SuccessConsole Output

Started by upstream project "bdg-utils-prb" build number 162
originally caused by:
 GitHub pull request #158 of commit 4370762222c3e5cc4d6194d147477bc6f204206d automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on research-jenkins-worker-07 (research-07 ubuntu) in workspace /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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 5b87e5d20757ff83948685f57dc61a6027c952e7 (origin/pr/158/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 5b87e5d20757ff83948685f57dc61a6027c952e7
First time build. Skipping changelog.
[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/hudson757040910499726291.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/:/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/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/utilsTestMvn0tnZ6FE

# 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/utilsTestMvn0tnZ6FE: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/:/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/:/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 ${BASH_SOURCE[0]} 
+++ dirname ./scripts/jenkins-test
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.3.0-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 2.11 ]]

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
+ '[' 2.11 == 2.11 ']'
+ set +e
+ ./scripts/move_to_scala_2.11.sh
Scala version is already set to 2.11 (Scala artifacts have _2.11 version suffix in artifact name).
Cowardly refusing to move to Scala 2.11 a second time...
+ [[ 1 == 0 ]]
+ set -e

if [ ${SCALA_VERSION} == 2.12 ];
then
    ./scripts/move_to_scala_2.12.sh
fi
+ '[' 2.11 == 2.12 ']'

# print versions
echo "Testing UTILS version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION} and Scala ${SCALA_VERSION}"
+ echo 'Testing UTILS version 0.3.0-SNAPSHOT on Spark 2.4.0 and Hadoop 2.7.5 and Scala 2.11'
Testing UTILS version 0.3.0-SNAPSHOT on Spark 2.4.0 and Hadoop 2.7.5 and Scala 2.11

# 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 158 ]]
+ COVERALLS_PRB_OPTION=-DpullRequest=158

# 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_2.11: Miscellaneous Spark utility code
[INFO] utils-minhash-spark2_2.11: MinHash-based Jaccard similarity estimator
[INFO] utils-metrics-spark2_2.11: tools for collecting metrics on top of RDDs
[INFO] utils-io-spark2_2.11: I/O utils
[INFO] utils-statistics-spark2_2.11: Spark code for fitting statistical models
[INFO] utils-cli-spark2_2.11: utilities for building command line applications
[INFO] utils-serialization-spark2_2.11: tools for serializing data
[INFO] utils-intervalrdd-spark2_2.11: IntervalRDD based on interval tree
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-parent-spark2_2.11 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-misc-spark2_2.11: Miscellaneous Spark utility code 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-misc-spark2_2.11 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-minhash-spark2_2.11: MinHash-based Jaccard similarity estimator 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-minhash-spark2_2.11 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-metrics-spark2_2.11: tools for collecting metrics on top of RDDs 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-metrics-spark2_2.11 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-io-spark2_2.11: I/O utils 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-io-spark2_2.11 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-statistics-spark2_2.11: Spark code for fitting statistical models 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-statistics-spark2_2.11 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-cli-spark2_2.11: utilities for building command line applications 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-cli-spark2_2.11 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-serialization-spark2_2.11: tools for serializing data 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-serialization-spark2_2.11 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-intervalrdd-spark2_2.11: IntervalRDD based on interval tree 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-intervalrdd-spark2_2.11 ---
[INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] utils .............................................. SUCCESS [  0.200 s]
[INFO] utils-misc-spark2_2.11: Miscellaneous Spark utility code SUCCESS [  0.023 s]
[INFO] utils-minhash-spark2_2.11: MinHash-based Jaccard similarity estimator SUCCESS [  0.011 s]
[INFO] utils-metrics-spark2_2.11: tools for collecting metrics on top of RDDs SUCCESS [  0.038 s]
[INFO] utils-io-spark2_2.11: I/O utils .................... SUCCESS [  0.008 s]
[INFO] utils-statistics-spark2_2.11: Spark code for fitting statistical models SUCCESS [  0.011 s]
[INFO] utils-cli-spark2_2.11: utilities for building command line applications SUCCESS [  0.017 s]
[INFO] utils-serialization-spark2_2.11: tools for serializing data SUCCESS [  0.006 s]
[INFO] utils-intervalrdd-spark2_2.11: IntervalRDD based on interval tree SUCCESS [  0.013 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.542 s
[INFO] Finished at: 2020-02-17T14:34:11-08:00
[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_2.11: Miscellaneous Spark utility code
[INFO] utils-minhash-spark2_2.11: MinHash-based Jaccard similarity estimator
[INFO] utils-metrics-spark2_2.11: tools for collecting metrics on top of RDDs
[INFO] utils-io-spark2_2.11: I/O utils
[INFO] utils-statistics-spark2_2.11: Spark code for fitting statistical models
[INFO] utils-cli-spark2_2.11: utilities for building command line applications
