Console Output

Started by upstream project "bdg-utils-prb" build number 145
originally caused by:
 GitHub pull request #134 of commit 5f1474cd853aadcd564b59bdda1da2a97391ddc6 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-staging-worker-02 (ubuntu staging-02 staging) in workspace /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/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/utils.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/utils.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/bigdatagenomics/utils.git +refs/pull/*:refs/remotes/origin/pr/*
Checking out Revision 29043ec7bab98ff94dc851939fe8f867b4caad76 (origin/pr/134/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 29043ec7bab98ff94dc851939fe8f867b4caad76
 > git rev-list 8ac4c5fcdc8682fd2651a079a6781ac7577f74ca # timeout=10
[EnvInject] - Executing scripts and injecting environment variables after the SCM step.
[EnvInject] - Injecting as environment variables the properties content 
JAVA_HOME=/usr/lib/jvm/java-8-oracle

[EnvInject] - Variables injected successfully.
[ubuntu] $ /bin/bash /tmp/hudson9041039988282418504.sh
+ set -e
+ export JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ export PATH=/usr/lib/jvm/java-8-oracle/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/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
+ ./scripts/jenkins-test

# make a tempdir for writing maven cruft to
UTILS_MVN_TMP_DIR=$(mktemp -d -t utilsTestMvnXXXXXXX)
mktemp -d -t utilsTestMvnXXXXXXX
++ mktemp -d -t utilsTestMvnXXXXXXX
+ UTILS_MVN_TMP_DIR=/tmp/utilsTestMvnJm5otYY

# 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=${UTILS_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/utilsTestMvnJm5otYY: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/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/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 ${BASH_SOURCE[0]} 
+++ dirname ./scripts/jenkins-test
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/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/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.2.15-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 2.4.0 ]]

# is the scala version set?
if ! [[ ${SCALA_VERSION} ]];
then
    echo "SCALA_VERSION environment variable is not set."
    echo "Please set this variable before running."
    exit 1
fi
+ [[ -n 2.12 ]]

if [ ${SCALA_VERSION} == 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
+ '[' 2.12 == 2.11 ']'

if [ ${SCALA_VERSION} == 2.12 ];
then
    ./scripts/move_to_scala_2.12.sh
fi
+ '[' 2.12 == 2.12 ']'
+ ./scripts/move_to_scala_2.12.sh

# print versions
echo "Testing UTILS version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION} and Scala ${SCALA_VERSION}"
+ echo 'Testing UTILS version 0.2.15-SNAPSHOT on Spark 2.4.0 and Hadoop 2.7.5 and Scala 2.12'
Testing UTILS version 0.2.15-SNAPSHOT on Spark 2.4.0 and Hadoop 2.7.5 and Scala 2.12

