Started by upstream project "bdg-utils-prb" build number 158 originally caused by: GitHub pull request #148 of commit 53cfc29e770b34f05786c299d576d6432ebbf6a3 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/2.12/SPARK_VERSION/2.4.0/label/ubuntu > git rev-parse --is-inside-work-tree # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/utils.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/utils.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/utils.git +refs/pull/*:refs/remotes/origin/pr/* Checking out Revision 76c6cd4309c3a4f9711e2fd089347912b1fab981 (origin/pr/148/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 76c6cd4309c3a4f9711e2fd089347912b1fab981 > git rev-list 0f99ef4d169db20d1e56f9c6250493413a8dab55 # timeout=10 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/hudson4162418701455458552.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=$(mktemp -d -t utilsTestMvnXXXXXXX) mktemp -d -t utilsTestMvnXXXXXXX ++ mktemp -d -t utilsTestMvnXXXXXXX + UTILS_MVN_TMP_DIR=/tmp/utilsTestMvnCBL5Wn6 # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/utilsTestMvnCBL5Wn6: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 ${BASH_SOURCE[0]} +++ dirname ./scripts/jenkins-test ++ cd ./scripts ++ pwd + DIR=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/scripts/.. VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g') grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g' ++ grep '<version>' /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.2.16-SNAPSHOT # is the hadoop version set? if ! [[ ${HADOOP_VERSION} ]]; then echo "HADOOP_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.7.5 ]] # is the spark version set? if ! [[ ${SPARK_VERSION} ]]; then echo "SPARK_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.4.0 ]] # is the scala version set? if ! [[ ${SCALA_VERSION} ]]; then echo "SCALA_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.12 ]] if [ ${SCALA_VERSION} == 2.11 ]; then # shouldn't be able to move to scala 2.11 twice set +e ./scripts/move_to_scala_2.11.sh if [[ $? == 0 ]]; then echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)." exit 1 fi set -e fi + '[' 2.12 == 2.11 ']' if [ ${SCALA_VERSION} == 2.12 ]; then ./scripts/move_to_scala_2.12.sh fi + '[' 2.12 == 2.12 ']' + ./scripts/move_to_scala_2.12.sh # print versions echo "Testing UTILS version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION} and Scala ${SCALA_VERSION}" + echo 'Testing UTILS version 0.2.16-SNAPSHOT on Spark 2.4.0 and Hadoop 2.7.5 and Scala 2.12' Testing UTILS version 0.2.16-SNAPSHOT on Spark 2.4.0 and Hadoop 2.7.5 and Scala 2.12 # if this is a pull request, we need to set the coveralls pr id if [[ ! -z $ghprbPullId ]]; then COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}" fi + [[ ! -z 148 ]] + COVERALLS_PRB_OPTION=-DpullRequest=148 # 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_2.12: Miscellaneous Spark utility code [INFO] utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator [INFO] utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs [INFO] utils-io-spark2_2.12: I/O utils [INFO] utils-statistics-spark2_2.12: Spark code for fitting statistical models [INFO] utils-cli-spark2_2.12: utilities for building command line applications [INFO] utils-serialization-spark2_2.12: tools for serializing data [INFO] utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-parent-spark2_2.12 --- [INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-misc-spark2_2.12: Miscellaneous Spark utility code 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-misc-spark2_2.12 --- [INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-minhash-spark2_2.12 --- [INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-metrics-spark2_2.12 --- [INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-io-spark2_2.12: I/O utils 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-io-spark2_2.12 --- [INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-statistics-spark2_2.12: Spark code for fitting statistical models 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-statistics-spark2_2.12 --- [INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-cli-spark2_2.12: utilities for building command line applications 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-cli-spark2_2.12 --- [INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-serialization-spark2_2.12: tools for serializing data 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-serialization-spark2_2.12 --- [INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-intervalrdd-spark2_2.12 --- [INFO] Deleting /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] utils .............................................. SUCCESS [ 0.301 s] [INFO] utils-misc-spark2_2.12: Miscellaneous Spark utility code SUCCESS [ 0.034 s] [INFO] utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 0.007 s] [INFO] utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs SUCCESS [ 0.015 s] [INFO] utils-io-spark2_2.12: I/O utils .................... SUCCESS [ 0.006 s] [INFO] utils-statistics-spark2_2.12: Spark code for fitting statistical models SUCCESS [ 0.006 s] [INFO] utils-cli-spark2_2.12: utilities for building command line applications SUCCESS [ 0.005 s] [INFO] utils-serialization-spark2_2.12: tools for serializing data SUCCESS [ 0.004 s] [INFO] utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree SUCCESS [ 0.010 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.708 s [INFO] Finished at: 2020-02-10T14:17:06-08:00 [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_2.12: Miscellaneous Spark utility code [INFO] utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator [INFO] utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs [INFO] utils-io-spark2_2.12: I/O utils [INFO] utils-statistics-spark2_2.12: Spark code for fitting statistical models [INFO] utils-cli-spark2_2.12: utilities for building command line applications [INFO] utils-serialization-spark2_2.12: tools for serializing data [INFO] utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-parent-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-parent-spark2_2.12 --- [INFO] Modified 0 of 81 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-parent-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-parent-spark2_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-parent-spark2_2.12 --- [INFO] Modified 0 of 81 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-parent-spark2_2.12 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-parent-spark2_2.12 --- [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-parent-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-parent-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-misc-spark2_2.12: Miscellaneous Spark utility code 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-misc-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-misc-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-misc-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-misc-spark2_2.12 --- [INFO] Modified 0 of 7 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-misc-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-misc-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/main/scala:-1: info: compiling [INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/2.12.8/classes at 1581373036995 [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-misc-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-misc-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-misc-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-misc-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/test/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/target/2.12.8/test-classes