[INFO] utils-serialization-spark2_2.11: tools for serializing data
[INFO] utils-intervalrdd-spark2_2.11: IntervalRDD based on interval tree
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-parent-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-parent-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-parent-spark2_2.11 ---
[INFO] Modified 0 of 82 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-parent-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-parent-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-parent-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-parent-spark2_2.11 ---
[INFO] Modified 0 of 82 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-parent-spark2_2.11 ---
[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_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-parent-spark2_2.11 ---
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-parent-spark2_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-parent-spark2_2.11 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-misc-spark2_2.11: Miscellaneous Spark utility code 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-misc-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-misc-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-misc-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-misc-spark2_2.11 ---
[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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/2.11.12/classes at 1581978859498
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-misc-spark2_2.11 ---
[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_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/2.11.12/test-classes at 1581978863542
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-misc-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-misc-spark2_2.11 ---
Discovery starting.
Discovery completed in 105 milliseconds.
Run starting. Expected test count is: 11
SparkFunSuiteSuite:
2020-02-17 14:34:29 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:34:29 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:34:29 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 2 seconds, 565 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_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-misc-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-misc-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-misc-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-misc-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-misc-spark2_2.11 ---
[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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/2.11.12/scoverage-classes at 1581978873418
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [27 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-misc-spark2_2.11 ---
[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_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-misc-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-misc-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-misc-spark2_2.11 ---
Discovery starting.
Discovery completed in 112 milliseconds.
Run starting. Expected test count is: 11
SparkFunSuiteSuite:
2020-02-17 14:34:37 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:34:37 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:34:38 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 2 seconds, 588 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_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-misc-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-minhash-spark2_2.11: MinHash-based Jaccard similarity estimator 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-minhash-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-minhash-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-minhash-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-minhash-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/2.11.12/classes at 1581978881508
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-minhash-spark2_2.11 ---
[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_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/2.11.12/test-classes at 1581978885815
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-minhash-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-minhash-spark2_2.11 ---
Discovery starting.
Discovery completed in 136 milliseconds.
Run starting. Expected test count is: 5
MinHashSignatureSuite:
- compute the similarity of signatures
- compute buckets for a simple signature
MinHashSuite:
2020-02-17 14:34:51 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:34:51 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:34:51 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
Run completed in 3 seconds, 866 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_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-minhash-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-minhash-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-minhash-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-minhash-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-minhash-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/2.11.12/scoverage-classes at 1581978895492
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [134 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-minhash-spark2_2.11 ---
[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_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-minhash-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-minhash-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-minhash-spark2_2.11 ---
Discovery starting.
Discovery completed in 136 milliseconds.