# 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 134 ]]
+ COVERALLS_PRB_OPTION=-DpullRequest=134

# coveralls token should not be visible
set +x +v
+ set +x +v
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] utils
[INFO] utils-misc-spark2_2.12: Miscellaneous Spark utility code
[INFO] utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator
[INFO] utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs
[INFO] utils-io-spark2_2.12: I/O utils
[INFO] utils-statistics-spark2_2.12: Spark code for fitting statistical models
[INFO] utils-cli-spark2_2.12: utilities for building command line applications
[INFO] utils-serialization-spark2_2.12: tools for serializing data
[INFO] utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-parent-spark2_2.12 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-misc-spark2_2.12: Miscellaneous Spark utility code 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-misc-spark2_2.12 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-minhash-spark2_2.12 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-metrics-spark2_2.12 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-io-spark2_2.12: I/O utils 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-io-spark2_2.12 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-statistics-spark2_2.12: Spark code for fitting statistical models 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-statistics-spark2_2.12 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-cli-spark2_2.12: utilities for building command line applications 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-cli-spark2_2.12 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-serialization-spark2_2.12: tools for serializing data 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-serialization-spark2_2.12 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] utils .............................................. SUCCESS [  0.240 s]
[INFO] utils-misc-spark2_2.12: Miscellaneous Spark utility code SUCCESS [  0.024 s]
[INFO] utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator SUCCESS [  0.005 s]
[INFO] utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs SUCCESS [  0.010 s]
[INFO] utils-io-spark2_2.12: I/O utils .................... SUCCESS [  0.005 s]
[INFO] utils-statistics-spark2_2.12: Spark code for fitting statistical models SUCCESS [  0.005 s]
[INFO] utils-cli-spark2_2.12: utilities for building command line applications SUCCESS [  0.004 s]
[INFO] utils-serialization-spark2_2.12: tools for serializing data SUCCESS [  0.003 s]
[INFO] utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree SUCCESS [  0.005 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.565 s
[INFO] Finished at: 2019-03-21T09:44:08-07:00
[INFO] Final Memory: 22M/1472M
[INFO] ------------------------------------------------------------------------
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] utils
[INFO] utils-misc-spark2_2.12: Miscellaneous Spark utility code
[INFO] utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator
[INFO] utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs
[INFO] utils-io-spark2_2.12: I/O utils
[INFO] utils-statistics-spark2_2.12: Spark code for fitting statistical models
[INFO] utils-cli-spark2_2.12: utilities for building command line applications
[INFO] utils-serialization-spark2_2.12: tools for serializing data
[INFO] utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-parent-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-parent-spark2_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-parent-spark2_2.12 ---
[INFO] Modified 0 of 81 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-parent-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-parent-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-parent-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-parent-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-parent-spark2_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-parent-spark2_2.12 ---
[INFO] Modified 0 of 81 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-parent-spark2_2.12 ---
[INFO] Skipping SCoverage execution for project with packaging type 'pom'
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-parent-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-parent-spark2_2.12 ---
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-parent-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-parent-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-parent-spark2_2.12 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-misc-spark2_2.12: Miscellaneous Spark utility code 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-misc-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-misc-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-misc-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-misc-spark2_2.12 ---
[INFO] Modified 0 of 7 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-misc-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-misc-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/main/scala:-1: info: compiling
[INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/2.12.6/classes at 1553186656816
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-misc-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-misc-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-misc-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-misc-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/test/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/2.12.6/test-classes at 1553186662683
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-misc-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-misc-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-misc-spark2_2.12 ---
Discovery starting.
Discovery completed in 125 milliseconds.
Run starting. Expected test count is: 11
SparkFunSuiteSuite:
2019-03-21 09:44:29 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)
2019-03-21 09:44:29 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:44:30 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- a simple test using spark
- copying a resource should pass equivalence testing
- load a resource file
MathUtilsSuite:
- check equality with floating point comparison
- check inequality with floating point comparison
- compute factorials
- test array aggregation in isolation
- use array aggregator with an rdd
- safe wrapped log should work
- softmax an array
- multiply an array by a scalar
Run completed in 3 seconds, 721 milliseconds.
Total number of tests run: 11
Suites: completed 3, aborted 0
Tests: succeeded 11, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-misc-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-misc-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-misc-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-misc-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-misc-spark2_2.12 ---
[INFO] Modified 0 of 7 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-misc-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-misc-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-misc-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-misc-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-misc-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-misc-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-misc-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-misc-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-misc-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-misc-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-misc-spark2_2.12 ---
Discovery starting.
Discovery completed in 169 milliseconds.
Run starting. Expected test count is: 11
SparkFunSuiteSuite:
2019-03-21 09:44:37 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)
2019-03-21 09:44:37 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:44:37 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- a simple test using spark
- copying a resource should pass equivalence testing
- load a resource file
MathUtilsSuite:
- check equality with floating point comparison
- check inequality with floating point comparison
- compute factorials
- test array aggregation in isolation
- use array aggregator with an rdd
- safe wrapped log should work
- softmax an array
- multiply an array by a scalar
Run completed in 4 seconds, 64 milliseconds.
Total number of tests run: 11
Suites: completed 3, aborted 0
Tests: succeeded 11, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-misc-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-misc-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-minhash-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-minhash-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-minhash-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-minhash-spark2_2.12 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-minhash-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-minhash-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/scala:-1: info: compiling
[INFO] Compiling 6 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/2.12.6/classes at 1553186681859
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-minhash-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-minhash-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-minhash-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-minhash-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/scala:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/2.12.6/test-classes at 1553186686998
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-minhash-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-minhash-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-minhash-spark2_2.12 ---
Discovery starting.
Discovery completed in 179 milliseconds.
Run starting. Expected test count is: 5
MinHashSuite:
2019-03-21 09:44:53 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)
2019-03-21 09:44:53 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:44:53 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- compute exact overlap for ten 1000 bp reads
- compute approximate overlap for ten 1000 bp reads across different band sizes
- should throw exception if we pick an illegal band count
MinHashSignatureSuite:
