.FSManifestIterable$3
[WARNING]   - org.apache.ivy.util.url.HttpClientHandler
[WARNING]   - 734 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-cli-spark2_2.11-0.2.13.jar, mango-cli-0.0.3-SNAPSHOT.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.cli.Args4j
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$4
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$3
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$class
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$2
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$run$1
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs$class
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$1
[WARNING]   - org.bdgenomics.utils.cli.SaveArgs
[WARNING]   - 13 more...
[WARNING] scalate-util_2.11-1.9.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 219 overlapping classes: 
[WARNING]   - org.fusesource.scalate.util.StringResource
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$12$$anonfun$apply$3$$anonfun$apply$19
[WARNING]   - org.fusesource.scalate.util.ClassPathBuilder$$anonfun$findManifestEntries$1$$anonfun$apply$3
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$18
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$12$$anonfun$apply$3$$anonfun$apply$5$$anonfun$apply$6$$anonfun$apply$9$$anonfun$apply$10
[WARNING]   - org.fusesource.scalate.util.ResourceLoader
[WARNING]   - org.fusesource.scalate.util.SourceMapStratum$$anonfun$7
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$20$$anonfun$apply$45
[WARNING]   - org.fusesource.scalate.util.ProductReflector$
[WARNING]   - org.fusesource.scalate.util.ClassFinder$$anonfun$discoverCommandClasses$1
[WARNING]   - 209 more...
[WARNING] commons-compress-1.8.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 64 overlapping classes: 
[WARNING]   - org.apache.commons.compress.archivers.sevenz.Coders$LZMADecoder
[WARNING]   - org.apache.commons.compress.archivers.sevenz.SevenZArchiveEntry
[WARNING]   - org.apache.commons.compress.archivers.sevenz.SevenZOutputFile$1
[WARNING]   - org.apache.commons.compress.changes.ChangeSetPerformer$ArchiveEntryIterator
[WARNING]   - org.apache.commons.compress.archivers.sevenz.Coder
[WARNING]   - org.apache.commons.compress.archivers.sevenz.Coders$BCJDecoder$1
[WARNING]   - org.apache.commons.compress.compressors.gzip.GzipParameters
[WARNING]   - org.apache.commons.compress.compressors.lzma.LZMACompressorInputStream
[WARNING]   - org.apache.commons.compress.compressors.snappy.SnappyCompressorInputStream
[WARNING]   - org.apache.commons.compress.archivers.sevenz.Coders$BCJDecoder
[WARNING]   - 54 more...
[WARNING] rl_2.11-0.4.10.jar, mango-cli-0.0.3-SNAPSHOT.jar define 126 overlapping classes: 
[WARNING]   - rl.StringQueryString$
[WARNING]   - rl.PathOps$class
[WARNING]   - rl.MapQueryString$$anonfun$mkString$1$$anonfun$apply$4
[WARNING]   - rl.EmptyFragment$
[WARNING]   - rl.StringFragment
[WARNING]   - rl.IPv6Address$$anon$3
[WARNING]   - rl.DomainParser$PublicSuffix$
[WARNING]   - rl.DomainParser$PublicSuffix
[WARNING]   - rl.MapQueryString$$anonfun$10
[WARNING]   - rl.EmptyHost$$anon$5
[WARNING]   - 116 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-codec-1.12.jar, mango-cli-0.0.3-SNAPSHOT.jar define 92 overlapping classes: 
[WARNING]   - org.apache.commons.codec.language.Nysiis
[WARNING]   - org.apache.commons.codec.language.bm.Rule$1
[WARNING]   - org.apache.commons.codec.language.bm.Rule$RPattern
[WARNING]   - org.apache.commons.codec.language.ColognePhonetic$CologneInputBuffer
[WARNING]   - org.apache.commons.codec.digest.HmacUtils
[WARNING]   - org.apache.commons.codec.language.bm.BeiderMorseEncoder
[WARNING]   - org.apache.commons.codec.digest.UnixCrypt
[WARNING]   - org.apache.commons.codec.language.Soundex
[WARNING]   - org.apache.commons.codec.binary.BinaryCodec
[WARNING]   - org.apache.commons.codec.language.bm.Languages$1
[WARNING]   - 82 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, convert-0.6.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 23 overlapping classes: 
[WARNING]   - org.bdgenomics.convert.bdgenomics.SliceToRead
[WARNING]   - org.bdgenomics.convert.bdgenomics.SliceToSequence
[WARNING]   - org.bdgenomics.convert.bdgenomics.BdgenomicsModule
[WARNING]   - org.bdgenomics.convert.ConversionException
[WARNING]   - org.bdgenomics.convert.bdgenomics.OntologyTermToString
[WARNING]   - org.bdgenomics.convert.bdgenomics.StringToVariantAnnotationMessage
[WARNING]   - org.bdgenomics.convert.ConversionStringency
[WARNING]   - org.bdgenomics.convert.bdgenomics.ReadToSlice
[WARNING]   - org.bdgenomics.convert.Converter
[WARNING]   - org.bdgenomics.convert.bdgenomics.ReadToSequence
[WARNING]   - 13 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, aopalliance-repackaged-2.4.0-b34.jar define 17 overlapping classes: 
[WARNING]   - org.aopalliance.reflect.ClassLocator
[WARNING]   - org.aopalliance.reflect.Metadata
[WARNING]   - org.aopalliance.instrument.Instrumentation
[WARNING]   - org.aopalliance.reflect.Field
[WARNING]   - org.aopalliance.intercept.FieldInterceptor
[WARNING]   - org.aopalliance.reflect.Method
[WARNING]   - org.aopalliance.reflect.CodeLocator
[WARNING]   - org.aopalliance.intercept.FieldAccess
[WARNING]   - org.aopalliance.reflect.ProgramUnit
[WARNING]   - org.aopalliance.instrument.UndoNotSupportedException
[WARNING]   - 7 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-module-paranamer-2.7.9.jar, mango-cli-0.0.3-SNAPSHOT.jar define 26 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.NullParanamer
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.ParameterNamesNotFoundException
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$1
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$MethodCollector
[WARNING]   - com.fasterxml.jackson.module.paranamer.SerializableParanamer
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.JavadocParanamer$DirJavadocProvider
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$Type
[WARNING]   - com.fasterxml.jackson.module.paranamer.ParanamerAnnotationIntrospector
[WARNING]   - com.fasterxml.jackson.module.paranamer.shaded.CachingParanamer$WithoutWeakReferences
[WARNING]   - com.fasterxml.jackson.module.paranamer.ParanamerOnJacksonAnnotationIntrospector
[WARNING]   - 16 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, curator-recipes-2.6.0.jar define 190 overlapping classes: 
[WARNING]   - org.apache.curator.framework.recipes.atomic.DistributedAtomicNumber
[WARNING]   - org.apache.curator.framework.recipes.locks.Reaper$State
[WARNING]   - org.apache.curator.framework.recipes.locks.InterProcessReadWriteLock
[WARNING]   - org.apache.curator.framework.recipes.queue.QueueBase
[WARNING]   - org.apache.curator.framework.recipes.locks.ChildReaper$1
[WARNING]   - org.apache.curator.framework.recipes.cache.Operation
[WARNING]   - org.apache.curator.framework.recipes.shared.SharedValue$1
[WARNING]   - org.apache.curator.framework.recipes.locks.Revoker
[WARNING]   - org.apache.curator.framework.recipes.queue.QueueSharderPolicies
[WARNING]   - org.apache.curator.framework.recipes.locks.StandardLockInternalsDriver
[WARNING]   - 180 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, commons-io-2.6.jar define 127 overlapping classes: 
[WARNING]   - org.apache.commons.io.FileCleaningTracker
[WARNING]   - org.apache.commons.io.comparator.SizeFileComparator
[WARNING]   - org.apache.commons.io.input.CloseShieldInputStream
[WARNING]   - org.apache.commons.io.ByteOrderParser
[WARNING]   - org.apache.commons.io.filefilter.EmptyFileFilter
[WARNING]   - org.apache.commons.io.monitor.FileEntry
[WARNING]   - org.apache.commons.io.output.ThresholdingOutputStream
[WARNING]   - org.apache.commons.io.input.TailerListener
[WARNING]   - org.apache.commons.io.IOExceptionWithCause
[WARNING]   - org.apache.commons.io.filefilter.NotFileFilter
[WARNING]   - 117 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, json4s-ast_2.11-3.2.11.jar define 68 overlapping classes: 
[WARNING]   - org.json4s.Merge$Mergeable
[WARNING]   - org.json4s.Merge$Mergeable$MergeSyntax
[WARNING]   - org.json4s.Merge$$anonfun$mergeRec$2$1
[WARNING]   - org.json4s.BigDecimalMode$class
[WARNING]   - org.json4s.JsonAST$JBool$
[WARNING]   - org.json4s.JsonAST$JField$
[WARNING]   - org.json4s.DoubleMode$class
[WARNING]   - org.json4s.JsonAST$JString
[WARNING]   - org.json4s.LowPriorityMergeDep$class
[WARNING]   - org.json4s.JsonAST
[WARNING]   - 58 more...
[WARNING] curator-client-2.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 56 overlapping classes: 
[WARNING]   - org.apache.curator.HandleHolder$Helper
[WARNING]   - org.apache.curator.utils.PathUtils
[WARNING]   - org.apache.curator.ensemble.exhibitor.ExhibitorEnsembleProvider$1
[WARNING]   - org.apache.curator.utils.CloseableScheduledExecutorService
[WARNING]   - org.apache.curator.utils.EnsurePath$InitialHelper$1
[WARNING]   - org.apache.curator.SessionFailRetryLoop$2
[WARNING]   - org.apache.curator.utils.ZKPaths$PathAndNode
[WARNING]   - org.apache.curator.ensemble.exhibitor.DefaultExhibitorRestClient
[WARNING]   - org.apache.curator.TimeTrace
[WARNING]   - org.apache.curator.HandleHolder$1$1
[WARNING]   - 46 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, scala-parser-combinators_2.11-1.0.4.jar define 352 overlapping classes: 
[WARNING]   - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$whitespace$1$$anonfun$apply$20$$anonfun$apply$21
[WARNING]   - scala.util.parsing.combinator.ImplicitConversions$$anonfun$flatten5$1
[WARNING]   - scala.util.parsing.combinator.Parsers$$anonfun$rep$1
[WARNING]   - scala.util.parsing.json.Lexer$$anonfun$number$1$$anonfun$apply$16
[WARNING]   - scala.util.parsing.combinator.Parsers$NoSuccess$$anonfun$1
[WARNING]   - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$3$$anonfun$apply$3$$anonfun$apply$4
[WARNING]   - scala.util.parsing.combinator.token.StdTokens$class
[WARNING]   - scala.util.parsing.json.Lexer$$anonfun$charSeq$10
[WARNING]   - scala.util.parsing.combinator.Parsers$Parser$$anonfun$$tilde$greater$1
[WARNING]   - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$5
[WARNING]   - 342 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, hk2-api-2.4.0-b34.jar, mango-cli-0.0.3-SNAPSHOT.jar define 165 overlapping classes: 
[WARNING]   - org.glassfish.hk2.api.ActiveDescriptor
[WARNING]   - org.glassfish.hk2.api.Proxiable
[WARNING]   - org.glassfish.hk2.utilities.InjecteeImpl
[WARNING]   - org.glassfish.hk2.api.ProxyCtl
[WARNING]   - org.glassfish.hk2.api.DynamicConfiguration
[WARNING]   - org.glassfish.hk2.internal.ImmediateHelper$1
[WARNING]   - org.glassfish.hk2.api.InjectionResolver
[WARNING]   - org.glassfish.hk2.utilities.ServiceLocatorUtilities$3
[WARNING]   - org.glassfish.hk2.api.Validator
[WARNING]   - org.glassfish.hk2.api.PopulatorPostProcessor
[WARNING]   - 155 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, activation-1.1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 38 overlapping classes: 
[WARNING]   - javax.activation.DataContentHandlerFactory
[WARNING]   - javax.activation.ObjectDataContentHandler
[WARNING]   - javax.activation.DataContentHandler
[WARNING]   - com.sun.activation.registries.MimeTypeEntry
[WARNING]   - com.sun.activation.viewers.TextViewer
[WARNING]   - com.sun.activation.registries.LogSupport
[WARNING]   - javax.activation.CommandObject
[WARNING]   - javax.activation.SecuritySupport$2
[WARNING]   - com.sun.activation.viewers.TextEditor
[WARNING]   - com.sun.activation.viewers.ImageViewerCanvas
[WARNING]   - 28 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, kryo-shaded-3.0.3.jar, kryo-2.24.0.jar define 193 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.BeanSerializer$1
[WARNING]   - com.esotericsoftware.kryo.Registration
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.kryo.util.IntMap$Values
[WARNING]   - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl
[WARNING]   - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField
[WARNING]   - com.esotericsoftware.kryo.serializers.JavaSerializer
[WARNING]   - 183 more...
[WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1955 overlapping classes: 
[WARNING]   - com.google.common.collect.CompactHashMap$Itr
[WARNING]   - com.google.common.collect.ImmutableMapValues$1
[WARNING]   - com.google.common.util.concurrent.AbstractService$5
[WARNING]   - com.google.common.io.LineProcessor
[WARNING]   - com.google.common.io.BaseEncoding$StandardBaseEncoding$2
[WARNING]   - com.google.common.io.ByteProcessor
[WARNING]   - com.google.common.math.package-info
[WARNING]   - com.google.common.util.concurrent.SimpleTimeLimiter
[WARNING]   - com.google.common.cache.AbstractCache$StatsCounter
[WARNING]   - com.google.common.util.concurrent.CycleDetectingLockFactory$Policies
[WARNING]   - 1945 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, guice-4.2.0.jar define 572 overlapping classes: 
[WARNING]   - com.google.inject.Scope
[WARNING]   - com.google.inject.Binding
[WARNING]   - com.google.inject.internal.cglib.core.$EmitUtils$3
[WARNING]   - com.google.inject.spi.TypeConverter
[WARNING]   - com.google.inject.internal.ConstructionProxy
[WARNING]   - com.google.inject.spi.InjectionPoint
[WARNING]   - com.google.inject.spi.StaticInjectionRequest
[WARNING]   - com.google.inject.internal.cglib.proxy.$FixedValueGenerator
[WARNING]   - com.google.inject.internal.cglib.proxy.$DispatcherGenerator
[WARNING]   - com.google.inject.spi.Elements$ElementsAsModule
[WARNING]   - 562 more...
[WARNING] commons-math3-3.4.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1215 overlapping classes: 
[WARNING]   - org.apache.commons.math3.optim.linear.LinearOptimizer
[WARNING]   - org.apache.commons.math3.linear.LUDecomposition$Solver
[WARNING]   - org.apache.commons.math3.analysis.function.Gaussian$Parametric
[WARNING]   - org.apache.commons.math3.stat.descriptive.WeightedEvaluation
[WARNING]   - org.apache.commons.math3.analysis.FunctionUtils$3
[WARNING]   - org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic
[WARNING]   - org.apache.commons.math3.ml.clustering.FuzzyKMeansClusterer
[WARNING]   - org.apache.commons.math3.analysis.FunctionUtils$3$1
[WARNING]   - org.apache.commons.math3.ode.nonstiff.MidpointStepInterpolator
[WARNING]   - org.apache.commons.math3.ode.ParameterConfiguration
[WARNING]   - 1205 more...
[WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, spark-launcher_2.11-2.3.3.jar, spark-tags_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, spark-kvstore_2.11-2.3.3.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: 
[WARNING]   - org.apache.spark.unused.UnusedStubClass
[WARNING] commons-compress-1.8.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 127 overlapping classes: 
[WARNING]   - org.apache.commons.compress.archivers.dump.ShortFileException
[WARNING]   - org.apache.commons.compress.utils.CountingInputStream
[WARNING]   - org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream
[WARNING]   - org.apache.commons.compress.compressors.bzip2.CRC
[WARNING]   - org.apache.commons.compress.archivers.dump.DumpArchiveEntry
[WARNING]   - org.apache.commons.compress.compressors.bzip2.BlockSort
[WARNING]   - org.apache.commons.compress.archivers.tar.TarArchiveEntry
[WARNING]   - org.apache.commons.compress.archivers.dump.UnsupportedCompressionAlgorithmException
[WARNING]   - org.apache.commons.compress.archivers.zip.AbstractUnicodeExtraField
[WARNING]   - org.apache.commons.compress.archivers.dump.InvalidFormatException
[WARNING]   - 117 more...
[WARNING] jackson-module-scala_2.11-2.6.7.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 403 overlapping classes: 
[WARNING]   - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializer$$anonfun$2
[WARNING]   - com.fasterxml.jackson.module.scala.deser.UnsortedSetDeserializerModule
[WARNING]   - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializerModule$class
[WARNING]   - com.fasterxml.jackson.module.scala.JacksonModule$$anonfun$1
[WARNING]   - com.fasterxml.jackson.module.scala.deser.SortedSetDeserializer$$anonfun$4
[WARNING]   - com.fasterxml.jackson.module.scala.util.Options$class
[WARNING]   - com.fasterxml.jackson.module.scala.util.EnumResolver$
[WARNING]   - com.fasterxml.jackson.module.scala.ser.OptionSerializer$$anonfun$serialize$1
[WARNING]   - com.fasterxml.jackson.module.scala.ser.OptionSerializerModule
[WARNING]   - com.fasterxml.jackson.module.scala.modifiers.CollectionLikeTypeModifier$$anonfun$modifyType$3
[WARNING]   - 393 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jets3t-0.9.4.jar define 616 overlapping classes: 
[WARNING]   - org.jets3t.service.acl.GroupGrantee
[WARNING]   - org.jets3t.service.multithread.CreateObjectsEvent
[WARNING]   - org.jets3t.service.model.S3BucketLoggingStatus
[WARNING]   - contribs.com.centerkey.utils.BareBonesBrowserLaunch
[WARNING]   - org.jets3t.service.impl.rest.CloudFrontXmlResponsesSaxParser$CacheBehaviorHandler
[WARNING]   - org.jets3t.apps.uploader.XmlGenerator$ObjectAndSignatureRequestDetails
[WARNING]   - org.jets3t.service.MultipartUploadChunk
[WARNING]   - org.jets3t.apps.cockpit.Cockpit$27
[WARNING]   - org.jets3t.service.model.S3DeleteMarker
[WARNING]   - org.jets3t.gui.TableSorter$Row
[WARNING]   - 606 more...
[WARNING] mango-cli-0.0.3-SNAPSHOT.jar, scala-compiler-2.11.12.jar define 11 overlapping classes: 
[WARNING]   - scala.tools.asm.CurrentFrame
[WARNING]   - scala.tools.nsc.transform.patmat.MatchCodeGen$OptimizedCodegen$optimizedCodegen$$anonfun$2$$anonfun$3
[WARNING]   - scala.tools.nsc.symtab.classfile.ICodeReader$$anonfun$parseInstruction$1$2
[WARNING]   - scala.tools.nsc.interpreter.jline.FileBackedHistory$$anonfun$2
[WARNING]   - scala.tools.nsc.interpreter.jline.FileBackedHistory$$anonfun$secure$1
[WARNING]   - scala.tools.nsc.interpreter.jline_embedded.FileBackedHistory$$anonfun$2
[WARNING]   - scala.tools.nsc.GenericRunnerSettings$$anonfun$1
[WARNING]   - scala.tools.nsc.transform.patmat.MatchCodeGen$OptimizedCodegen$optimizedCodegen$$anonfun$2$$anonfun$4
[WARNING]   - scala.tools.nsc.interpreter.jline_embedded.FileBackedHistory$$anonfun$secure$1
[WARNING]   - scala.tools.util.PathResolverBase$Calculated$$anonfun$okay$1$1
[WARNING]   - 1 more...
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jul-to-slf4j-1.7.16.jar define 1 overlapping classes: 
[WARNING]   - org.slf4j.bridge.SLF4JBridgeHandler
[WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, xbean-asm5-shaded-4.4.jar define 81 overlapping classes: 
[WARNING]   - org.apache.xbean.asm5.FieldWriter
[WARNING]   - org.apache.xbean.asm5.commons.GeneratorAdapter
[WARNING]   - org.apache.xbean.asm5.AnnotationWriter
[WARNING]   - org.apache.xbean.asm5.tree.IntInsnNode
[WARNING]   - org.apache.xbean.asm5.Type
[WARNING]   - org.apache.xbean.asm5.commons.RemappingClassAdapter
[WARNING]   - org.apache.xbean.asm5.tree.FieldInsnNode
[WARNING]   - org.apache.xbean.asm5.tree.MultiANewArrayInsnNode
[WARNING]   - org.apache.xbean.asm5.tree.IincInsnNode
[WARNING]   - org.apache.xbean.asm5.tree.InsnList$InsnListIterator
[WARNING]   - 71 more...
[WARNING] mango-cli-0.0.3-SNAPSHOT.jar, grizzled-slf4j_2.11-1.0.2.jar define 4 overlapping classes: 
[WARNING]   - grizzled.slf4j.Logger$
[WARNING]   - grizzled.slf4j.Logging
[WARNING]   - grizzled.slf4j.Logging$class
[WARNING]   - grizzled.slf4j.Logger
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar with /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT-shaded.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-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:2.2.1: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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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 ---
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: Distribution 0.0.3-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-shade-plugin:3.1.0:shade (default) @ mango-distribution ---
[INFO] Replacing original artifact with shaded artifact.
[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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.tar.gz
[INFO] Building tar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  3.286 s]
[INFO] mango: CORE ........................................ SUCCESS [ 41.221 s]
[INFO] mango: CLI ......................................... SUCCESS [ 56.166 s]
[INFO] Mango: Assembly .................................... SUCCESS [ 49.703 s]
[INFO] mango: Distribution ................................ SUCCESS [ 34.619 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:05 min
[INFO] Finished at: 2019-05-10T15:01:29-07:00
[INFO] Final Memory: 95M/1503M
[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-0.0.3-SNAPSHOT-bin.tar.gz
+ grep jar
+ grep -v -e sources -e javadoc
-rw-r--r-- jenkins/jenkins 126866907 2019-05-10 15:00 mango-distribution-0.0.3-SNAPSHOT/repo/mango-assembly-0.0.3-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvnpmmz3Bo
/tmp/mangoTestMvnpmmz3Bo
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/._references.avro.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/_SUCCESS
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/_partitionedByStartPos
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/referenceName=1
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/referenceName=1/positionBin=0/.part-00000-5245bde5-875a-489b-b821-51d64a565d97.c000.snappy.parquet.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/referenceName=1/positionBin=0/part-00000-5245bde5-875a-489b-b821-51d64a565d97.c000.snappy.parquet
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/_references.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/_samples.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/._SUCCESS.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/._samples.avro.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/._header.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253.adam/_header
/tmp/mangoTestMvnpmmz3Bo/invalidBuild.genome2800409261822372935
/tmp/mangoTestMvnpmmz3Bo/scalate-2899127126144848871-workdir
/tmp/mangoTestMvnpmmz3Bo/scalate-2899127126144848871-workdir/classes
/tmp/mangoTestMvnpmmz3Bo/scalate-2899127126144848871-workdir/src
/tmp/mangoTestMvnpmmz3Bo/scalate-2899127126144848871-workdir/src/WEB-INF
/tmp/mangoTestMvnpmmz3Bo/scalate-2899127126144848871-workdir/src/WEB-INF/layouts
/tmp/mangoTestMvnpmmz3Bo/scalate-2899127126144848871-workdir/src/WEB-INF/layouts/overall.ssp.scala
/tmp/mangoTestMvnpmmz3Bo/8048024201891087246
/tmp/mangoTestMvnpmmz3Bo/8048024201891087246/anoGam1.genome
/tmp/mangoTestMvnpmmz3Bo/genomes7159719231813865298
/tmp/mangoTestMvnpmmz3Bo/genomes7159719231813865298/hg19.genome
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/._references.avro.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/_SUCCESS
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/_partitionedByStartPos
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/referenceName=1
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/referenceName=1/positionBin=0/part-00000-49ce6b38-d353-45c2-8ef5-59919fbea270.c000.snappy.parquet
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/referenceName=1/positionBin=0/.part-00000-49ce6b38-d353-45c2-8ef5-59919fbea270.c000.snappy.parquet.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/_references.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/_samples.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/._SUCCESS.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/._samples.avro.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/._header.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337.adam/_header
/tmp/mangoTestMvnpmmz3Bo/TempSuite1586578071857724253
/tmp/mangoTestMvnpmmz3Bo/TempSuite6474262242702813337
/tmp/mangoTestMvnpmmz3Bo/mmbroken4370101029681894134.genome
/tmp/mangoTestMvnpmmz3Bo/4089925925851420529
/tmp/mangoTestMvnpmmz3Bo/4089925925851420529/anoGam1.genome
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612
/tmp/mangoTestMvnpmmz3Bo/scalate-4333254086040186203-workdir
/tmp/mangoTestMvnpmmz3Bo/scalate-4333254086040186203-workdir/classes
/tmp/mangoTestMvnpmmz3Bo/scalate-4333254086040186203-workdir/src
/tmp/mangoTestMvnpmmz3Bo/scalate-4333254086040186203-workdir/src/WEB-INF
/tmp/mangoTestMvnpmmz3Bo/scalate-4333254086040186203-workdir/src/WEB-INF/layouts
/tmp/mangoTestMvnpmmz3Bo/scalate-4333254086040186203-workdir/src/WEB-INF/layouts/browser.ssp.scala
/tmp/mangoTestMvnpmmz3Bo/1145169549209131454
/tmp/mangoTestMvnpmmz3Bo/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvnpmmz3Bo/invalidBuild.genome2666997290444567285
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/._references.avro.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/_readGroups.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/_processingSteps.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/_SUCCESS
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/_partitionedByStartPos
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=1
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=1/positionBin=26/part-00000-d1f670b5-6b99-4052-9c3b-6379cddb7779.c000.snappy.parquet
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=1/positionBin=26/.part-00000-d1f670b5-6b99-4052-9c3b-6379cddb7779.c000.snappy.parquet.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=1/positionBin=240/part-00000-d1f670b5-6b99-4052-9c3b-6379cddb7779.c000.snappy.parquet
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=1/positionBin=240/.part-00000-d1f670b5-6b99-4052-9c3b-6379cddb7779.c000.snappy.parquet.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/_references.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=2
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=2/positionBin=189/part-00000-d1f670b5-6b99-4052-9c3b-6379cddb7779.c000.snappy.parquet
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/referenceName=2/positionBin=189/.part-00000-d1f670b5-6b99-4052-9c3b-6379cddb7779.c000.snappy.parquet.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/._SUCCESS.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5443035721675086612.adam/._readGroups.avro.crc
/tmp/mangoTestMvnpmmz3Bo/mmbroken5585197884556400807.genome
/tmp/mangoTestMvnpmmz3Bo/genomes7029077670046578833
/tmp/mangoTestMvnpmmz3Bo/genomes7029077670046578833/hg19.genome
/tmp/mangoTestMvnpmmz3Bo/scalate-2201335394200449856-workdir
/tmp/mangoTestMvnpmmz3Bo/scalate-2201335394200449856-workdir/classes
/tmp/mangoTestMvnpmmz3Bo/scalate-2201335394200449856-workdir/src
/tmp/mangoTestMvnpmmz3Bo/scalate-2201335394200449856-workdir/src/WEB-INF
/tmp/mangoTestMvnpmmz3Bo/scalate-2201335394200449856-workdir/src/WEB-INF/layouts
/tmp/mangoTestMvnpmmz3Bo/scalate-2201335394200449856-workdir/src/WEB-INF/layouts/overall.ssp.scala
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/._references.avro.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/_readGroups.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/_processingSteps.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/_SUCCESS
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/_partitionedByStartPos
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=1
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=1/positionBin=26/.part-00000-4d763f3c-c2c4-4ba0-a4f9-9d8306bdf991.c000.snappy.parquet.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=1/positionBin=26/part-00000-4d763f3c-c2c4-4ba0-a4f9-9d8306bdf991.c000.snappy.parquet
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=1/positionBin=240/.part-00000-4d763f3c-c2c4-4ba0-a4f9-9d8306bdf991.c000.snappy.parquet.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=1/positionBin=240/part-00000-4d763f3c-c2c4-4ba0-a4f9-9d8306bdf991.c000.snappy.parquet
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/_references.avro
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=2
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=2/positionBin=189/.part-00000-4d763f3c-c2c4-4ba0-a4f9-9d8306bdf991.c000.snappy.parquet.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/referenceName=2/positionBin=189/part-00000-4d763f3c-c2c4-4ba0-a4f9-9d8306bdf991.c000.snappy.parquet
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/._SUCCESS.crc
/tmp/mangoTestMvnpmmz3Bo/TempSuite5438912678443126016.adam/._readGroups.avro.crc
/tmp/mangoTestMvnpmmz3Bo/8047877454177010518
/tmp/mangoTestMvnpmmz3Bo/scalate-3400614593681916399-workdir
/tmp/mangoTestMvnpmmz3Bo/scalate-3400614593681916399-workdir/classes
/tmp/mangoTestMvnpmmz3Bo/scalate-3400614593681916399-workdir/src
/tmp/mangoTestMvnpmmz3Bo/scalate-3400614593681916399-workdir/src/WEB-INF
/tmp/mangoTestMvnpmmz3Bo/scalate-3400614593681916399-workdir/src/WEB-INF/layouts
/tmp/mangoTestMvnpmmz3Bo/scalate-3400614593681916399-workdir/src/WEB-INF/layouts/browser.ssp.scala
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvnpmmz3Bo