Run starting. Expected test count is: 5
MinHashSignatureSuite:
- compute the similarity of signatures
- compute buckets for a simple signature
MinHashSuite:
2020-02-17 14:35:01 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:35:01 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:35:01 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
Run completed in 18 seconds, 331 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_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-minhash-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-metrics-spark2_2.11: tools for collecting metrics on top of RDDs 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-metrics-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-metrics-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-metrics-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 42 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-metrics-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala:-1: info: compiling
[INFO] Compiling 25 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/2.11.12/classes at 1581978920332
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimer.scala:45: warning: no valid targets for annotation on value tags - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class ServoTimer(name: String, @transient tags: Tag*) extends ConfigurableMonitor(name, tags)
[WARNING]                                 ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimer.scala:166: warning: no valid targets for annotation on value tags - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]   private class LongValueStatMonitor(name: String, @transient tags: Seq[Tag], function: () => Long)
[WARNING]                                                     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimer.scala:176: warning: no valid targets for annotation on value tags - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]   private class ConditionalGauge(name: String, @transient tags: Seq[Tag], condition: (Long, Long) => Boolean)
[WARNING]                                                 ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimer.scala:221: warning: no valid targets for annotation on value tags - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] abstract class ConfigurableMonitor(val name: String, @transient tags: Seq[Tag])
[WARNING]                                                       ^
[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 57 deprecation warnings; re-run with -deprecation for details
[WARNING] warning: there were three feature warnings; re-run with -feature for details
[WARNING] 7 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 10 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-metrics-spark2_2.11 ---
[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_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/2.11.12/test-classes at 1581978930782
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:28: warning: class ASCIITableHeader in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col1", alignment = Alignment.Left),
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:28: warning: object Alignment in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col1", alignment = Alignment.Left),
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:29: warning: class ASCIITableHeader in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col2", alignment = Alignment.Right),
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:29: warning: object Alignment in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col2", alignment = Alignment.Right),
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:30: warning: class ASCIITableHeader in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col3 Really Quite A Long Column", alignment = Alignment.Center))
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:30: warning: object Alignment in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col3 Really Quite A Long Column", alignment = Alignment.Center))
[WARNING]                                                                                  ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:36: warning: class ASCIITable in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val asciiTable = new ASCIITable(header, rows)
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:47: warning: class ASCIITableHeader in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col1", alignment = Alignment.Left),
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:47: warning: object Alignment in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col1", alignment = Alignment.Left),
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:48: warning: class ASCIITableHeader in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col2", alignment = Alignment.Right))
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:48: warning: object Alignment in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITableHeader(name = "Col2", alignment = Alignment.Right))
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:56: warning: class ASCIITable in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ASCIITable(header, rows)
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ASCIITableSuite.scala:61: warning: class ASCIITable in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   private def getRenderedTable(table: ASCIITable): String = {
[WARNING]                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/DurationFormattingSuite.scala:105: warning: object DurationFormatting in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     formatDuration(Duration.fromNanos(durationNanos))
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentationTestingUtil.scala:50: warning: class StageTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   def renderTableFromMetricsObject(sparkStageTimings: Option[Seq[StageTiming]] = None): String = {
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentationTestingUtil.scala:53: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.print(out, sparkStageTimings)
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedOrderedRDDFunctionsSuite.scala:28: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.initialize(sc)
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedOrderedRDDFunctionsSuite.scala:32: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.stopRecording()
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedOrderedRDDFunctionsSuite.scala:40: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.Recorder.value.foreach(recorder => {
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedPairRDDFunctionsSuite.scala:36: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.initialize(sc)
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedPairRDDFunctionsSuite.scala:40: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.stopRecording()
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedPairRDDFunctionsSuite.scala:58: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedPairRDDFunctionsSuite.scala:73: warning: class Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING] object DummyTimers extends Metrics {
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedPairRDDFunctionsSuite.scala:73: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING] object DummyTimers extends Metrics {
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:30: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.initialize(sc)
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:34: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.stopRecording()
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:41: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val timers = Metrics.Recorder.value.get.accumulable.value.timerMap
[WARNING]                  ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:54: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     assert(recorder ne Metrics.Recorder.value) // This should be a copy
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:61: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]         Metrics.Recorder.value = None
[WARNING]         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:99: warning: class Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING] object OtherTimers extends Metrics {
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:99: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING] object OtherTimers extends Metrics {
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsListenerSuite.scala:27: warning: class RecordedMetrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val metrics = new RecordedMetrics()
