Started by upstream project "bdg-utils-prb" build number 160 originally caused by: GitHub pull request #156 of commit 777e9ba8f203388274d5a198e6b67880a9747393 automatically merged. [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-09 (ubuntu ubuntu-gpu research-09 ubuntu-avx2) in workspace /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu Cloning the remote Git repository Cloning repository https://github.com/bigdatagenomics/utils.git > git init /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.0/label/ubuntu # 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/heads/*:refs/remotes/origin/* > git config remote.origin.url https://github.com/bigdatagenomics/utils.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/utils.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/utils.git > git fetch --tags --progress https://github.com/bigdatagenomics/utils.git +refs/pull/*:refs/remotes/origin/pr/* Checking out Revision 7f8836eb4001daad053692261eccd380b72c303b (origin/pr/156/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 7f8836eb4001daad053692261eccd380b72c303b 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/hudson6559672835543718546.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=$(mktemp -d -t utilsTestMvnXXXXXXX) mktemp -d -t utilsTestMvnXXXXXXX ++ mktemp -d -t utilsTestMvnXXXXXXX + UTILS_MVN_TMP_DIR=/tmp/utilsTestMvnVYYqqCJ # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/utilsTestMvnVYYqqCJ: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 ++ sed 's/ *<version>//g' ++ tail -1 ++ 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 156 ]] + COVERALLS_PRB_OPTION=-DpullRequest=156 # coveralls token should not be visible set +x +v + set +x +v OpenJDK 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] [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] [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] [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] [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] [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] [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] [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] [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] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] utils .............................................. SUCCESS [ 0.279 s] [INFO] utils-misc-spark2_2.11: Miscellaneous Spark utility code SUCCESS [ 0.024 s] [INFO] utils-minhash-spark2_2.11: MinHash-based Jaccard similarity estimator SUCCESS [ 0.002 s] [INFO] utils-metrics-spark2_2.11: tools for collecting metrics on top of RDDs SUCCESS [ 0.002 s] [INFO] utils-io-spark2_2.11: I/O utils .................... SUCCESS [ 0.002 s] [INFO] utils-statistics-spark2_2.11: Spark code for fitting statistical models SUCCESS [ 0.002 s] [INFO] utils-cli-spark2_2.11: utilities for building command line applications SUCCESS [ 0.001 s] [INFO] utils-serialization-spark2_2.11: tools for serializing data SUCCESS [ 0.002 s] [INFO] utils-intervalrdd-spark2_2.11: IntervalRDD based on interval tree SUCCESS [ 0.002 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.583 s [INFO] Finished at: 2020-02-17T13:39:37-08:00 [INFO] Final Memory: 22M/1472M [INFO] ------------------------------------------------------------------------ OpenJDK 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 84 .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 84 .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 7 .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 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-misc/target/2.11.12/classes at 1581975586867 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-misc-spark2_2.11 --- [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 1581975593099 [INFO] prepare-compile in 0 s [INFO] compile in 6 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 119 milliseconds. Run starting. Expected test count is: 11 SparkFunSuiteSuite: 2020-02-17 13:40:00 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:40:00 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:40:00 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - a simple test using spark - copying a resource should pass equivalence testing - load a resource file MathUtilsSuite: - check equality with floating point comparison - check inequality with floating point comparison - compute factorials - test array aggregation in isolation - use array aggregator with an rdd - safe wrapped log should work - softmax an array - multiply an array by a scalar Run completed in 3 seconds, 558 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 7 .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 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-misc/target/2.11.12/scoverage-classes at 1581975606096 [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 [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [INFO] [info] Instrumentation completed [141 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 4 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 163 milliseconds. Run starting. Expected test count is: 11 SparkFunSuiteSuite: 2020-02-17 13:40:13 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:40:13 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:40:13 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - a simple test using spark - copying a resource should pass equivalence testing - load a resource file MathUtilsSuite: - check equality with floating point comparison - check inequality with floating point comparison - compute factorials - test