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/mangoTestMvnpmmz3Bo: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

    # make a temp directory
    MANGO_TMP_DIR=$(mktemp -d -t mangoTestXXXXXXX)

    MANGO_TMP_DIR=$MANGO_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
    mkdir $MANGO_TMP_DIR

    # 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}

    # add pyspark to the python path
    PY4J_ZIP="$(ls -1 "${SPARK_HOME}/python/lib" | grep py4j)"
    export PYTHONPATH=${SPARK_HOME}/python:${SPARK_HOME}/python/lib/${PY4J_ZIP}:${PYTHONPATH}

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

    # create a conda environment for python build, if necessary
    pythons=( 2.7 3.6 )
    for python in ${pythons[*]}
    do
        uuid=$(uuidgen)
        conda create -y -q -n mango-build-${uuid} python=${python}
        source activate mango-build-${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}
            # clean up
            rm -rf ${MANGO_TMP_DIR}
            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-${uuid} --all

    done

    # test mango submit
    MANGO_BROWSER_LOGS=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 \
    --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

    curl \
    --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

    # 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}
        # clean up
        rm -rf ${MANGO_TMP_DIR}
        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

    rm -rf ${MANGO_TMP_DIR}/${TEST_GENOME}*

    # clean up
    rm -rf ${MANGO_TMP_DIR}

fi
+ [[ 2.11 == 2.11 ]]
mktemp -d -t mangoTestXXXXXXX
++ mktemp -d -t mangoTestXXXXXXX
+ MANGO_TMP_DIR=/tmp/mangoTestY2ahf2b
+ MANGO_TMP_DIR=/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded
+ mkdir /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded
+ export TMPDIR=/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded
+ pushd /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/..
~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ cp -r . /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded
+ popd
~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ pushd /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded
/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ [[ 2.7.5 =~ ^2\.6 ]]
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7
+ SPARK=spark-2.3.3
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.3.3/spark-2.3.3-bin-hadoop2.7.tgz' -o spark-2.3.3-bin-hadoop2.7.tgz
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+ tar xzvf spark-2.3.3-bin-hadoop2.7.tgz
spark-2.3.3-bin-hadoop2.7/
spark-2.3.3-bin-hadoop2.7/bin/
spark-2.3.3-bin-hadoop2.7/bin/beeline
spark-2.3.3-bin-hadoop2.7/bin/beeline.cmd
spark-2.3.3-bin-hadoop2.7/bin/docker-image-tool.sh
spark-2.3.3-bin-hadoop2.7/bin/find-spark-home
spark-2.3.3-bin-hadoop2.7/bin/find-spark-home.cmd
spark-2.3.3-bin-hadoop2.7/bin/load-spark-env.cmd
spark-2.3.3-bin-hadoop2.7/bin/load-spark-env.sh
spark-2.3.3-bin-hadoop2.7/bin/pyspark
spark-2.3.3-bin-hadoop2.7/bin/pyspark.cmd
spark-2.3.3-bin-hadoop2.7/bin/pyspark2.cmd
spark-2.3.3-bin-hadoop2.7/bin/run-example
spark-2.3.3-bin-hadoop2.7/bin/run-example.cmd
spark-2.3.3-bin-hadoop2.7/bin/spark-class
spark-2.3.3-bin-hadoop2.7/bin/spark-class.cmd
spark-2.3.3-bin-hadoop2.7/bin/spark-class2.cmd
spark-2.3.3-bin-hadoop2.7/bin/spark-shell
spark-2.3.3-bin-hadoop2.7/bin/spark-shell.cmd
spark-2.3.3-bin-hadoop2.7/bin/spark-shell2.cmd
spark-2.3.3-bin-hadoop2.7/bin/spark-sql
spark-2.3.3-bin-hadoop2.7/bin/spark-sql.cmd
spark-2.3.3-bin-hadoop2.7/bin/spark-sql2.cmd
spark-2.3.3-bin-hadoop2.7/bin/spark-submit
spark-2.3.3-bin-hadoop2.7/bin/spark-submit.cmd
spark-2.3.3-bin-hadoop2.7/bin/spark-submit2.cmd
spark-2.3.3-bin-hadoop2.7/bin/sparkR
spark-2.3.3-bin-hadoop2.7/bin/sparkR.cmd
spark-2.3.3-bin-hadoop2.7/bin/sparkR2.cmd
spark-2.3.3-bin-hadoop2.7/conf/
spark-2.3.3-bin-hadoop2.7/conf/docker.properties.template
spark-2.3.3-bin-hadoop2.7/conf/fairscheduler.xml.template
spark-2.3.3-bin-hadoop2.7/conf/log4j.properties.template
spark-2.3.3-bin-hadoop2.7/conf/metrics.properties.template
spark-2.3.3-bin-hadoop2.7/conf/slaves.template
spark-2.3.3-bin-hadoop2.7/conf/spark-defaults.conf.template
spark-2.3.3-bin-hadoop2.7/conf/spark-env.sh.template
spark-2.3.3-bin-hadoop2.7/data/
spark-2.3.3-bin-hadoop2.7/data/graphx/
spark-2.3.3-bin-hadoop2.7/data/graphx/followers.txt
spark-2.3.3-bin-hadoop2.7/data/graphx/users.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/
spark-2.3.3-bin-hadoop2.7/data/mllib/als/
spark-2.3.3-bin-hadoop2.7/data/mllib/als/sample_movielens_ratings.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/als/test.data
spark-2.3.3-bin-hadoop2.7/data/mllib/gmm_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/images/
spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/
spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/29.5.a_b_EGDP022204.jpg
spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/54893.jpg
spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/DP153539.jpg
spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/DP802813.jpg
spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/not-image.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/images/license.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/
spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/BGRA.png
spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/BGRA_alpha_60.png
spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/chr30.4.184.jpg
spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/grayscale.jpg
spark-2.3.3-bin-hadoop2.7/data/mllib/iris_libsvm.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/kmeans_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/pagerank_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/pic_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/ridge-data/
spark-2.3.3-bin-hadoop2.7/data/mllib/ridge-data/lpsa.data
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_binary_classification_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_fpgrowth.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_isotonic_regression_libsvm_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_kmeans_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_lda_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_lda_libsvm_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_libsvm_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_linear_regression_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_movielens_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_multiclass_classification_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/sample_svm_data.txt
spark-2.3.3-bin-hadoop2.7/data/mllib/streaming_kmeans_data_test.txt
spark-2.3.3-bin-hadoop2.7/data/streaming/
spark-2.3.3-bin-hadoop2.7/data/streaming/AFINN-111.txt
spark-2.3.3-bin-hadoop2.7/examples/
spark-2.3.3-bin-hadoop2.7/examples/jars/
spark-2.3.3-bin-hadoop2.7/examples/jars/scopt_2.11-3.7.0.jar
spark-2.3.3-bin-hadoop2.7/examples/jars/spark-examples_2.11-2.3.3.jar
spark-2.3.3-bin-hadoop2.7/examples/src/
spark-2.3.3-bin-hadoop2.7/examples/src/main/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaHdfsLR.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaLogQuery.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaPageRank.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaSparkPi.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaStatusTrackerDemo.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaTC.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaWordCount.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaALSExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBinarizerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBisectingKMeansExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBucketedRandomProjectionLSHExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBucketizerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaChiSqSelectorExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaChiSquareTestExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaCorrelationExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaCountVectorizerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDCTExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDecisionTreeClassificationExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDecisionTreeRegressionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDocument.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaElementwiseProductExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaEstimatorTransformerParamExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaFeatureHasherExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaFPGrowthExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGaussianMixtureExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGeneralizedLinearRegressionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeClassifierExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeRegressorExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaImputerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaIndexToStringExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaInteractionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaIsotonicRegressionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaKMeansExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLabeledDocument.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLDAExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLinearRegressionWithElasticNetExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLinearSVCExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionSummaryExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionWithElasticNetExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMaxAbsScalerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMinHashLSHExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMinMaxScalerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaModelSelectionViaCrossValidationExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaModelSelectionViaTrainValidationSplitExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMulticlassLogisticRegressionWithElasticNetExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMultilayerPerceptronClassifierExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaNaiveBayesExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaNGramExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaNormalizerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaOneHotEncoderEstimatorExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaOneVsRestExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPCAExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPipelineExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPolynomialExpansionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaQuantileDiscretizerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaRandomForestClassifierExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaRandomForestRegressorExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaRFormulaExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaSQLTransformerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaStandardScalerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaStopWordsRemoverExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaStringIndexerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaTfIdfExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaTokenizerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorAssemblerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorIndexerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorSizeHintExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorSlicerExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaWord2VecExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaALS.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaAssociationRulesExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaBinaryClassificationMetricsExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaBisectingKMeansExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaChiSqSelectorExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaCorrelationsExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaDecisionTreeClassificationExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaDecisionTreeRegressionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaElementwiseProductExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaGaussianMixtureExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaGradientBoostingClassificationExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaGradientBoostingRegressionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaHypothesisTestingExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaHypothesisTestingKolmogorovSmirnovTestExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaIsotonicRegressionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaKernelDensityEstimationExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaKMeansExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLatentDirichletAllocationExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLBFGSExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLinearRegressionWithSGDExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLogisticRegressionWithLBFGSExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaMulticlassClassificationMetricsExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaMultiLabelClassificationMetricsExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaNaiveBayesExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaPCAExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaPowerIterationClusteringExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaPrefixSpanExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRandomForestClassificationExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRandomForestRegressionExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRankingMetricsExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRecommendationExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRegressionMetricsExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaSimpleFPGrowth.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaStratifiedSamplingExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaStreamingTestExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaSummaryStatisticsExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaSVDExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaSVMWithSGDExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/hive/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/hive/JavaSparkHiveExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaSparkSQLExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaSQLDataSourceExample.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaUserDefinedTypedAggregation.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaUserDefinedUntypedAggregation.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredKafkaWordCount.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredNetworkWordCount.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredNetworkWordCountWindowed.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredSessionization.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaCustomReceiver.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaDirectKafkaWordCount.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaNetworkWordCount.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaQueueStream.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaRecord.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaRecoverableNetworkWordCount.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaSqlNetworkWordCount.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaStatefulNetworkWordCount.java
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/als.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/avro_inputformat.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/kmeans.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/logistic_regression.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/aft_survival_regression.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/als_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/binarizer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/bisecting_k_means_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/bucketed_random_projection_lsh_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/bucketizer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/chi_square_test_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/chisq_selector_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/correlation_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/count_vectorizer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/cross_validator.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/dataframe_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/dct_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/decision_tree_classification_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/decision_tree_regression_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/elementwise_product_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/estimator_transformer_param_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/feature_hasher_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/fpgrowth_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/gaussian_mixture_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/generalized_linear_regression_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/gradient_boosted_tree_classifier_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/gradient_boosted_tree_regressor_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/imputer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/index_to_string_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/isotonic_regression_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/kmeans_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/lda_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/linear_regression_with_elastic_net.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/linearsvc.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/logistic_regression_summary_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/logistic_regression_with_elastic_net.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/max_abs_scaler_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/min_hash_lsh_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/min_max_scaler_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/multiclass_logistic_regression_with_elastic_net.