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsListenerSuite.scala:28: warning: class MetricsListener in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val listener = new MetricsListener(metrics)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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: use AccumulatorV2
[WARNING]     val accumulator = sc.accumulator(0)
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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: use AccumulatorV2
[WARNING]     val accumulator = sc.accumulator(0)
[WARNING]                                     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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: use AccumulatorV2
[WARNING]     val accumulator = sc.accumulator(0)
[WARNING]                                     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/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: use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:30: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:30: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:31: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val recorder = new MetricsRecorder(accumulable)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:34: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val timingPath = new TimingPath("Timer 1", None, sequenceId = 1)
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:35: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     verify(accumulable).+=(new RecordedTiming(100000, timingPath))
[WARNING]                                ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/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: use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:39: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:39: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:40: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val recorder = new MetricsRecorder(accumulable)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:47: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val timingPath1 = new TimingPath("Timer 1", None, sequenceId = 1)
[WARNING]                           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:48: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val timingPath2 = new TimingPath("Timer 2", Some(timingPath1), sequenceId = 1)
[WARNING]                           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:49: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val timingPath3 = new TimingPath("Timer 3", Some(timingPath1), sequenceId = 1)
[WARNING]                           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:50: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     verify(accumulable).+=(new RecordedTiming(200000, timingPath2))
[WARNING]                                ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:51: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     verify(accumulable).+=(new RecordedTiming(300000, timingPath3))
[WARNING]                                ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:52: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     verify(accumulable).+=(new RecordedTiming(100000, timingPath1))
[WARNING]                                ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/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: use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:56: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:56: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:57: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val recorder = new MetricsRecorder(accumulable)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/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: use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:70: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:70: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:71: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val recorder = new MetricsRecorder(accumulable)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/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: use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:84: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:84: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:85: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val recorder = new MetricsRecorder(accumulable)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/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: use AccumulatorV2
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:95: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:95: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]]
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:96: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val recorder = new MetricsRecorder(accumulable)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:107: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val timingPath1 = new TimingPath("Timer 1", None, sequenceId = 1)
[WARNING]                           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:108: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val timingPath2 = new TimingPath("Timer 2", Some(timingPath1), sequenceId = 1, isRDDOperation = true)
[WARNING]                           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:109: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val timingPath5 = new TimingPath("Timer 5", Some(timingPath2), sequenceId = 1)
[WARNING]                           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:113: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     verify(accumulable).+=(new RecordedTiming(100000, timingPath1))
[WARNING]                                ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:114: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     verify(accumulable).+=(new RecordedTiming(500000, timingPath5))
[WARNING]                                ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:115: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     verify(accumulable).+=(new RecordedTiming(200000, timingPath2))
[WARNING]                                ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsSuite.scala:30: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.initialize(sc)
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsSuite.scala:34: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.stopRecording()
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsSuite.scala:195: warning: class StageTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   private def getRenderedTable(sparkStageTimings: Option[Seq[StageTiming]]): String = {
[WARNING]                                                   ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsSuite.scala:198: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.print(out, sparkStageTimings)
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsSuite.scala:203: warning: class Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   class TestTimers(testingClock: TestingClock) extends Metrics(testingClock) {
[WARNING]                                                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:30: warning: class TableHeader in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new TableHeader(name = "Col1", valueExtractor = ValueExtractor.forTagValueWithKey("TagKey1"), None, alignment = Alignment.Left),
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:30: warning: object ValueExtractor in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new TableHeader(name = "Col1", valueExtractor = ValueExtractor.forTagValueWithKey("TagKey1"), None, alignment = Alignment.Left),
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:30: warning: object Alignment in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new TableHeader(name = "Col1", valueExtractor = ValueExtractor.forTagValueWithKey("TagKey1"), None, alignment = Alignment.Left),
[WARNING]                                                                                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:31: warning: class TableHeader in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new TableHeader(name = "Col2", valueExtractor = ValueExtractor.forMonitorMatchingTag(ServoTimer.TotalTimeTag), formatFunction = Some(formatFunction1)),
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:31: warning: object ValueExtractor in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new TableHeader(name = "Col2", valueExtractor = ValueExtractor.forMonitorMatchingTag(ServoTimer.TotalTimeTag), formatFunction = Some(formatFunction1)),
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:31: warning: object ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new TableHeader(name = "Col2", valueExtractor = ValueExtractor.forMonitorMatchingTag(ServoTimer.TotalTimeTag), formatFunction = Some(formatFunction1)),
