FailedConsole Output

Started by upstream project "mango-prb" build number 835
originally caused by:
 GitHub pull request #494 of commit 88fa02ddabeb8a52c0fe83db18f141e14c482b20 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on research-jenkins-worker-08 (ubuntu research-08) 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 947143833269f805a6056320b28b14c521f11375 (origin/pr/494/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 947143833269f805a6056320b28b14c521f11375
 > git rev-list 1edf11fb172c57fbbe2f4178da4596eed4d18027 # timeout=10
First time build. Skipping changelog.
[ubuntu] $ /bin/bash /tmp/hudson327576552624740652.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/mangoTestMvnUnptd5V

# 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/mangoTestMvnUnptd5V: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
++ tail -1
++ sed 's/ *<version>//g'
++ 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 [  0.236 s]
[INFO] mango: CORE ........................................ SUCCESS [  0.064 s]
[INFO] mango: CLI ......................................... SUCCESS [  0.386 s]
[INFO] Mango: Assembly .................................... SUCCESS [  0.042 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.931 s
[INFO] Finished at: 2019-05-13T17:53:28-07:00
[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 1 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://repository.apache.org/snapshots/commons-codec/commons-codec/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/repositories/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 1557795217879
[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 17 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 1557795237233
[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.
*** RUN ABORTED ***
  java.lang.RuntimeException: Unable to load a Suite class that was discovered in the runpath: org.bdgenomics.mango.io.VcfReaderSuite
  at org.scalatest.tools.DiscoverySuite$.getSuiteInstance(DiscoverySuite.scala:84)
  at org.scalatest.tools.DiscoverySuite$$anonfun$1.apply(DiscoverySuite.scala:38)
  at org.scalatest.tools.DiscoverySuite$$anonfun$1.apply(DiscoverySuite.scala:37)
  at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
  at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
  at scala.collection.Iterator$class.foreach(Iterator.scala:891)
  at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
  at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
  at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
  at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
  at scala.collection.AbstractTraversable.map(Traversable.scala:104)
  at org.scalatest.tools.DiscoverySuite.<init>(DiscoverySuite.scala:37)
  at org.scalatest.tools.Runner$.genDiscoSuites$1(Runner.scala:2390)
  at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2475)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
  at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
  at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
  Cause: java.lang.NullPointerException:
  at org.bdgenomics.mango.util.MangoFunSuite$class.resourcePath(MangoFunSuite.scala:37)
  at org.bdgenomics.mango.io.VcfReaderSuite.resourcePath(VcfReaderSuite.scala:26)
  at org.bdgenomics.mango.io.VcfReaderSuite.<init>(VcfReaderSuite.scala:34)
  at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
  at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
  at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
  at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
  at java.lang.Class.newInstance(Class.java:442)
  at org.scalatest.tools.DiscoverySuite$.getSuiteInstance(DiscoverySuite.scala:69)
  at org.scalatest.tools.DiscoverySuite$$anonfun$1.apply(DiscoverySuite.scala:38)
  at org.scalatest.tools.DiscoverySuite$$anonfun$1.apply(DiscoverySuite.scala:37)
  at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
  at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
  at scala.collection.Iterator$class.foreach(Iterator.scala:891)
  at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
  at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
  at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
  at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
  at scala.collection.AbstractTraversable.map(Traversable.scala:104)
  at org.scalatest.tools.DiscoverySuite.<init>(DiscoverySuite.scala:37)
  at org.scalatest.tools.Runner$.genDiscoSuites$1(Runner.scala:2390)
  at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2475)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
  at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
  at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Skipping mango
[INFO] This project has been banned from the build due to previous failures.
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  3.175 s]
[INFO] mango: CORE ........................................ FAILURE [ 33.426 s]
[INFO] mango: CLI ......................................... SKIPPED
[INFO] Mango: Assembly .................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 36.879 s
[INFO] Finished at: 2019-05-13T17:54:06-07:00
[INFO] Final Memory: 41M/1484M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.scalatest:scalatest-maven-plugin:1.0:test (test) on project mango-core: There are test failures -> [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/MojoFailureException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :mango-core
Build step 'Execute shell' marked build as failure
Finished: FAILURE