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/multilayer_perceptron_classification.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/n_gram_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/naive_bayes_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/normalizer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/one_vs_rest_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/onehot_encoder_estimator_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/pca_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/pipeline_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/polynomial_expansion_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/quantile_discretizer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/random_forest_classifier_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/random_forest_regressor_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/rformula_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/sql_transformer.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/standard_scaler_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/stopwords_remover_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/string_indexer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/tf_idf_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/tokenizer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/train_validation_split.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/vector_assembler_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/vector_indexer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/vector_size_hint_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/vector_slicer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/word2vec_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/binary_classification_metrics_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/bisecting_k_means_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/correlations.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/correlations_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/decision_tree_classification_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/decision_tree_regression_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/elementwise_product_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/fpgrowth_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/gaussian_mixture_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/gaussian_mixture_model.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/gradient_boosting_classification_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/gradient_boosting_regression_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/hypothesis_testing_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/hypothesis_testing_kolmogorov_smirnov_test_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/isotonic_regression_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/k_means_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/kernel_density_estimation_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/kmeans.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/latent_dirichlet_allocation_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/linear_regression_with_sgd_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/logistic_regression.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/logistic_regression_with_lbfgs_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/multi_class_metrics_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/multi_label_metrics_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/naive_bayes_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/normalizer_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/pca_rowmatrix_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/power_iteration_clustering_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/random_forest_classification_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/random_forest_regression_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/random_rdd_generation.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/ranking_metrics_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/recommendation_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/regression_metrics_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/sampled_rdds.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/standard_scaler_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/stratified_sampling_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/streaming_k_means_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/streaming_linear_regression_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/summary_statistics_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/svd_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/svm_with_sgd_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/tf_idf_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/word2vec.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/word2vec_example.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/pagerank.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/parquet_inputformat.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/pi.py
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spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/arrow.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/basic.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/datasource.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/hive.py
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spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/streaming/structured_kafka_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/streaming/structured_network_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/streaming/structured_network_wordcount_windowed.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/status_api_demo.py
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spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/direct_kafka_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/flume_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/hdfs_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/kafka_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/network_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/network_wordjoinsentiments.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/queue_stream.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/recoverable_network_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/sql_network_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/stateful_network_wordcount.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/transitive_closure.py
spark-2.3.3-bin-hadoop2.7/examples/src/main/python/wordcount.py
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spark-2.3.3-bin-hadoop2.7/examples/src/main/r/data-manipulation.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/dataframe.R
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spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/als.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/bisectingKmeans.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/decisionTree.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/fpm.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/gaussianMixture.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/gbt.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/glm.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/isoreg.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/kmeans.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/kstest.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/lda.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/logit.R
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spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/mlp.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/naiveBayes.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/randomForest.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/survreg.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/svmLinear.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/RSparkSQLExample.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/streaming/
spark-2.3.3-bin-hadoop2.7/examples/src/main/r/streaming/structured_network_wordcount.R
spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/
spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/employees.json
spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/full_user.avsc
spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/kv1.txt
spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/people.csv
spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/people.json
spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/people.txt
spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/user.avsc
spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/users.avro
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spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/BroadcastTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/DFSReadWriteTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/DriverSubmissionTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ExceptionHandlingTest.scala
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spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/AggregateMessagesExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/Analytics.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/ComprehensiveExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/ConnectedComponentsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/LiveJournalPageRank.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/PageRankExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/SSSPExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/SynthBenchmark.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/TriangleCountingExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/GroupByTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/HdfsTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalALS.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalFileLR.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalKMeans.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalLR.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalPi.scala
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spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/AFTSurvivalRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ALSExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BinarizerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BisectingKMeansExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BucketedRandomProjectionLSHExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BucketizerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ChiSqSelectorExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ChiSquareTestExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/CorrelationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/CountVectorizerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DataFrameExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DCTExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeClassificationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DeveloperApiExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ElementwiseProductExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/EstimatorTransformerParamExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/FeatureHasherExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/FPGrowthExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GaussianMixtureExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GBTExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GeneralizedLinearRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GradientBoostedTreeClassifierExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GradientBoostedTreeRegressorExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ImputerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/IndexToStringExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/InteractionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/IsotonicRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/KMeansExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LDAExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LinearRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LinearRegressionWithElasticNetExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LinearSVCExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LogisticRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LogisticRegressionSummaryExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LogisticRegressionWithElasticNetExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MaxAbsScalerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MinHashLSHExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MinMaxScalerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ModelSelectionViaCrossValidationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ModelSelectionViaTrainValidationSplitExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MulticlassLogisticRegressionWithElasticNetExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MultilayerPerceptronClassifierExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/NaiveBayesExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/NGramExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/NormalizerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/OneHotEncoderEstimatorExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/OneVsRestExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PCAExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PipelineExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PolynomialExpansionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/QuantileDiscretizerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RandomForestClassifierExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RandomForestExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RandomForestRegressorExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RFormulaExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/SQLTransformerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/StandardScalerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/StopWordsRemoverExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/StringIndexerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/TfIdfExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/TokenizerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/UnaryTransformerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorAssemblerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorIndexerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorSizeHintExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorSlicerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/Word2VecExample.scala
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spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/AbstractParams.scala
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spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/BinaryClassification.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/BinaryClassificationMetricsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/BisectingKMeansExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/ChiSqSelectorExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/Correlations.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/CorrelationsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/CosineSimilarity.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/DecisionTreeClassificationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/DecisionTreeRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/DecisionTreeRunner.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/DenseKMeans.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/ElementwiseProductExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/FPGrowthExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GaussianMixtureExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostedTreesRunner.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostingClassificationExample.scala