array aggregation in isolation - use array aggregator with an rdd - safe wrapped log should work - softmax an array - multiply an array by a scalar Run completed in 3 seconds, 711 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 1581975617917 [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-minhash-spark2_2.11 --- [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 1581975623486 [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-minhash-spark2_2.11 --- [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 146 milliseconds. Run starting. Expected test count is: 5 MinHashSignatureSuite: - compute the similarity of signatures - compute buckets for a simple signature MinHashSuite: 2020-02-17 13:40:30 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:40:30 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:40:30 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 4 seconds, 727 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 1581975635344 [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 5 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 163 milliseconds. Run starting. Expected test count is: 5 MinHashSignatureSuite: - compute the similarity of signatures - compute buckets for a simple signature MinHashSuite: 2020-02-17 13:40:42 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:40:42 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:40:42 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 23 seconds, 880 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 1581975666771 [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 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] --- 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 1581975678703 [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 10 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 282 milliseconds. Run starting. Expected test count is: 43 InstrumentedRDDSuite: 2020-02-17 13:41:30 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:41:30 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:41:30 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 8 seconds, 73 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 1581975698831 [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 13 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 337 milliseconds. Run starting. Expected test count is: 43 InstrumentedRDDSuite: 2020-02-17 13:41:53 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:41:53 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:41:54 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 8 seconds, 747 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 1581975723421 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-spark2_2.11 --- [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 1581975728056 [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 103 milliseconds. Run starting. Expected test count is: 7 LocalFileLocatorSuite: - parentLocator retrieves the parent directory - relativeLocator retrieves a subdirectory - bytes accesses the named underlying file ByteArrayLocatorSuite: - byte access can be wrapped in a locator correctly FileLocatorSuite: - parseSlash can correctly parse a one-slash string - parseSlash can correctly parse a two-slash string - parseSlash can correctly parse a no-slash string Run completed in 234 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 1581975733164 [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 4 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 99 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 246 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 1581975739070 [INFO] prepare-compile in 0 s [INFO] compile in 6 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 1581975745270 [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 150 milliseconds. Run starting. Expected test count is: 6 PoissonMixtureModelSuite: 2020-02-17 13:42:30 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:42:30 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:42:31 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 13:42:34 WARN KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2020-02-17 13:42:34 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2020-02-17 13:42:34 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS 2020-02-17 13:42:35 WARN KMeans:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached. - fit a poisson to several thousand points ZScoreNormalizationSuite: - compute mean of a set of samples - compute variance of a set of samples - variance should be 0 if all elements are the same - check z-score for a varying rdd Run completed in 6 seconds, 632 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 1581975757823 [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 7 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 192 milliseconds. Run starting. Expected test count is: 6 PoissonMixtureModelSuite: 2020-02-17 13:42:46 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:42:46 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:42:46 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 13:42:49 WARN KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2020-02-17 13:42:49 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2020-02-17 13:42:49 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS 2020-02-17 13:42:50 WARN KMeans:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached. - fit a poisson to several thousand points ZScoreNormalizationSuite: - compute mean of a set of samples - compute variance of a set of samples - variance should be 0 if all elements are the same - check z-score for a varying rdd Run completed in 6 seconds, 530 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 1581975773095 [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 4 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 1581975777300 [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 4 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 1581975782651 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark2_2.11 --- [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 76 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 109 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 1581975786972 [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 97 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 164 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 1581975790647 [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 1581975796088 [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 180 milliseconds. Run starting. Expected test count is: 31 IntervalRDDSuite: 2020-02-17 13:43:23 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:43:23 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:43:24 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 6 seconds, 201 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 1581975810452 [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 6 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 177 milliseconds. Run starting. Expected test count is: 31 IntervalRDDSuite: 2020-02-17 13:43:37 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-02-17 13:43:37 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-17 13:43:37 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - create IntervalRDD from RDD of datatype string - merge new values into existing IntervalRDD - call put multiple times on data with same interval - test filterByInterval - verify no data is lost in conversion from rdd to intervalrdd - count data where chromosome partitions overlap - get data where chromosome partitions overlap - apply predicate to the RDD - testing collect - test before and after toRDD sizes are the same - testing mapValues - Attempt to access data from non existing key - Delete values from rdd - Repartitions IntervalRDD IntervalPartitionSuite: - create new partition - create partition from iterator - get values from iterator-created partition - correctly fetches data that is initially unsorted - put some for iterator of intervals and key-values - get some for iterator of intervals - selectively getting intervals - putting differing number of reads into different regions - putting then getting a region that overlaps 3 regions - applying a predicate - applying a map IntervalArraySuite: - succeeds in searching empty IntervalArray - build a IntervalArray with a single item and retrieve data - build a IntervalArray out of multiple datapoints and retrieve data - verify get with requireOverlap set to false on IntervalArray retrieves nearest data - verify IntervalArray fetches all valid ranges - inserts new elements into IntervalArray Run completed in 6 seconds, 367 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 (160 / 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/160/) [INFO] Using repository token <secret> [INFO] Git commit 7f8836e in pr/156/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 146ms [INFO] Gathered code coverage metrics for 50 source files with 6274 lines of code: [INFO] - 1548 relevant lines [INFO] - 842 covered lines [INFO] - 706 missed lines [INFO] Submitting Coveralls data to API [INFO] Successfully submitted Coveralls data in 696ms for Job #160.1 [INFO] https://coveralls.io/jobs/59072624 [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 [ 1.306 s] [INFO] utils-misc-spark2_2.11: Miscellaneous Spark utility code SUCCESS [ 33.671 s] [INFO] utils-minhash-spark2_2.11: MinHash-based Jaccard similarity estimator SUCCESS [ 48.519 s] [INFO] utils-metrics-spark2_2.11: tools for collecting metrics on top of RDDs SUCCESS [ 57.175 s] [INFO] utils-io-spark2_2.11: I/O utils .................... SUCCESS [ 15.658 s] [INFO] utils-statistics-spark2_2.11: Spark code for fitting statistical models SUCCESS [ 33.995 s] [INFO] utils-cli-spark2_2.11: utilities for building command line applications SUCCESS [ 8.857 s] [INFO] utils-serialization-spark2_2.11: tools for serializing data SUCCESS [ 8.688 s] [INFO] utils-intervalrdd-spark2_2.11: IntervalRDD based on interval tree SUCCESS [ 35.154 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 04:07 min [INFO] Finished at: 2020-02-17T13:43:46-08:00 [INFO] Final Memory: 58M/1331M [INFO] ------------------------------------------------------------------------ # we are done with maven, so clean up the maven temp dir find ${UTILS_MVN_TMP_DIR} + find /tmp/utilsTestMvnVYYqqCJ /tmp/utilsTestMvnVYYqqCJ /tmp/utilsTestMvnVYYqqCJ/LocalFileLocatorSuite4182102204511282711test /tmp/utilsTestMvnVYYqqCJ/LocalFileLocatorSuite5521799818507059210test /tmp/utilsTestMvnVYYqqCJ/LocalFileLocatorSuite7781711585946853687test /tmp/utilsTestMvnVYYqqCJ/test.txt9026519581048504333.txt /tmp/utilsTestMvnVYYqqCJ/LocalFileLocatorSuite4381638773617260801test /tmp/utilsTestMvnVYYqqCJ/LocalFileLocatorSuite1984885909594767749test /tmp/utilsTestMvnVYYqqCJ/test.txt332594142233671260.txt /tmp/utilsTestMvnVYYqqCJ/LocalFileLocatorSuite236085161376715298test rm -rf ${UTILS_MVN_TMP_DIR} + rm -rf /tmp/utilsTestMvnVYYqqCJ 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/7f8836eb4001daad053692261eccd380b72c303b Finished: SUCCESS