- compute the similarity of signatures
- compute buckets for a simple signature
Run completed in 4 seconds, 950 milliseconds.
Total number of tests run: 5
Suites: completed 3, aborted 0
Tests: succeeded 5, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-minhash-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-minhash-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-minhash-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-minhash-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-minhash-spark2_2.12 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-minhash-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-minhash-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-minhash-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-minhash-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-minhash-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-minhash-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-minhash-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-minhash-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-minhash-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-minhash-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-minhash-spark2_2.12 ---
Discovery starting.
Discovery completed in 138 milliseconds.
Run starting. Expected test count is: 5
MinHashSuite:
2019-03-21 09:44:59 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)
2019-03-21 09:44:59 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:45:00 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- compute exact overlap for ten 1000 bp reads
- compute approximate overlap for ten 1000 bp reads across different band sizes
- should throw exception if we pick an illegal band count
MinHashSignatureSuite:
- compute the similarity of signatures
- compute buckets for a simple signature
Run completed in 5 seconds, 21 milliseconds.
Total number of tests run: 5
Suites: completed 3, aborted 0
Tests: succeeded 5, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-minhash-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-minhash-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-metrics-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-metrics-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-metrics-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-metrics-spark2_2.12 ---
[INFO] Modified 0 of 39 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-metrics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-metrics-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala:-1: info: compiling
[INFO] Compiling 22 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/2.12.6/classes at 1553186705316
[WARNING] warning: non-variable type argument com.netflix.servo.monitor.Monitor[_] in type pattern scala.runtime.NonLocalReturnControl[com.netflix.servo.monitor.Monitor[_]] is unchecked since it is eliminated by erasure
[WARNING] warning: there were 5 deprecation warnings (since 2.0.0)
[WARNING] warning: there were two deprecation warnings (since 2.12.0)
[WARNING] warning: there were 7 deprecation warnings in total; re-run with -deprecation for details
[WARNING] warning: there were three feature warnings; re-run with -feature for details
[WARNING] 5 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 10 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-metrics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-metrics-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-metrics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-metrics-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala:-1: info: compiling
[INFO] Compiling 17 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/2.12.6/test-classes at 1553186715649
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedOrderedRDDFunctionsSuite.scala:44: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       val timerNames = timerMap.keys().map(_.timerName).toSet
[WARNING]                                     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedPairRDDFunctionsSuite.scala:58: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val timers = Metrics.Recorder.value.get.accumulable.value.timerMap.filter(entry =>
[WARNING]                                                               ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:86: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assertOnNameAndCountInTimingsTable(dataRows.get(1), "map at InstrumentedRDDSuite.scala", 1)
[WARNING]                                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:87: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assertOnNameAndCountInTimingsTable(dataRows.get(2), "function call", 10)
[WARNING]                                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:88: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assertOnNameAndCountInTimingsTable(dataRows.get(3), "timer 1", 10)
[WARNING]                                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:89: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assertOnNameAndCountInTimingsTable(dataRows.get(4), "timer 2", 10)
[WARNING]                                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsListenerSuite.scala:32: warning: method accumulator in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     val accumulator = sc.accumulator(0)
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsListenerSuite.scala:32: warning: object IntAccumulatorParam in object AccumulatorParam is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     val accumulator = sc.accumulator(0)
[WARNING]                                     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsListenerSuite.scala:32: warning: object AccumulatorParam in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     val accumulator = sc.accumulator(0)
[WARNING]                                     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:30: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:30: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:39: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:39: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:56: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:56: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:70: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:70: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:84: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:84: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:95: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:95: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:94: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     timer.getMonitors.foreach(monitor => {
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:30: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     var accumulable: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers())
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:30: warning: method accumulable in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     var accumulable: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers())
[WARNING]                                                                    ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:70: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     var accumulable: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers())
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:70: warning: method accumulable in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     var accumulable: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers())
[WARNING]                                                                    ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:108: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     var accumulable1: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers())
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:108: warning: method accumulable in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     var accumulable1: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers())
[WARNING]                                                                     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:114: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     var accumulable2: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers())
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:114: warning: method accumulable in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2
[WARNING]     var accumulable2: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers())
[WARNING]                                                                     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TimerSuite.scala:34: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead
[WARNING]     val recorder = mock[MetricsRecorder]
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TimerSuite.scala:41: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead
[WARNING]     val recorder = mock[MetricsRecorder]
[WARNING]                    ^
[WARNING] 32 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-metrics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-metrics-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-metrics-spark2_2.12 ---
Discovery starting.
Discovery completed in 236 milliseconds.
Run starting. Expected test count is: 43
InstrumentedRDDSuite:
2019-03-21 09:45:25 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)
2019-03-21 09:45:25 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:45:26 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- Operation is recorded correctly
- Function call is recorded correctly
- Instrumented Spark operation works correctly
InstrumentedOrderedRDDFunctionsSuite:
- Nested timings are not recorded for sortByKey operation
InstrumentedPairRDDFunctionsSuite:
- Persisting to Hadoop file is instrumented correctly
+-------------------------+--------------------+--------+
|          Col1           |        Col2        |  Col3  |
+-------------------------+--------------------+--------+
| Col1Value1              |    100 nanoseconds |    100 |
| Col1Value2 A Bit Longer | 200000 nanoseconds | 200000 |
+-------------------------+--------------------+--------+