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spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/KernelDensityEstimationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/KMeansExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LatentDirichletAllocationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LBFGSExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LDAExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LinearRegression.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LinearRegressionWithSGDExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LogisticRegressionWithLBFGSExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MovieLensALS.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MulticlassMetricsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MultiLabelMetricsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MultivariateSummarizer.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/NaiveBayesExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/NormalizerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnRowMatrixExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnSourceVectorExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PMMLModelExportExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PowerIterationClusteringExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PrefixSpanExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestClassificationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomRDDGeneration.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RankingMetricsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RecommendationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RegressionMetricsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SampledRDDs.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SimpleFPGrowth.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SparseNaiveBayes.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StandardScalerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StratifiedSamplingExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingKMeansExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLinearRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLogisticRegression.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SummaryStatisticsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SVDExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SVMWithSGDExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnyPCA.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnySVD.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TFIDFExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/Word2VecExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/MultiBroadcastTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/pythonconverters/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/pythonconverters/AvroConverters.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SimpleSkewedGroupByTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SkewedGroupByTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkALS.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkHdfsLR.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkKMeans.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkLR.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkPageRank.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkPi.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkTC.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/hive/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/hive/SparkHiveExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/RDDRelation.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/SparkSQLExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/SQLDataSourceExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredKafkaWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCountWindowed.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredSessionization.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedTypedAggregation.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedUntypedAggregation.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewGenerator.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewStream.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/CustomReceiver.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/DirectKafkaWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/HdfsWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/NetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/QueueStream.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/RawNetworkGrep.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/RecoverableNetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/SqlNetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/StatefulNetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/StreamingExamples.scala
spark-2.3.3-bin-hadoop2.7/jars/
spark-2.3.3-bin-hadoop2.7/jars/activation-1.1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/aircompressor-0.8.jar
spark-2.3.3-bin-hadoop2.7/jars/antlr-2.7.7.jar
spark-2.3.3-bin-hadoop2.7/jars/antlr-runtime-3.4.jar
spark-2.3.3-bin-hadoop2.7/jars/antlr4-runtime-4.7.jar
spark-2.3.3-bin-hadoop2.7/jars/aopalliance-1.0.jar
spark-2.3.3-bin-hadoop2.7/jars/aopalliance-repackaged-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/apache-log4j-extras-1.2.17.jar
spark-2.3.3-bin-hadoop2.7/jars/apacheds-i18n-2.0.0-M15.jar
spark-2.3.3-bin-hadoop2.7/jars/apacheds-kerberos-codec-2.0.0-M15.jar
spark-2.3.3-bin-hadoop2.7/jars/api-asn1-api-1.0.0-M20.jar
spark-2.3.3-bin-hadoop2.7/jars/api-util-1.0.0-M20.jar
spark-2.3.3-bin-hadoop2.7/jars/arpack_combined_all-0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/arrow-format-0.8.0.jar
spark-2.3.3-bin-hadoop2.7/jars/arrow-memory-0.8.0.jar
spark-2.3.3-bin-hadoop2.7/jars/arrow-vector-0.8.0.jar
spark-2.3.3-bin-hadoop2.7/jars/automaton-1.11-8.jar
spark-2.3.3-bin-hadoop2.7/jars/avro-1.7.7.jar
spark-2.3.3-bin-hadoop2.7/jars/avro-ipc-1.7.7.jar
spark-2.3.3-bin-hadoop2.7/jars/avro-mapred-1.7.7-hadoop2.jar
spark-2.3.3-bin-hadoop2.7/jars/base64-2.3.8.jar
spark-2.3.3-bin-hadoop2.7/jars/bcprov-jdk15on-1.58.jar
spark-2.3.3-bin-hadoop2.7/jars/bonecp-0.8.0.RELEASE.jar
spark-2.3.3-bin-hadoop2.7/jars/breeze-macros_2.11-0.13.2.jar
spark-2.3.3-bin-hadoop2.7/jars/breeze_2.11-0.13.2.jar
spark-2.3.3-bin-hadoop2.7/jars/calcite-avatica-1.2.0-incubating.jar
spark-2.3.3-bin-hadoop2.7/jars/calcite-core-1.2.0-incubating.jar
spark-2.3.3-bin-hadoop2.7/jars/calcite-linq4j-1.2.0-incubating.jar
spark-2.3.3-bin-hadoop2.7/jars/chill-java-0.8.4.jar
spark-2.3.3-bin-hadoop2.7/jars/chill_2.11-0.8.4.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-beanutils-1.7.0.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-beanutils-core-1.8.0.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-cli-1.2.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-codec-1.10.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-collections-3.2.2.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-compiler-3.0.8.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-compress-1.4.1.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-configuration-1.6.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-crypto-1.0.0.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-dbcp-1.4.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-digester-1.8.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-httpclient-3.1.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-io-2.4.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-lang-2.6.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-lang3-3.5.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-logging-1.1.3.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-math3-3.4.1.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-net-2.2.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-pool-1.5.4.jar
spark-2.3.3-bin-hadoop2.7/jars/compress-lzf-1.0.3.jar
spark-2.3.3-bin-hadoop2.7/jars/core-1.1.2.jar
spark-2.3.3-bin-hadoop2.7/jars/curator-client-2.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/curator-framework-2.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/curator-recipes-2.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/datanucleus-api-jdo-3.2.6.jar
spark-2.3.3-bin-hadoop2.7/jars/datanucleus-core-3.2.10.jar
spark-2.3.3-bin-hadoop2.7/jars/datanucleus-rdbms-3.2.9.jar
spark-2.3.3-bin-hadoop2.7/jars/derby-10.12.1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/eigenbase-properties-1.1.5.jar
spark-2.3.3-bin-hadoop2.7/jars/flatbuffers-1.2.0-3f79e055.jar
spark-2.3.3-bin-hadoop2.7/jars/generex-1.0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/gson-2.2.4.jar
spark-2.3.3-bin-hadoop2.7/jars/guava-14.0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/guice-3.0.jar
spark-2.3.3-bin-hadoop2.7/jars/guice-servlet-3.0.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-annotations-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-auth-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-client-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-common-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-hdfs-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-app-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-common-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-core-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-jobclient-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-shuffle-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-api-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-client-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-common-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-server-common-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-server-web-proxy-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-beeline-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-cli-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-exec-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-jdbc-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-metastore-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hk2-api-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/hk2-locator-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/hk2-utils-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/hppc-0.7.2.jar
spark-2.3.3-bin-hadoop2.7/jars/htrace-core-3.1.0-incubating.jar
spark-2.3.3-bin-hadoop2.7/jars/httpclient-4.5.4.jar
spark-2.3.3-bin-hadoop2.7/jars/httpcore-4.4.8.jar
spark-2.3.3-bin-hadoop2.7/jars/ivy-2.4.0.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-annotations-2.6.7.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-core-2.6.7.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-core-asl-1.9.13.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-databind-2.6.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-dataformat-yaml-2.6.7.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-jaxrs-1.9.13.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-mapper-asl-1.9.13.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-module-jaxb-annotations-2.6.7.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-module-paranamer-2.7.9.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-module-scala_2.11-2.6.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-xc-1.9.13.jar
spark-2.3.3-bin-hadoop2.7/jars/janino-3.0.8.jar
spark-2.3.3-bin-hadoop2.7/jars/java-xmlbuilder-1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/JavaEWAH-0.3.2.jar
spark-2.3.3-bin-hadoop2.7/jars/javassist-3.18.1-GA.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.annotation-api-1.2.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.inject-1.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.inject-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.servlet-api-3.1.0.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.ws.rs-api-2.0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/javolution-5.5.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jaxb-api-2.2.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jcl-over-slf4j-1.7.16.jar
spark-2.3.3-bin-hadoop2.7/jars/jdo-api-3.0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-client-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-common-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-container-servlet-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-container-servlet-core-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-guava-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-media-jaxb-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-server-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jets3t-0.9.4.jar
spark-2.3.3-bin-hadoop2.7/jars/jetty-6.1.26.jar
spark-2.3.3-bin-hadoop2.7/jars/jetty-util-6.1.26.jar
spark-2.3.3-bin-hadoop2.7/jars/jline-2.12.1.jar
spark-2.3.3-bin-hadoop2.7/jars/joda-time-2.9.3.jar
spark-2.3.3-bin-hadoop2.7/jars/jodd-core-3.5.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jpam-1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/json4s-ast_2.11-3.2.11.jar
spark-2.3.3-bin-hadoop2.7/jars/json4s-core_2.11-3.2.11.jar
spark-2.3.3-bin-hadoop2.7/jars/json4s-jackson_2.11-3.2.11.jar
spark-2.3.3-bin-hadoop2.7/jars/jsp-api-2.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jsr305-1.3.9.jar
spark-2.3.3-bin-hadoop2.7/jars/jta-1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jtransforms-2.4.0.jar
spark-2.3.3-bin-hadoop2.7/jars/jul-to-slf4j-1.7.16.jar
spark-2.3.3-bin-hadoop2.7/jars/kryo-shaded-3.0.3.jar
spark-2.3.3-bin-hadoop2.7/jars/kubernetes-client-3.0.0.jar
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spark-2.3.3-bin-hadoop2.7/python/test_support/hello/hello.txt
spark-2.3.3-bin-hadoop2.7/python/test_support/hello/sub_hello/
spark-2.3.3-bin-hadoop2.7/python/test_support/hello/sub_hello/sub_hello.txt
spark-2.3.3-bin-hadoop2.7/python/test_support/SimpleHTTPServer.py
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/ages.csv
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/ages_newlines.csv
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/_SUCCESS
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/c=0/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/c=0/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/c=0/part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/c=1/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/c=1/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/c=1/part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/_common_metadata
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/_metadata
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/_SUCCESS
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/.part-r-00008.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/part-r-00008.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/.part-r-00002.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/.part-r-00004.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/part-r-00002.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/part-r-00004.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/.part-r-00005.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/part-r-00005.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/.part-r-00007.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/part-r-00007.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/people.json
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/people1.json
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/people_array.json
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/streaming/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/streaming/text-test.txt
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/text-test.txt
spark-2.3.3-bin-hadoop2.7/python/test_support/userlib-0.1.zip
spark-2.3.3-bin-hadoop2.7/python/test_support/userlibrary.py
spark-2.3.3-bin-hadoop2.7/R/
spark-2.3.3-bin-hadoop2.7/R/lib/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/DESCRIPTION
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/index.html
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/sparkr-vignettes.html
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/sparkr-vignettes.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/sparkr-vignettes.Rmd
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/aliases.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/AnIndex
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/paths.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdb
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdx
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/html/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/html/00Index.html
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/html/R.css
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/INDEX
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/features.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/hsearch.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/links.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/nsInfo.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/package.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/Rd.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/vignette.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/NAMESPACE
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/profile/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/profile/general.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/profile/shell.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/SparkR
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdb
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdx
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/tests/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/tests/testthat/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/tests/testthat/test_basic.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/worker/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/worker/daemon.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/worker/worker.R
spark-2.3.3-bin-hadoop2.7/R/lib/sparkr.zip
spark-2.3.3-bin-hadoop2.7/README.md
spark-2.3.3-bin-hadoop2.7/RELEASE
spark-2.3.3-bin-hadoop2.7/sbin/
spark-2.3.3-bin-hadoop2.7/sbin/slaves.sh
spark-2.3.3-bin-hadoop2.7/sbin/spark-config.sh
spark-2.3.3-bin-hadoop2.7/sbin/spark-daemon.sh
spark-2.3.3-bin-hadoop2.7/sbin/spark-daemons.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-all.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-history-server.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-master.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-mesos-dispatcher.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-mesos-shuffle-service.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-shuffle-service.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-slave.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-slaves.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-thriftserver.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-all.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-history-server.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-master.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-mesos-dispatcher.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-mesos-shuffle-service.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-shuffle-service.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-slave.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-slaves.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-thriftserver.sh
spark-2.3.3-bin-hadoop2.7/yarn/
spark-2.3.3-bin-hadoop2.7/yarn/spark-2.3.3-yarn-shuffle.jar
+ export SPARK_HOME=/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7
+ SPARK_HOME=/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7
ls -1 "${SPARK_HOME}/python/lib" | grep py4j
++ ls -1 /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python/lib
++ grep py4j
+ PY4J_ZIP=py4j-0.10.7-src.zip
+ export PYTHONPATH=/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python:/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip:
+ PYTHONPATH=/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python:/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip:
+ ASSEMBLY_DIR=/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target
ls -1 "$ASSEMBLY_DIR" | grep "^mango-assembly[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true
++ ls -1 /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target
++ grep '^mango-assembly[0-9A-Za-z\_\.-]*\.jar$'
++ grep -v javadoc
++ grep -v sources
+ ASSEMBLY_JAR=mango-assembly-0.0.3-SNAPSHOT.jar
+ export 'PYSPARK_SUBMIT_ARGS=--jars /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar --driver-class-path /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar pyspark-shell'
+ PYSPARK_SUBMIT_ARGS='--jars /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar --driver-class-path /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar pyspark-shell'
+ pythons=(2.7 3.6)
+ for python in '${pythons[*]}'
uuidgen
++ uuidgen
+ uuid=129ba419-7f8e-494a-82f0-32306f465bed
+ conda create -y -q -n mango-build-129ba419-7f8e-494a-82f0-32306f465bed python=2.7