[WARNING]                                                                                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:32: warning: class TableHeader in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new TableHeader(name = "Col3", valueExtractor = ValueExtractor.forMonitorValue()))
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:32: warning: object ValueExtractor in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new TableHeader(name = "Col3", valueExtractor = ValueExtractor.forMonitorValue()))
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:35: warning: class ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ServoTimer("timer1"),
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:36: warning: class ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]       new ServoTimer("timer2"))
[WARNING]           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:38: warning: class ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     rows(0).asInstanceOf[ServoTimer].addTag(Tags.newTag("TagKey1", "Col1Value1"))
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:39: warning: class ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     rows(1).asInstanceOf[ServoTimer].addTag(Tags.newTag("TagKey1", "Col1Value2 A Bit Longer"))
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:41: warning: class ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     rows(0).asInstanceOf[ServoTimer].recordNanos(100)
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:42: warning: class ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     rows(1).asInstanceOf[ServoTimer].recordNanos(200000)
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:44: warning: class MonitorTable in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val monitorTable = new MonitorTable(headers, rows)
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MonitorTableSuite.scala:54: warning: class MonitorTable in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   private def getRenderedTable(table: MonitorTable): String = {
[WARNING]                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:34: warning: object ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     assert(fromNanos(getTaggedValue(timer, TotalTimeTag).longValue()) === 300)
[WARNING]                                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:42: warning: object ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     assert(getTaggedValue(timer, CountTag).longValue() === 2)
[WARNING]                                  ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:50: warning: object ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     assert(fromNanos(getTaggedValue(timer, MeanTag).longValue()) === 150)
[WARNING]                                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:59: warning: object ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     assert(fromNanos(getTaggedValue(timer, MaxTag).longValue()) === 201)
[WARNING]                                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:69: warning: object ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     assert(fromNanos(getTaggedValue(timer, MinTag).longValue()) === 99)
[WARNING]                                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:86: warning: object ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     assert(getTaggedValue(timer, TotalTimeTag).longValue() === 30000)
[WARNING]                                  ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:93: warning: class ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   def getTaggedValue(timer: ServoTimer, tag: Tag): Number = {
[WARNING]                             ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:105: warning: class ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   def createTimer(): ServoTimer = {
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:106: warning: class ServoTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     new ServoTimer("testTimer")
[WARNING]         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:28: warning: class ServoTimersAccumulableParam in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     implicit val accumulableParam = new ServoTimersAccumulableParam()
[WARNING]                                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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: 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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:30: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:30: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/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: 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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:30: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:32: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val root = new TimingPath("Timer 1", None)
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:33: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val child1 = new TimingPath("Timer 2", Some(root))
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:34: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val child2 = new TimingPath("Timer 3", Some(root))
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:36: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val grandchild1 = new TimingPath("Timer 2", Some(child1))
[WARNING]                           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:39: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(100000, root)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:40: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(200000, child1)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:41: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(300000, child2)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:42: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(400000, grandchild1)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:55: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(50000, root)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:56: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(50000, child2)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:68: warning: class ServoTimersAccumulableParam in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     implicit val accumulableParam = new ServoTimersAccumulableParam()
[WARNING]                                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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: 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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:70: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:70: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/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: 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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:70: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:72: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val root = new TimingPath("Timer 1", None)
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:75: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val child1 = new TimingPath("Timer 2", Some(root), sequenceId = 101)
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:76: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val child2 = new TimingPath("Timer 3", Some(root), sequenceId = 102)
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:77: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val child3 = new TimingPath("Timer 4", Some(root), sequenceId = 101, isRDDOperation = true)
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:80: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(100000, root)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:81: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(200000, child1)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:82: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(300000, child2)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:83: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable += new RecordedTiming(400000, child3)
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:99: warning: class ServoTimersAccumulableParam in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     implicit val accumulableParam = new ServoTimersAccumulableParam()
[WARNING]                                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:101: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val root = new TimingPath("Timer 1", None)
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:102: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val child1 = new TimingPath("Timer 2", Some(root))