MonitorTableSuite:
- Table is rendered correctly
TimerSuite:
- Time method does not error when no recorder is defined
- Function times are recorded correctly with explicit recorder
- Function times are recorded correctly with thread-local recorder
DurationFormattingSuite:
- Values with hours formatted correctly
- Values with minutes formatted correctly
- Values with seconds formatted correctly
- Values with milliseconds formatted correctly
- Values with microseconds formatted correctly
- Values with nanoseconds formatted correctly
- Negative duration does not throw an error
HistogramSuite:
- Histogram addition works
ServoTimerSuite:
- Total time computed correctly
- Count computed correctly
- Mean computed correctly
- Max computed correctly
- Min computed correctly
- Timer and sub-monitors tagged correctly
- Nanosecond timings recorded correctly
MetricsSuite:
- Timer metrics are computed correctly
- Timer metrics are computed correctly for RDD operations
MetricsListenerSuite:
- Listener accumulates metrics when registered with Spark
MetricsRecorderSuite:
- Timings are recorded correctly
- Nested timings are recorded correctly
- New top-level operations get new sequence IDs
- Repeated top-level operations get new sequence IDs
- Non-matching timer name causes assertion error
- Nested RDD operations are not recorded
ASCIITableSuite:
- Table is rendered correctly
- Inequal sizes between header and rows are rejected
AggregatorSuite:
- UniqueAggregator only collects unique values
- HistogramAggregator counts values correctly
ServoTimersAccumulableParamSuite:
- Values accumulated correctly
- Paths with different properties are treated as distinct timers
- Accumulable params can be merged together
SparkMetricsSuite:
- Task metrics are captured correctly
- Stage metrics are captured correctly
- Metrics are rendered correctly
Run completed in 7 seconds, 540 milliseconds.
Total number of tests run: 43
Suites: completed 16, aborted 0
Tests: succeeded 43, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-metrics-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-metrics-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-metrics-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-metrics-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-metrics-spark2_2.12 ---
[INFO] Modified 0 of 39 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-metrics-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-metrics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-metrics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-metrics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-metrics-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-metrics-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-metrics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-metrics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-metrics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-metrics-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-metrics-spark2_2.12 ---
Discovery starting.
Discovery completed in 193 milliseconds.
Run starting. Expected test count is: 43
InstrumentedRDDSuite:
2019-03-21 09:45:34 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)
2019-03-21 09:45:34 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:45:35 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- Operation is recorded correctly
- Function call is recorded correctly
- Instrumented Spark operation works correctly
InstrumentedOrderedRDDFunctionsSuite:
- Nested timings are not recorded for sortByKey operation
InstrumentedPairRDDFunctionsSuite:
- Persisting to Hadoop file is instrumented correctly
+-------------------------+--------------------+--------+
|          Col1           |        Col2        |  Col3  |
+-------------------------+--------------------+--------+
| Col1Value1              |    100 nanoseconds |    100 |
| Col1Value2 A Bit Longer | 200000 nanoseconds | 200000 |
+-------------------------+--------------------+--------+