Package plan for installation in environment /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed:

The following NEW packages will be INSTALLED:

    ca-certificates: 2019.1.23-0            
    certifi:         2019.3.9-py27_0        
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       8.2.0-hdf63c60_1       
    libstdcxx-ng:    8.2.0-hdf63c60_1       
    ncurses:         6.1-he6710b0_1         
    openssl:         1.1.1b-h7b6447c_1      
    pip:             19.1.1-py27_0          
    python:          2.7.16-h9bab390_0      
    readline:        7.0-h7b6447c_5         
    setuptools:      41.0.1-py27_0          
    sqlite:          3.28.0-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.2-py27_0          
    zlib:            1.2.11-h7b6447c_3      


+ source activate mango-build-129ba419-7f8e-494a-82f0-32306f465bed
#!/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-129ba419-7f8e-494a-82f0-32306f465bed

"$_CONDA_DIR/conda" ..checkenv $_SHELL$EXT "$args"
++ /home/anaconda/bin/conda ..checkenv bash mango-build-129ba419-7f8e-494a-82f0-32306f465bed
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-129ba419-7f8e-494a-82f0-32306f465bed
+++ 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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/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-129ba419-7f8e-494a-82f0-32306f465bed
++ _NEW_PART=/home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/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-129ba419-7f8e-494a-82f0-32306f465bed/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-129ba419-7f8e-494a-82f0-32306f465bed/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-129ba419-7f8e-494a-82f0-32306f465bed
++ CONDA_DEFAULT_ENV=mango-build-129ba419-7f8e-494a-82f0-32306f465bed
++ firstpath=/home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/bin
echo ${firstpath} | sed "s|/bin$||"
+++ echo /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed
"$_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-129ba419-7f8e-494a-82f0-32306f465bed) '
++ PS1='(mango-build-129ba419-7f8e-494a-82f0-32306f465bed) '
++ _CONDA_D=/home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/etc/conda/activate.d
++ [[ -d /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/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-129ba419-7f8e-494a-82f0-32306f465bed:

The following NEW packages will be INSTALLED:

    nodejs: 10.13.0-he6710b0_0

+ pushd mango-python
/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ make prepare
pip install pytest==3.9.1
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
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 atomicwrites>=1.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/52/90/6155aa926f43f2b2a22b01be7241be3bfd1ceaf7d0b3267213e8127d41f4/atomicwrites-1.3.0-py2.py3-none-any.whl
Collecting more-itertools>=4.0.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/2f/9d/dcfe59e213093695f108508af1214cf9cd95cc5489e46877ec5cb56369e5/more_itertools-5.0.0-py2-none-any.whl
Collecting pluggy>=0.7 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/cc/e4/2003a5e4e445424602c8f06a436eeed9e78bcae4947128f64741c66c7216/pluggy-0.11.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from pytest==3.9.1) (41.0.1)
Collecting attrs>=17.4.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/23/96/d828354fa2dbdf216eaa7b7de0db692f12c234f7ef888cc14980ef40d1d2/attrs-19.1.0-py2.py3-none-any.whl
Collecting pathlib2>=2.2.0; python_version < "3.6" (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/2a/46/c696dcf1c7aad917b39b875acdc5451975e3a9b4890dca8329983201c97a/pathlib2-2.3.3-py2.py3-none-any.whl
Collecting py>=1.5.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/76/bc/394ad449851729244a97857ee14d7cba61ddb268dce3db538ba2f2ba1f0f/py-1.8.0-py2.py3-none-any.whl
Collecting six>=1.10.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting funcsigs; python_version < "3.0" (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting scandir; python_version < "3.5" (from pathlib2>=2.2.0; python_version < "3.6"->pytest==3.9.1)
Installing collected packages: atomicwrites, six, more-itertools, pluggy, attrs, scandir, pathlib2, py, funcsigs, pytest
Successfully installed atomicwrites-1.3.0 attrs-19.1.0 funcsigs-1.0.2 more-itertools-5.0.0 pathlib2-2.3.3 pluggy-0.11.0 py-1.8.0 pytest-3.9.1 scandir-1.10.0 six-1.12.0
# ipython version required for python 2.7
pip install jupyter_contrib_nbextensions
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
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 notebook>=4.0 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/f6/36/89ebfffc9dd8c8dbd81c1ffb53e3d4233ee666414c143959477cb07cc5f5/notebook-5.7.8-py2.py3-none-any.whl
Collecting traitlets>=4.1 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/93/d6/abcb22de61d78e2fc3959c964628a5771e47e7cc60d53e9342e21ed6cc9a/traitlets-4.3.2-py2.py3-none-any.whl
Collecting ipython-genutils (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl
Collecting nbconvert>=4.2 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/35/e7/f46c9d65f149271e47fca6ab084ef5c6e4cb1870f4c5cce6690feac55231/nbconvert-5.5.0-py2.py3-none-any.whl
Collecting pyyaml (from jupyter_contrib_nbextensions)
Collecting jupyter-nbextensions-configurator>=0.4.0 (from jupyter_contrib_nbextensions)
Collecting jupyter-latex-envs>=1.3.8 (from jupyter_contrib_nbextensions)
Collecting jupyter-core (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/1d/44/065d2d7bae7bebc06f1dd70d23c36da8c50c0f08b4236716743d706762a8/jupyter_core-4.4.0-py2.py3-none-any.whl
Collecting lxml (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/89/51/a8a6cdb8a084d32dbc9bda94623dc35310ae2002be57de8702a1703c0026/lxml-4.3.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting tornado (from jupyter_contrib_nbextensions)
Collecting jupyter-contrib-core>=0.3.3 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/e6/8f/04a752a8b66a66e7092c035e5d87d2502ac7ec07f9fb6059059b6c0dc272/jupyter_contrib_core-0.3.3-py2.py3-none-any.whl
Collecting jupyter-highlight-selected-word>=0.1.1 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/50/d7/19ab7cfd60bf268d2abbacc52d4295a40f52d74dfc0d938e4761ee5e598b/jupyter_highlight_selected_word-0.2.0-py2.py3-none-any.whl
Collecting jupyter-client>=5.2.0 (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/3b/c3/3043fe9ffd140d03c9d091a056794ccdc427c56ec19b8eea74f9ea0a498f/jupyter_client-5.2.4-py2.py3-none-any.whl
Collecting nbformat (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/da/27/9a654d2b6cc1eaa517d1c5a4405166c7f6d72f04f6e7eea41855fe808a46/nbformat-4.4.0-py2.py3-none-any.whl
Collecting prometheus-client (from notebook>=4.0->jupyter_contrib_nbextensions)
Collecting Send2Trash (from notebook>=4.0->jupyter_contrib_nbextensions)
Collecting pyzmq>=17 (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/91/f5/c9bef3768d6f8d71aae8f44f1ddbee90162dad909560fa6c13e4872e28c9/pyzmq-18.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting jinja2 (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl
Collecting terminado>=0.8.1 (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/a7/56/80ea7fa66565fa75ae21ce0c16bc90067530e5d15e48854afcc86585a391/terminado-0.8.2-py2.py3-none-any.whl
Collecting ipykernel (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/00/47/764e4fa1b1b89598426b8d79b1c4fbe8042432621b0f8e1991aeb3c24806/ipykernel-4.10.0-py2-none-any.whl
Collecting ipaddress; python_version == "2.7" (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting enum34; python_version == "2.7" (from traitlets>=4.1->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Requirement already satisfied: six in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from traitlets>=4.1->jupyter_contrib_nbextensions) (1.12.0)
Collecting decorator (from traitlets>=4.1->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl
Collecting entrypoints>=0.2.2 (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl
Collecting pygments (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/6e/00/c5cb5fc7c047da4af049005d0146b3a961b1a25d9cefbbe24bf0882a11ad/Pygments-2.4.0-py2.py3-none-any.whl
Collecting bleach (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/ab/05/27e1466475e816d3001efb6e0a85a819be17411420494a1e602c36f8299d/bleach-3.1.0-py2.py3-none-any.whl
Collecting testpath (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/be/a4/162f9ebb6489421fe46dcca2ae420369edfee4b563c668d93cb4605d12ba/testpath-0.4.2-py2.py3-none-any.whl
Collecting defusedxml (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/06/74/9b387472866358ebc08732de3da6dc48e44b0aacd2ddaa5cb85ab7e986a2/defusedxml-0.6.0-py2.py3-none-any.whl
Collecting mistune>=0.8.1 (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl
Collecting pandocfilters>=1.4.1 (from nbconvert>=4.2->jupyter_contrib_nbextensions)
Collecting ipython (from jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/b0/88/d996ab8be22cea1eaa18baee3678a11265e18cf09974728d683c51102148/ipython-5.8.0-py2-none-any.whl
Collecting futures (from tornado->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/2d/99/b2c4e9d5a30f6471e410a146232b4118e697fa3ffc06d6a65efde84debd0/futures-3.2.0-py2-none-any.whl
Collecting singledispatch (from tornado->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/c5/10/369f50bcd4621b263927b0a1519987a04383d4a98fb10438042ad410cf88/singledispatch-3.4.0.3-py2.py3-none-any.whl
Collecting backports-abc>=0.4 (from tornado->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/7d/56/6f3ac1b816d0cd8994e83d0c4e55bc64567532f7dc543378bd87f81cebc7/backports_abc-0.5-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jupyter-contrib-core>=0.3.3->jupyter_contrib_nbextensions) (41.0.1)
Collecting python-dateutil>=2.1 (from jupyter-client>=5.2.0->notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl
Collecting jsonschema!=2.5.0,>=2.4 (from nbformat->notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/aa/69/df679dfbdd051568b53c38ec8152a3ab6bc533434fc7ed11ab034bf5e82f/jsonschema-3.0.1-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from jinja2->notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/fb/40/f3adb7cf24a8012813c5edb20329eb22d5d8e2a0ecf73d21d6b85865da11/MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ptyprocess; os_name != "nt" (from terminado>=0.8.1->notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl
Collecting configparser>=3.5; python_version == "2.7" (from entrypoints>=0.2.2->nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/ba/05/6c96328e92e625fc31445d24d75a2c92ef9ba34fc5b037fe69693c362a0d/configparser-3.7.4-py2.py3-none-any.whl
Collecting webencodings (from bleach->nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (2.3.3)
Collecting backports.shutil-get-terminal-size; python_version == "2.7" (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/7d/cd/1750d6c35fe86d35f8562091737907f234b78fdffab42b29c72b1dd861f4/backports.shutil_get_terminal_size-1.0.0-py2.py3-none-any.whl
Collecting simplegeneric>0.8 (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
Collecting pexpect; sys_platform != "win32" (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/0e/3e/377007e3f36ec42f1b84ec322ee12141a9e10d808312e5738f52f80a232c/pexpect-4.7.0-py2.py3-none-any.whl
Collecting prompt-toolkit<2.0.0,>=1.0.4 (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/4e/4e/e5545e8bebf89790455b31112a0f886580c7b3624a05abec416efa5c3a08/prompt_toolkit-1.0.16-py2-none-any.whl
Collecting pickleshare (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl
Collecting functools32; python_version < "3" (from jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions)
Collecting pyrsistent>=0.14.0 (from jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions) (19.1.0)
Requirement already satisfied: scandir; python_version < "3.5" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (1.10.0)
Collecting wcwidth (from prompt-toolkit<2.0.0,>=1.0.4->ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl
Installing collected packages: python-dateutil, enum34, ipython-genutils, decorator, traitlets, pyzmq, jupyter-core, futures, singledispatch, backports-abc, tornado, jupyter-client, functools32, pyrsistent, jsonschema, nbformat, configparser, entrypoints, MarkupSafe, jinja2, pygments, webencodings, bleach, testpath, defusedxml, mistune, pandocfilters, nbconvert, prometheus-client, Send2Trash, ptyprocess, terminado, backports.shutil-get-terminal-size, simplegeneric, pexpect, wcwidth, prompt-toolkit, pickleshare, ipython, ipykernel, ipaddress, notebook, pyyaml, jupyter-contrib-core, jupyter-nbextensions-configurator, jupyter-latex-envs, lxml, jupyter-highlight-selected-word, jupyter-contrib-nbextensions
Successfully installed MarkupSafe-1.1.1 Send2Trash-1.5.0 backports-abc-0.5 backports.shutil-get-terminal-size-1.0.0 bleach-3.1.0 configparser-3.7.4 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 enum34-1.1.6 functools32-3.2.3.post2 futures-3.2.0 ipaddress-1.0.22 ipykernel-4.10.0 ipython-5.8.0 ipython-genutils-0.2.0 jinja2-2.10.1 jsonschema-3.0.1 jupyter-client-5.2.4 jupyter-contrib-core-0.3.3 jupyter-contrib-nbextensions-0.5.1 jupyter-core-4.4.0 jupyter-highlight-selected-word-0.2.0 jupyter-latex-envs-1.4.6 jupyter-nbextensions-configurator-0.4.1 lxml-4.3.3 mistune-0.8.4 nbconvert-5.5.0 nbformat-4.4.0 notebook-5.7.8 pandocfilters-1.4.2 pexpect-4.7.0 pickleshare-0.7.5 prometheus-client-0.6.0 prompt-toolkit-1.0.16 ptyprocess-0.6.0 pygments-2.4.0 pyrsistent-0.15.1 python-dateutil-2.8.0 pyyaml-5.1 pyzmq-18.0.1 simplegeneric-0.8.1 singledispatch-3.4.0.3 terminado-0.8.2 testpath-0.4.2 tornado-5.1.1 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1
pip install -r requirements.txt
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting cigar==0.1.3 (from -r requirements.txt (line 1))
Collecting matplotlib==2.0.2 (from -r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/2c/69/362c0a5eca37225c7d451e6c57f07c4fee85a5b6cb3aedf16fe649f411ea/matplotlib-2.0.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ipython==5.5.0 (from -r requirements.txt (line 3))
  Using cached https://files.pythonhosted.org/packages/08/2c/6285504003b4eadce5540f3ee3adc081468b26723f3eef07d9d5d7d97ed8/ipython-5.5.0-py2-none-any.whl
Collecting jupyter==1.0.0 (from -r requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl
Collecting bdgenomics.mango.pileup==0.0.2a0 (from -r requirements.txt (line 5))
Collecting bdgenomics.adam==0.26.0 (from -r requirements.txt (line 6))
Collecting ipywidgets==7.0.0 (from -r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/14/ea/793f6588d5be295d103fb868e26ba8671686b70bd855a21d02302f8dcd37/ipywidgets-7.0.0-py2.py3-none-any.whl
Collecting psutil (from -r requirements.txt (line 8))
Collecting subprocess32 (from matplotlib==2.0.2->-r requirements.txt (line 2))
Collecting cycler>=0.10 (from matplotlib==2.0.2->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Requirement already satisfied: functools32 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (3.2.3.post2)
Requirement already satisfied: six>=1.10 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.12.0)
Collecting pytz (from matplotlib==2.0.2->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib==2.0.2->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/dd/d9/3ec19e966301a6e25769976999bd7bbe552016f0d32b577dc9d63d2e0c49/pyparsing-2.4.0-py2.py3-none-any.whl
Collecting numpy>=1.7.1 (from matplotlib==2.0.2->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/e1/72/179a78b565ecf01fe98dab6417581d30acac15c2d93c49f93169ebea99b1/numpy-1.16.3-cp27-cp27mu-manylinux1_x86_64.whl
Requirement already satisfied: python-dateutil in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.8.0)
Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (2.3.3)
Requirement already satisfied: backports.shutil-get-terminal-size; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (1.0.0)
Requirement already satisfied: simplegeneric>0.8 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (0.8.1)
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (2.4.0)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (4.7.0)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (41.0.1)
Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (1.0.16)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (0.7.5)
Requirement already satisfied: traitlets>=4.2 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (4.3.2)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (4.4.0)
Collecting qtconsole (from jupyter==1.0.0->-r requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/c7/45/1a50288305797fbca7c2039f9baefff1a9df603322874743fbb8408d8ec2/qtconsole-4.4.4-py2.py3-none-any.whl
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.7.8)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.5.0)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (4.10.0)
Collecting jupyter-console (from jupyter==1.0.0->-r requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/77/82/6469cd7fccf7958cbe5dce2e623f1e3c5e27f1bb1ad36d90519bc2d5d370/jupyter_console-5.2.0-py2.py3-none-any.whl
Requirement already satisfied: pyspark>=1.6.0 in /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python (from bdgenomics.adam==0.26.0->-r requirements.txt (line 6)) (2.3.3)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 7)) (4.4.0)
Collecting widgetsnbextension~=3.0.0 (from ipywidgets==7.0.0->-r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/8d/f2/c8bcccccbed39d51d3e237fb0c0f0c9bbc845d12afc41f5ca5f5728fffc7/widgetsnbextension-3.0.8-py2.py3-none-any.whl
Requirement already satisfied: scandir; python_version < "3.5" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython==5.5.0->-r requirements.txt (line 3)) (1.10.0)
Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from pexpect; sys_platform != "win32"->ipython==5.5.0->-r requirements.txt (line 3)) (0.6.0)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython==5.5.0->-r requirements.txt (line 3)) (0.1.7)
Requirement already satisfied: enum34; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->-r requirements.txt (line 3)) (1.1.6)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->-r requirements.txt (line 3)) (0.2.0)
Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (4.4.0)
Requirement already satisfied: jupyter-client>=4.1 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (5.2.4)
Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.2)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.5.0)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (18.0.1)
Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (2.10.1)
Requirement already satisfied: tornado<7,>=4.1 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (5.1.1)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.6.0)
Requirement already satisfied: ipaddress; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.0.22)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.3)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.4.2)
Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.1.0)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.4.2)
Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.6.0)
Requirement already satisfied: mistune>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.4)
Collecting py4j==0.10.7 (from pyspark>=1.6.0->bdgenomics.adam==0.26.0->-r requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/e3/53/c737818eb9a7dc32a7cd4f1396e787bd94200c3997c72c1dbe028587bd76/py4j-0.10.7-py2.py3-none-any.whl
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (3.0.1)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jinja2->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.1.1)
Requirement already satisfied: futures in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (3.2.0)
Requirement already satisfied: singledispatch in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (3.4.0.3)
Requirement already satisfied: backports-abc>=0.4 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5)
Requirement already satisfied: configparser>=3.5; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from entrypoints>=0.2.2->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.7.4)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5.1)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (0.15.1)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (19.1.0)
Installing collected packages: cigar, subprocess32, cycler, pytz, pyparsing, numpy, matplotlib, ipython, qtconsole, widgetsnbextension, ipywidgets, jupyter-console, jupyter, bdgenomics.mango.pileup, bdgenomics.adam, psutil, py4j
  Found existing installation: ipython 5.8.0
    Uninstalling ipython-5.8.0:
      Successfully uninstalled ipython-5.8.0
Successfully installed bdgenomics.adam-0.26.0 bdgenomics.mango.pileup-0.0.2a0 cigar-0.1.3 cycler-0.10.0 ipython-5.5.0 ipywidgets-7.0.0 jupyter-1.0.0 jupyter-console-5.2.0 matplotlib-2.0.2 numpy-1.16.3 psutil-5.6.2 py4j-0.10.7 pyparsing-2.4.0 pytz-2019.1 qtconsole-4.4.4 subprocess32-3.5.3 widgetsnbextension-3.0.8
+ popd
/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ mvn -U -P python,distribution package -DskipTests -Dhadoop.version=2.7.5 -Dspark.version=2.3.3
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-python:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-python:[unknown-version], /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-python/pom.xml, line 21, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-cli:[unknown-version], /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-cli/pom.xml, line 39, column 15
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango
[INFO] mango: CORE
[INFO] Mango: Python APIs
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO] mango: Distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.3-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 144 of 226 .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-shade-plugin:3.1.0:shade (default) @ mango-parent ---
[INFO] Replacing original artifact with shaded artifact.
[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 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/repositories/snapshots/commons-codec/commons-codec/maven-metadata.xml
Downloading: https://repository.apache.org/snapshots/commons-codec/commons-codec/maven-metadata.xml
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Downloaded: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml (672 B at 2.1 KB/sec)
            