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:103: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val child2 = new TimingPath("Timer 3", Some(root))
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:105: warning: class TimingPath in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val grandchild1 = new TimingPath("Timer 2", Some(child1))
[WARNING]                           ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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: 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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:108: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:108: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/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: 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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:108: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:109: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable1 += new RecordedTiming(100000, root)
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:110: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable1 += new RecordedTiming(200000, child1)
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:111: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable1 += new RecordedTiming(300000, child2)
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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: 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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:114: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:114: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/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: 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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:114: warning: class ServoTimers in package instrumentation is deprecated: to be removed in version 0.3.0
[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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:115: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable2 += new RecordedTiming(400000, grandchild1)
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:116: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable2 += new RecordedTiming(50000, root)
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:117: warning: class RecordedTiming in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     accumulable2 += new RecordedTiming(50000, child2)
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/SparkMetricsSuite.scala:134: warning: class TaskTimer in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   private def addValue(timer: TaskTimer, value: Long, host: String, stage: Int) {
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/SparkMetricsSuite.scala:151: warning: class SparkMetrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   private class MyMetrics extends SparkMetrics {
[WARNING]                                   ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TestingClock.scala:20: warning: class Clock in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING] class TestingClock extends Clock {
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TimerSuite.scala:34: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val recorder = mock[MetricsRecorder]
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TimerSuite.scala:41: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     val recorder = mock[MetricsRecorder]
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TimerSuite.scala:42: warning: object Metrics in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]     Metrics.Recorder.withValue(Some(recorder)) {
[WARNING]     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TimerSuite.scala:47: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   def doTest(testingClock: TestingClock, recorder: MetricsRecorder, explicitRecorder: Option[MetricsRecorder]) {
[WARNING]                                                    ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TimerSuite.scala:47: warning: class MetricsRecorder in package instrumentation is deprecated: to be removed in version 0.3.0
[WARNING]   def doTest(testingClock: TestingClock, recorder: MetricsRecorder, explicitRecorder: Option[MetricsRecorder]) {
[WARNING]                                                                                       ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/metrics/HistogramSuite.scala:24: warning: object Histogram in package metrics is deprecated: to be removed in version 0.3.0
[WARNING]     assert((Histogram[Long](1) ++ Histogram[Long](1)).valueToCount(1) === 2)
[WARNING]             ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/metrics/HistogramSuite.scala:24: warning: object Histogram in package metrics is deprecated: to be removed in version 0.3.0
[WARNING]     assert((Histogram[Long](1) ++ Histogram[Long](1)).valueToCount(1) === 2)
[WARNING]                                   ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/metrics/aggregators/AggregatorSuite.scala:25: warning: class UniqueAggregator in package aggregators is deprecated: to be removed in version 0.3.0
[WARNING]     val agg = new UniqueAggregator[String]()
[WARNING]                   ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/metrics/aggregators/AggregatorSuite.scala:35: warning: class HistogramAggregator in package aggregators is deprecated: to be removed in version 0.3.0
[WARNING]     val agg = new HistogramAggregator[Int]()
[WARNING]                   ^
[WARNING] 175 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_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-metrics-spark2_2.11 ---
Discovery starting.
Discovery completed in 274 milliseconds.
Run starting. Expected test count is: 43
InstrumentedRDDSuite:
2020-02-17 14:35:39 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:35:39 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:35:40 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 5 seconds, 993 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_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-metrics-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-metrics-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-metrics-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 42 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-metrics-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-metrics-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala:-1: info: compiling
[INFO] Compiling 25 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/2.11.12/scoverage-classes at 1581978946272
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimer.scala:45: warning: no valid targets for annotation on value tags - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class ServoTimer(name: String, @transient tags: Tag*) extends ConfigurableMonitor(name, tags)
[WARNING]                                 ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimer.scala:166: warning: no valid targets for annotation on value tags - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]   private class LongValueStatMonitor(name: String, @transient tags: Seq[Tag], function: () => Long)
[WARNING]                                                     ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimer.scala:176: warning: no valid targets for annotation on value tags - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]   private class ConditionalGauge(name: String, @transient tags: Seq[Tag], condition: (Long, Long) => Boolean)
[WARNING]                                                 ^
[WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimer.scala:221: warning: no valid targets for annotation on value tags - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] abstract class ConfigurableMonitor(val name: String, @transient tags: Seq[Tag])
[WARNING]                                                       ^
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [1894 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/scoverage-data]
[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 57 deprecation warnings; re-run with -deprecation for details
[WARNING] warning: there were three feature warnings; re-run with -feature for details
[WARNING] 7 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 11 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-metrics-spark2_2.11 ---
[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_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-metrics-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-metrics-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-metrics-spark2_2.11 ---
Discovery starting.