MonitorTableSuite:
- Table is rendered correctly
TimerSuite:
- Time method does not error when no recorder is defined
- Function times are recorded correctly with explicit recorder
- Function times are recorded correctly with thread-local recorder
DurationFormattingSuite:
- Values with hours formatted correctly
- Values with minutes formatted correctly
- Values with seconds formatted correctly
- Values with milliseconds formatted correctly
- Values with microseconds formatted correctly
- Values with nanoseconds formatted correctly
- Negative duration does not throw an error
HistogramSuite:
- Histogram addition works
ServoTimerSuite:
- Total time computed correctly
- Count computed correctly
- Mean computed correctly
- Max computed correctly
- Min computed correctly
- Timer and sub-monitors tagged correctly
- Nanosecond timings recorded correctly
MetricsSuite:
- Timer metrics are computed correctly
- Timer metrics are computed correctly for RDD operations
MetricsListenerSuite:
- Listener accumulates metrics when registered with Spark
MetricsRecorderSuite:
- Timings are recorded correctly
- Nested timings are recorded correctly
- New top-level operations get new sequence IDs
- Repeated top-level operations get new sequence IDs
- Non-matching timer name causes assertion error
- Nested RDD operations are not recorded
ASCIITableSuite:
- Table is rendered correctly
- Inequal sizes between header and rows are rejected
AggregatorSuite:
- UniqueAggregator only collects unique values
- HistogramAggregator counts values correctly
ServoTimersAccumulableParamSuite:
- Values accumulated correctly
- Paths with different properties are treated as distinct timers
- Accumulable params can be merged together
SparkMetricsSuite:
- Task metrics are captured correctly
- Stage metrics are captured correctly
- Metrics are rendered correctly
Run completed in 7 seconds, 583 milliseconds.
Total number of tests run: 43
Suites: completed 16, aborted 0
Tests: succeeded 43, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-metrics-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-metrics-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-io-spark2_2.12: I/O utils 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-io-spark2_2.12 ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-io-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-io-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/scala:-1: info: compiling
[INFO] Compiling 8 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/2.12.6/classes at 1553186742546
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-io-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-io-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-io-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/2.12.6/test-classes at 1553186747237
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-io-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark2_2.12 ---
Discovery starting.
Discovery completed in 103 milliseconds.
Run starting. Expected test count is: 7
LocalFileLocatorSuite:
- parentLocator retrieves the parent directory
- relativeLocator retrieves a subdirectory
- bytes accesses the named underlying file
ByteArrayLocatorSuite:
- byte access can be wrapped in a locator correctly
FileLocatorSuite:
- parseSlash can correctly parse a one-slash string
- parseSlash can correctly parse a two-slash string
- parseSlash can correctly parse a no-slash string
Run completed in 214 milliseconds.
Total number of tests run: 7
Suites: completed 4, aborted 0
Tests: succeeded 7, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-io-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-io-spark2_2.12 ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-io-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-io-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-io-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-io-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-io-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-io-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-io-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark2_2.12 ---
Discovery starting.
Discovery completed in 138 milliseconds.
Run starting. Expected test count is: 7
LocalFileLocatorSuite:
- parentLocator retrieves the parent directory
- relativeLocator retrieves a subdirectory
- bytes accesses the named underlying file
ByteArrayLocatorSuite:
- byte access can be wrapped in a locator correctly
FileLocatorSuite:
- parseSlash can correctly parse a one-slash string
- parseSlash can correctly parse a two-slash string
- parseSlash can correctly parse a no-slash string
Run completed in 274 milliseconds.
Total number of tests run: 7
Suites: completed 4, aborted 0
Tests: succeeded 7, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-io-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-io-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-statistics-spark2_2.12: Spark code for fitting statistical models 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-statistics-spark2_2.12 ---
[INFO] Modified 0 of 6 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-statistics-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/2.12.6/classes at 1553186754072
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-statistics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-statistics-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-statistics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-statistics-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/scala:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/2.12.6/test-classes at 1553186759153
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-statistics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-statistics-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-statistics-spark2_2.12 ---
Discovery starting.
Discovery completed in 117 milliseconds.
Run starting. Expected test count is: 6
PoissonMixtureModelSuite:
2019-03-21 09:46:05 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)
2019-03-21 09:46:05 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:46:06 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- run the m step on a trivial example
2019-03-21 09:46:08 WARN  KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-03-21 09:46:09 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2019-03-21 09:46:09 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2019-03-21 09:46:10 WARN  KMeans:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- fit a poisson to several thousand points