            
[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/mangoTestY2ahf2b/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:3.0.1:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/scala-2.11.12/classes at 1557525825754
[WARNING] /tmp/mangoTestY2ahf2b/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/mangoTestY2ahf2b/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/mangoTestY2ahf2b/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/mangoTestY2ahf2b/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/mangoTestY2ahf2b/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:3.5.1: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/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 20 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala:-1: info: compiling
[INFO] Compiling 13 source files to /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/scala-2.11.12/test-classes at 1557525836860
[WARNING] /tmp/mangoTestY2ahf2b/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 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-core ---
[INFO] Building jar: /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-core ---
[INFO] Including com.github.samtools:htsjdk:jar:2.16.1 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 org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 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 org.scala-lang:scala-compiler: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.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.curator:curator-client:jar:2.7.1 in the shaded jar.
[INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar.
[INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 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 commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar.
[INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar.
[INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar.
[INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar.
[INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar.
[INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar.
[INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar.
[INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar.
[INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar.
[INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar.
[INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar.
[INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar.
[INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar.
[INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar.
[INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar.
[INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar.
[INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar.
[INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar.
[INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar.
[INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar.
[INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar.
[INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar.
[INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar.
[INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar.
[INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar.
[INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar.
[INFO] Including oro:oro:jar:2.0.8 in the shaded jar.
[INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar.
[INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar.
[INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 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.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 org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 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:0.26.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.2 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:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.1 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.
[WARNING] minlog-1.3.0.jar, minlog-1.2.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[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] aopalliance-1.0.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: 
[WARNING]   - org.aopalliance.intercept.ConstructorInterceptor
[WARNING]   - org.aopalliance.intercept.MethodInvocation
[WARNING]   - org.aopalliance.intercept.MethodInterceptor
[WARNING]   - org.aopalliance.intercept.Invocation
[WARNING]   - org.aopalliance.aop.AspectException
[WARNING]   - org.aopalliance.intercept.Interceptor
[WARNING]   - org.aopalliance.intercept.Joinpoint
[WARNING]   - org.aopalliance.aop.Advice
[WARNING]   - org.aopalliance.intercept.ConstructorInvocation
[WARNING] javax.inject-2.4.0-b34.jar, javax.inject-1.jar define 6 overlapping classes: 
[WARNING]   - javax.inject.Inject
[WARNING]   - javax.inject.Singleton
[WARNING]   - javax.inject.Named
[WARNING]   - javax.inject.Scope
[WARNING]   - javax.inject.Provider
[WARNING]   - javax.inject.Qualifier
[WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, spark-tags_2.11-2.3.3.jar, spark-launcher_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, spark-kvstore_2.11-2.3.3.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: 
[WARNING]   - org.apache.spark.unused.UnusedStubClass
[WARNING] commons-logging-1.1.1.jar, jcl-over-slf4j-1.7.16.jar define 6 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING]   - org.apache.commons.logging.Log
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING] kryo-shaded-3.0.3.jar, kryo-2.24.0.jar define 193 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.BeanSerializer$1
[WARNING]   - com.esotericsoftware.kryo.Registration
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.kryo.util.IntMap$Values
[WARNING]   - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl
[WARNING]   - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField
[WARNING]   - com.esotericsoftware.kryo.serializers.JavaSerializer
[WARNING]   - 183 more...
[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/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar with /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT-shaded.jar
[INFO] Dependency-reduced POM written at: /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/dependency-reduced-pom.xml
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core ---
[INFO] Building jar: /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-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/mangoTestY2ahf2b/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 ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[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/mangoTestY2ahf2b/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/mangoTestY2ahf2b/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/mangoTestY2ahf2b/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/mangoTestY2ahf2b/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/mangoTestY2ahf2b/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/mangoTestY2ahf2b/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/${GENOME}/database/refGene.txt.gz
                                                                                     ^
/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                  ^
/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                                    ^
/tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:51: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz
                                                                                   ^
/tmp/mangoTestY2ahf2b/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/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Python APIs 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml
741/741 B   
            
Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml (741 B at 65.8 KB/sec)
[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:3.0.1:resources (default-resources) @ mango-python ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestY2ahf2b/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 .
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Obtaining file:///tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-python
Requirement already satisfied: cigar==0.1.3 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (0.1.3)
Requirement already satisfied: matplotlib==2.0.2 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (2.0.2)
Requirement already satisfied: ipython==5.5.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (5.5.0)
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (1.0.0)
Requirement already satisfied: bdgenomics.mango.pileup==0.0.2a0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (0.0.2a0)
Requirement already satisfied: bdgenomics.adam==0.26.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (0.26.0)
Requirement already satisfied: ipywidgets==7.0.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (7.0.0)
Requirement already satisfied: psutil in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (5.6.2)
Requirement already satisfied: subprocess32 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (3.5.3)
Requirement already satisfied: cycler>=0.10 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (0.10.0)
Requirement already satisfied: functools32 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (3.2.3.post2)
Requirement already satisfied: six>=1.10 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (1.12.0)
Requirement already satisfied: pytz in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (2019.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (2.4.0)
Requirement already satisfied: numpy>=1.7.1 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (1.16.3)
Requirement already satisfied: python-dateutil in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (2.8.0)
Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (2.3.3)
Requirement already satisfied: backports.shutil-get-terminal-size; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.0.0)
Requirement already satisfied: simplegeneric>0.8 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.8.1)
Requirement already satisfied: traitlets>=4.2 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (4.3.2)
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (2.4.0)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (4.7.0)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (41.0.1)
Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.0.16)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.7.5)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (4.4.0)
Requirement already satisfied: qtconsole in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (4.4.4)
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.7.8)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.5.0)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (4.10.0)
Requirement already satisfied: jupyter-console in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.2.0)
Requirement already satisfied: pyspark>=1.6.0 in /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python (from bdgenomics.adam==0.26.0->bdgenomics.mango==0.0.3a0) (2.3.3)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (4.4.0)
Requirement already satisfied: widgetsnbextension~=3.0.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (3.0.8)
Requirement already satisfied: scandir; python_version < "3.5" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.10.0)
Requirement already satisfied: enum34; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.1.6)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.2.0)
Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from pexpect; sys_platform != "win32"->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.6.0)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.1.7)
Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (4.4.0)
Requirement already satisfied: jupyter-client>=4.1 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.2.4)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.6.0)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (1.5.0)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (18.0.1)
Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (2.10.1)
Requirement already satisfied: tornado<7,>=4.1 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.1.1)
Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.8.2)
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Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.5.1)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (0.15.1)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (19.1.0)
Installing collected packages: bdgenomics.mango
  Found existing installation: bdgenomics.mango 0.0.3a0
    Can't uninstall 'bdgenomics.mango'. No files were found to uninstall.
  Running setup.py develop for bdgenomics.mango
Successfully installed bdgenomics.mango
python setup.py sdist bdist_egg
Could not import pypandoc - required to package bdgenomics.mango
running sdist
running egg_info
writing requirements to bdgenomics.mango.egg-info/requires.txt
writing bdgenomics.mango.egg-info/PKG-INFO
writing top-level names to bdgenomics.mango.egg-info/top_level.txt
writing dependency_links to bdgenomics.mango.egg-info/dependency_links.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-0.0.3a0
creating bdgenomics.mango-0.0.3a0/bdgenomics
creating bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
creating bdgenomics.mango-0.0.3a0/bdgenomics/mango
creating bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying files to bdgenomics.mango-0.0.3a0...
copying MANIFEST.in -> bdgenomics.mango-0.0.3a0
copying README.md -> bdgenomics.mango-0.0.3a0
copying requirements.txt -> bdgenomics.mango-0.0.3a0
copying setup.py -> bdgenomics.mango-0.0.3a0
copying version.py -> bdgenomics.mango-0.0.3a0
copying bdgenomics/__init__.py -> bdgenomics.mango-0.0.3a0/bdgenomics
copying bdgenomics.mango.egg-info/PKG-INFO -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/SOURCES.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/dependency_links.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/requires.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/top_level.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics/mango/__init__.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/alignments.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/coverage.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/distribution.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/features.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/genotypes.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/utils.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/variants.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/test/__init__.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/alignment_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/coverage_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/distribution_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/feature_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/genotypes_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/notebook_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/variant_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
Writing bdgenomics.mango-0.0.3a0/setup.cfg
creating dist
Creating tar archive
removing 'bdgenomics.mango-0.0.3a0' (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/alignments.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/variants.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/distribution.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/coverage.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/utils.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/genotypes.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/features.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/__init__.py -> build/lib/bdgenomics/mango
creating build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/genotypes_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/notebook_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/variant_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/alignment_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/coverage_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/__init__.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
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/alignments.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/genotypes_test.py -> 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/variant_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/alignment_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/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/variants.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/mango/coverage.py -> 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/genotypes.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/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
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byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/alignment_test.py to alignment_test.pyc
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byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/__init__.py to __init__.pyc
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byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/genotypes.py to genotypes.pyc
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byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/__init__.py to __init__.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
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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.__init__: module references __path__
bdgenomics.mango.__init__: module references __path__
creating 'dist/bdgenomics.mango-0.0.3a0-py2.7.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:3.5.1:compile (default-compile) @ mango-python ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-python ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestY2ahf2b/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/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/example-files/notebooks /tmp/mangoTestY2ahf2b/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 1661 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
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux2 -- Python 2.7.16, pytest-3.9.1, py-1.8.0, pluggy-0.11.0 -- /home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/bin/python
cachedir: .pytest_cache
rootdir: /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-python, inifile:
collecting ... collected 24 items

bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_coverage_distribution PASSED [  4%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_fragment_distribution PASSED [  8%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution PASSED [ 12%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_maximal_bin_size PASSED [ 16%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_no_elements PASSED [ 20%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_mapq_distribution PASSED [ 25%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_visualize_alignments PASSED [ 29%]
bdgenomics/mango/test/coverage_test.py::CoverageTest::test_coverage_distribution PASSED [ 33%]
bdgenomics/mango/test/coverage_test.py::CoverageTest::test_example_coverage PASSED [ 37%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_cumulative_count_distribution PASSED [ 41%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_fail_on_invalid_sample PASSED [ 45%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_normalized_count_distribution PASSED [ 50%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_sampling PASSED [ 54%]
bdgenomics/mango/test/feature_test.py::FeatureTest::test_visualize_features PASSED [ 58%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeCallRatesDistribution PASSED [ 62%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeSummary PASSED [ 66%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_HetHomRatioDistribution PASSED [ 70%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistribution PASSED [ 75%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistributionSampling FAILED [ 79%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_alignment_example PASSED [ 83%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_coverage_example PASSED [ 87%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_example PASSED [ 91%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_variants_example PASSED [ 95%]
bdgenomics/mango/test/variant_test.py::VariantTest::test_visualize_variants PASSED [100%]

=================================== FAILURES ===================================
___________ GenotypesTest.test_VariantsPerSampleDistributionSampling ___________

self = <bdgenomics.mango.test.genotypes_test.GenotypesTest testMethod=test_VariantsPerSampleDistributionSampling>

    def test_VariantsPerSampleDistributionSampling(self):
        ac = ADAMContext(self.ss)
        testFile = self.resourceFile("genodata.v3.test.vcf")
    
        genotypes = ac.loadGenotypes(testFile)
        _, data = VariantsPerSampleDistribution(self.ss, genotypes, sample=0.9).plotDistributions(testMode= True)
    
        expected = [6, 8, 8, 1, 7, 8]
    
        # estimated counts should be around real counts
        dev = 8
>       assert(sum(expected) > sum(data) - dev and sum(expected) < sum(data) + dev)
E       AssertionError: assert (38 > (30 - 8) and 38 < (30 + 8))
E        +  where 38 = sum([6, 8, 8, 1, 7, 8])
E        +  and   30 = sum([6, 8, 5, 5, 6])
E        +  and   38 = sum([6, 8, 8, 1, 7, 8])
E        +  and   30 = sum([6, 8, 5, 5, 6])

bdgenomics/mango/test/genotypes_test.py:49: AssertionError
----------------------------- Captured stderr call -----------------------------

[Stage 0:>                                                          (0 + 1) / 1]
                                                                                
- generated xml file: /tmp/mangoTestY2ahf2b/deleteMePleaseThisIsNoLongerNeeded/mango-python/target/pytest-reports/tests.xml -
=============================== warnings summary ===============================
/home/jenkins/anaconda2/envs/mango-build-129ba419-7f8e-494a-82f0-32306f465bed/lib/python2.7/site-packages/ipywidgets/widgets/widget.py:287: DeprecationWarning: Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator.
  warnings.warn("Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator.", DeprecationWarning)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
=============== 1 failed, 23 passed, 1 warnings in 90.81 seconds ===============
Makefile:82: recipe for target 'test' failed
make: *** [test] Error 1
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 2 (Exit value: 2)
	at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
	at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:804)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:751)
	at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:313)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  4.932 s]
[INFO] mango: CORE ........................................ SUCCESS [01:03 min]
[INFO] Mango: Python APIs ................................. FAILURE [01:38 min]
[INFO] mango: CLI ......................................... SKIPPED
[INFO] Mango: Assembly .................................... SKIPPED
[INFO] mango: Distribution ................................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:47 min
[INFO] Finished at: 2019-05-10T15:06:22-07:00
[INFO] Final Memory: 52M/1509M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:exec (test-python) on project mango-python: Command execution failed. Process exited with an error: 2 (Exit value: 2) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :mango-python
Build step 'Execute shell' marked build as failure
Finished: FAILURE