Discovery completed in 263 milliseconds.
Run starting. Expected test count is: 43
InstrumentedRDDSuite:
2020-02-17 14:35:58 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:35:58 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:35:59 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 5 seconds, 969 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_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-metrics-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-io-spark2_2.11: I/O utils 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-io-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-io-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-io-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/2.11.12/classes at 1581978965681
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-spark2_2.11 ---
[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_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/2.11.12/test-classes at 1581978969219
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark2_2.11 ---
Discovery starting.
Discovery completed in 95 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 192 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_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-io-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-io-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-io-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-io-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/2.11.12/scoverage-classes at 1581978973253
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [136 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-spark2_2.11 ---
[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_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-io-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark2_2.11 ---
Discovery starting.
Discovery completed in 90 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 194 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_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-io-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-statistics-spark2_2.11: Spark code for fitting statistical models 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-statistics-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-statistics-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 6 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/2.11.12/classes at 1581978978073
[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_2.11 ---
[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_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/2.11.12/test-classes at 1581978983151
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-statistics-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-statistics-spark2_2.11 ---
Discovery starting.
Discovery completed in 122 milliseconds.
Run starting. Expected test count is: 6
PoissonMixtureModelSuite:
2020-02-17 14:36:28 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:36:28 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:36:28 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
2020-02-17 14:36:30 WARN  KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2020-02-17 14:36:30 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2020-02-17 14:36:30 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2020-02-17 14:36:31 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 5 seconds, 98 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_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-statistics-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-statistics-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 6 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-statistics-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/2.11.12/scoverage-classes at 1581978993624
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [287 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/scoverage-data]
[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_2.11 ---
[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_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-statistics-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-statistics-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-statistics-spark2_2.11 ---
Discovery starting.
Discovery completed in 129 milliseconds.
Run starting. Expected test count is: 6
PoissonMixtureModelSuite:
2020-02-17 14:36:40 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:36:40 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:36:40 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
2020-02-17 14:36:42 WARN  KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2020-02-17 14:36:42 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2020-02-17 14:36:42 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2020-02-17 14:36:43 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 5 seconds, 206 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_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-statistics-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-cli-spark2_2.11: utilities for building command line applications 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 3 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-cli-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target/2.11.12/classes at 1581979005544
[WARNING] warning: there were 9 deprecation warnings; re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-spark2_2.11 ---
[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_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-cli-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-cli-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-cli-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 3 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-cli-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target/2.11.12/scoverage-classes at 1581979008954
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [99 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target/scoverage-data]
[WARNING] warning: there were 9 deprecation warnings; re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-spark2_2.11 ---
[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_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-cli-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-cli-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-cli-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-cli-spark2_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-cli-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-serialization-spark2_2.11: tools for serializing data 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-serialization-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-serialization-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-serialization-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target/2.11.12/classes at 1581979013152
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark2_2.11 ---
[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_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-serialization-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-serialization-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-serialization-spark2_2.11 ---
Discovery starting.
Discovery completed in 58 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 85 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_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-serialization-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-serialization-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-serialization-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-serialization-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target/2.11.12/scoverage-classes at 1581979016738
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [3 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark2_2.11 ---
[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_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-serialization-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-serialization-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-serialization-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-serialization-spark2_2.11 ---
Discovery starting.
Discovery completed in 57 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 85 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_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-serialization-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-intervalrdd-spark2_2.11: IntervalRDD based on interval tree 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/2.11.12/classes at 1581979019948
[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_2.11 ---
[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_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/2.11.12/test-classes at 1581979025069
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-intervalrdd-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-intervalrdd-spark2_2.11 ---
Discovery starting.