ZScoreNormalizationSuite:
- compute mean of a set of samples
- compute variance of a set of samples
- variance should be 0 if all elements are the same
- check z-score for a varying rdd
Run completed in 6 seconds, 397 milliseconds.
Total number of tests run: 6
Suites: completed 3, aborted 0
Tests: succeeded 6, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-statistics-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-statistics-spark2_2.12 ---
[INFO] Modified 0 of 6 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-statistics-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-statistics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-statistics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-statistics-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-statistics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-statistics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-statistics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-statistics-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-statistics-spark2_2.12 ---
Discovery starting.
Discovery completed in 120 milliseconds.
Run starting. Expected test count is: 6
PoissonMixtureModelSuite:
2019-03-21 09:46:13 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)
2019-03-21 09:46:13 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:46:13 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- run the m step on a trivial example
2019-03-21 09:46:16 WARN  KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-03-21 09:46:17 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2019-03-21 09:46:17 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2019-03-21 09:46:18 WARN  KMeans:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- fit a poisson to several thousand points
ZScoreNormalizationSuite:
- compute mean of a set of samples
- compute variance of a set of samples
- variance should be 0 if all elements are the same
- check z-score for a varying rdd
Run completed in 6 seconds, 650 milliseconds.
Total number of tests run: 6
Suites: completed 3, aborted 0
Tests: succeeded 6, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-statistics-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-statistics-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-cli-spark2_2.12: utilities for building command line applications 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-cli-spark2_2.12 ---
[INFO] Modified 0 of 3 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-cli-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target/2.12.6/classes at 1553186780191
[WARNING] warning: there was one deprecation warning
[WARNING] warning: there was one deprecation warning (since 2.12.0)
[WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details
[WARNING] three warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-cli-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-cli-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-cli-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-cli-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-cli-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-cli-spark2_2.12 ---
[INFO] Modified 0 of 3 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-cli-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-cli-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-cli-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-cli-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-cli-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-cli-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-cli-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-cli-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-serialization-spark2_2.12: tools for serializing data 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-serialization-spark2_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-serialization-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-serialization-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target/2.12.6/classes at 1553186785094
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-serialization-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-serialization-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-serialization-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-serialization-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-serialization-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-serialization-spark2_2.12 ---
Discovery starting.
Discovery completed in 88 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 137 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-serialization-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-serialization-spark2_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-serialization-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-serialization-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-serialization-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-serialization-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-serialization-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-serialization-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-serialization-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-serialization-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-serialization-spark2_2.12 ---
Discovery starting.
Discovery completed in 104 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 162 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-serialization-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-serialization-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-intervalrdd-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/scala:-1: info: compiling
[INFO] Compiling 5 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/2.12.6/classes at 1553186792341
[WARNING] warning: there were two deprecation warnings (since 2.0.0); re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-intervalrdd-spark2_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/scala:-1: info: compiling
[INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/2.12.6/test-classes at 1553186798347
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-intervalrdd-spark2_2.12 ---
Discovery starting.
Discovery completed in 202 milliseconds.
Run starting. Expected test count is: 31
IntervalRDDSuite:
2019-03-21 09:46:47 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)
2019-03-21 09:46:47 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:46:47 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- create IntervalRDD from RDD of datatype string
- merge new values into existing IntervalRDD
- call put multiple times on data with same interval
- test filterByInterval
- verify no data is lost in conversion from rdd to intervalrdd
- count data where chromosome partitions overlap
- get data where chromosome partitions overlap
- apply predicate to the RDD
- testing collect
- test before and after toRDD sizes are the same
- testing mapValues
- Attempt to access data from non existing key
- Delete values from rdd
- Repartitions IntervalRDD
IntervalPartitionSuite:
- create new partition
- create partition from iterator
- get values from iterator-created partition
- correctly fetches data that is initially unsorted
- put some for iterator of intervals and key-values
- get some for iterator of intervals
- selectively getting intervals
- putting differing number of reads into different regions
- putting then getting a region that overlaps 3 regions
- applying a predicate
- applying a map
IntervalArraySuite:
- succeeds in searching empty IntervalArray
- build a IntervalArray with a single item and retrieve data
- build a IntervalArray out of multiple datapoints and retrieve data
- verify get with requireOverlap set to false on IntervalArray retrieves nearest data
- verify IntervalArray fetches all valid ranges
- inserts new elements into IntervalArray
Run completed in 6 seconds, 752 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 @ utils-intervalrdd-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-intervalrdd-spark2_2.12 ---
Discovery starting.
Discovery completed in 150 milliseconds.
Run starting. Expected test count is: 31
IntervalRDDSuite:
2019-03-21 09:46:55 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)
2019-03-21 09:46:55 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:46:55 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- create IntervalRDD from RDD of datatype string
- merge new values into existing IntervalRDD
- call put multiple times on data with same interval
- test filterByInterval
- verify no data is lost in conversion from rdd to intervalrdd
- count data where chromosome partitions overlap
- get data where chromosome partitions overlap
- apply predicate to the RDD
- testing collect
- test before and after toRDD sizes are the same
- testing mapValues
- Attempt to access data from non existing key
- Delete values from rdd
- Repartitions IntervalRDD
IntervalPartitionSuite:
- create new partition
- create partition from iterator
- get values from iterator-created partition
- correctly fetches data that is initially unsorted
- put some for iterator of intervals and key-values
- get some for iterator of intervals
- selectively getting intervals
- putting differing number of reads into different regions
- putting then getting a region that overlaps 3 regions
- applying a predicate
- applying a map
IntervalArraySuite:
- succeeds in searching empty IntervalArray
- build a IntervalArray with a single item and retrieve data
- build a IntervalArray out of multiple datapoints and retrieve data
- verify get with requireOverlap set to false on IntervalArray retrieves nearest data
- verify IntervalArray fetches all valid ranges
- inserts new elements into IntervalArray
Run completed in 6 seconds, 238 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 @ utils-intervalrdd-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ utils-parent-spark2_2.12 ---
[INFO] Starting Coveralls job for jenkins (145 / https://amplab.cs.berkeley.edu/jenkins/job/bdg-utils-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=2.4.0,label=ubuntu/145/)
[INFO] Using repository token <secret>
[INFO] Git commit 29043ec in pr/134/merge
[INFO] Writing Coveralls data to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/target/coveralls.json...
[INFO] Processing coverage report from /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 69ms
[INFO] Gathered code coverage metrics for 0 source files with 0 lines of code:
[INFO] - 0 relevant lines
[INFO] - 0 covered lines
[INFO] - 0 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 2062ms for Job #145.1
[INFO] https://coveralls.io/jobs/46449382
[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] utils .............................................. SUCCESS [  2.782 s]
[INFO] utils-misc-spark2_2.12: Miscellaneous Spark utility code SUCCESS [ 27.377 s]
[INFO] utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 23.258 s]
[INFO] utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs SUCCESS [ 37.665 s]
[INFO] utils-io-spark2_2.12: I/O utils .................... SUCCESS [ 11.537 s]
[INFO] utils-statistics-spark2_2.12: Spark code for fitting statistical models SUCCESS [ 26.128 s]
[INFO] utils-cli-spark2_2.12: utilities for building command line applications SUCCESS [  4.288 s]
[INFO] utils-serialization-spark2_2.12: tools for serializing data SUCCESS [  7.818 s]
[INFO] utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree SUCCESS [ 29.559 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:54 min
[INFO] Finished at: 2019-03-21T09:47:04-07:00
[INFO] Final Memory: 60M/1494M
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${UTILS_MVN_TMP_DIR}
+ find /tmp/utilsTestMvnJm5otYY
/tmp/utilsTestMvnJm5otYY
/tmp/utilsTestMvnJm5otYY/LocalFileLocatorSuite170536485133140330test
/tmp/utilsTestMvnJm5otYY/test.txt6465844398479047760.txt
/tmp/utilsTestMvnJm5otYY/LocalFileLocatorSuite5996504540289414023test
/tmp/utilsTestMvnJm5otYY/LocalFileLocatorSuite6476613227277475798test
/tmp/utilsTestMvnJm5otYY/LocalFileLocatorSuite615471844111162627test
/tmp/utilsTestMvnJm5otYY/test.txt1336047485040407995.txt
/tmp/utilsTestMvnJm5otYY/LocalFileLocatorSuite8822201739306448945test
/tmp/utilsTestMvnJm5otYY/LocalFileLocatorSuite1938421679027462834test
rm -rf ${UTILS_MVN_TMP_DIR}
+ rm -rf /tmp/utilsTestMvnJm5otYY

echo
+ echo

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

Recording test results
Setting commit status on GitHub for https://github.com/bigdatagenomics/utils/commit/29043ec7bab98ff94dc851939fe8f867b4caad76
Finished: SUCCESS