Discovery completed in 153 milliseconds.
Run starting. Expected test count is: 31
IntervalRDDSuite:
2020-02-17 14:37:12 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:37:12 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:37:12 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 5 seconds, 179 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_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-intervalrdd-spark2_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark2_2.11 ---
[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/2.11/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_2.11 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/2.11.12/scoverage-classes at 1581979037719
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [375 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/scoverage-data]
[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_2.11 ---
[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_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-intervalrdd-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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_2.11 ---
[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/2.11/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_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-intervalrdd-spark2_2.11 ---
[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_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-intervalrdd-spark2_2.11 ---
Discovery starting.
Discovery completed in 147 milliseconds.
Run starting. Expected test count is: 31
IntervalRDDSuite:
2020-02-17 14:37:24 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2020-02-17 14:37:24 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-02-17 14:37:24 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 5 seconds, 202 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_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-intervalrdd-spark2_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils 0.3.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ utils-parent-spark2_2.11 ---
[INFO] Starting Coveralls job for jenkins (162 / https://amplab.cs.berkeley.edu/jenkins/job/bdg-utils-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.11,SPARK_VERSION=2.4.0,label=ubuntu/162/)
[INFO] Using repository token <secret>
[INFO] Git commit 5b87e5d in pr/158/merge
[INFO] Writing Coveralls data to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/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/2.11/SPARK_VERSION/2.4.0/label/ubuntu/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 144ms
[INFO] Gathered code coverage metrics for 48 source files with 6066 lines of code:
[INFO] - 1505 relevant lines
[INFO] - 842 covered lines
[INFO] - 663 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 726ms for Job #162.1
[INFO] https://coveralls.io/jobs/59074178
[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 [  1.305 s]
[INFO] utils-misc-spark2_2.11: Miscellaneous Spark utility code SUCCESS [ 24.126 s]
[INFO] utils-minhash-spark2_2.11: MinHash-based Jaccard similarity estimator SUCCESS [ 38.581 s]
[INFO] utils-metrics-spark2_2.11: tools for collecting metrics on top of RDDs SUCCESS [ 45.840 s]
[INFO] utils-io-spark2_2.11: I/O utils .................... SUCCESS [ 12.350 s]
[INFO] utils-statistics-spark2_2.11: Spark code for fitting statistical models SUCCESS [ 27.507 s]
[INFO] utils-cli-spark2_2.11: utilities for building command line applications SUCCESS [  7.121 s]
[INFO] utils-serialization-spark2_2.11: tools for serializing data SUCCESS [  7.246 s]
[INFO] utils-intervalrdd-spark2_2.11: IntervalRDD based on interval tree SUCCESS [ 31.356 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:19 min
[INFO] Finished at: 2020-02-17T14:37:32-08:00
[INFO] Final Memory: 57M/1445M
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${UTILS_MVN_TMP_DIR}
+ find /tmp/utilsTestMvn0tnZ6FE
/tmp/utilsTestMvn0tnZ6FE
/tmp/utilsTestMvn0tnZ6FE/test.txt508392722251692034.txt
/tmp/utilsTestMvn0tnZ6FE/LocalFileLocatorSuite1876817468350951255test
/tmp/utilsTestMvn0tnZ6FE/LocalFileLocatorSuite289035590368902852test
/tmp/utilsTestMvn0tnZ6FE/test.txt2400461969587181354.txt
/tmp/utilsTestMvn0tnZ6FE/LocalFileLocatorSuite5061976244549916716test
/tmp/utilsTestMvn0tnZ6FE/LocalFileLocatorSuite2925222436342711703test
/tmp/utilsTestMvn0tnZ6FE/LocalFileLocatorSuite5800307105898779764test
/tmp/utilsTestMvn0tnZ6FE/LocalFileLocatorSuite1761879921897779052test
rm -rf ${UTILS_MVN_TMP_DIR}
+ rm -rf /tmp/utilsTestMvn0tnZ6FE

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/5b87e5d20757ff83948685f57dc61a6027c952e7
Finished: SUCCESS