at 1581373044008 [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-misc-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-misc-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-misc-spark2_2.12 --- Discovery starting. Discovery completed in 176 milliseconds. Run starting. Expected test count is: 11 SparkFunSuiteSuite: 2020-02-10 14:17:32 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) 2020-02-10 14:17:32 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:17:33 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - a simple test using spark - copying a resource should pass equivalence testing - load a resource file MathUtilsSuite: - check equality with floating point comparison - check inequality with floating point comparison - compute factorials - test array aggregation in isolation - use array aggregator with an rdd - safe wrapped log should work - softmax an array - multiply an array by a scalar Run completed in 4 seconds, 374 milliseconds. Total number of tests run: 11 Suites: completed 3, aborted 0 Tests: succeeded 11, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-misc-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-misc-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-misc-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-misc-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-misc-spark2_2.12 --- [INFO] Modified 0 of 7 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-misc-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-misc-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-misc-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-misc-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-misc-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-misc-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-misc/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-misc-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-misc-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-misc-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-misc-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-misc-spark2_2.12 --- Discovery starting. Discovery completed in 158 milliseconds. Run starting. Expected test count is: 11 SparkFunSuiteSuite: 2020-02-10 14:17:41 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) 2020-02-10 14:17:41 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:17:42 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - a simple test using spark - copying a resource should pass equivalence testing - load a resource file MathUtilsSuite: - check equality with floating point comparison - check inequality with floating point comparison - compute factorials - test array aggregation in isolation - use array aggregator with an rdd - safe wrapped log should work - softmax an array - multiply an array by a scalar Run completed in 4 seconds, 548 milliseconds. Total number of tests run: 11 Suites: completed 3, aborted 0 Tests: succeeded 11, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-misc-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-misc-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/2.4.5/spark-mllib_2.12-2.4.5.pom 3/10 KB 5/10 KB 8/10 KB 10/10 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/2.4.5/spark-mllib_2.12-2.4.5.pom (10 KB at 14.1 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/apache/spark/spark-streaming_2.12/2.4.5/spark-streaming_2.12-2.4.5.pom 3/10 KB 5/10 KB 8/10 KB 10/10 KB Downloaded: 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KB 5100/5181 KB 1128/1128 KB 5104/5181 KB 1128/1128 KB 5108/5181 KB 1128/1128 KB 5112/5181 KB 1128/1128 KB 5116/5181 KB 1128/1128 KB 5120/5181 KB 1128/1128 KB 5124/5181 KB 1128/1128 KB 5128/5181 KB 1128/1128 KB 5132/5181 KB 1128/1128 KB 5136/5181 KB 1128/1128 KB 5140/5181 KB 1128/1128 KB 5144/5181 KB 1128/1128 KB 5148/5181 KB 1128/1128 KB 5152/5181 KB 1128/1128 KB 5156/5181 KB 1128/1128 KB 5160/5181 KB 1128/1128 KB 5164/5181 KB 1128/1128 KB 5168/5181 KB 1128/1128 KB 5172/5181 KB 1128/1128 KB 5176/5181 KB 1128/1128 KB 5180/5181 KB 1128/1128 KB 5181/5181 KB 1128/1128 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/spark/spark-streaming_2.12/2.4.5/spark-streaming_2.12-2.4.5.jar (1128 KB at 1193.2 KB/sec) Downloaded: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/2.4.5/spark-mllib_2.12-2.4.5.jar (5181 KB at 4477.8 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-minhash-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-minhash-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-minhash-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-minhash-spark2_2.12 --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-minhash-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-minhash-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/scala:-1: info: compiling [INFO] Compiling 6 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/2.12.8/classes at 1581373069940 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-minhash-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-minhash-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-minhash-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-minhash-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/scala:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/target/2.12.8/test-classes at 1581373076472 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-minhash-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-minhash-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-minhash-spark2_2.12 --- Discovery starting. Discovery completed in 215 milliseconds. Run starting. Expected test count is: 5 MinHashSuite: 2020-02-10 14:18:04 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) 2020-02-10 14:18:04 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:18:04 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - compute exact overlap for ten 1000 bp reads - compute approximate overlap for ten 1000 bp reads across different band sizes - should throw exception if we pick an illegal band count MinHashSignatureSuite: - compute the similarity of signatures - compute buckets for a simple signature Run completed in 6 seconds, 487 milliseconds. Total number of tests run: 5 Suites: completed 3, aborted 0 Tests: succeeded 5, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-minhash-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-minhash-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-minhash-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-minhash-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-minhash-spark2_2.12 --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-minhash-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-minhash-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-minhash-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-minhash-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-minhash-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-minhash-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-minhash-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-minhash/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-minhash-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-minhash-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-minhash-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-minhash-spark2_2.12 --- Discovery starting. Discovery completed in 204 milliseconds. Run starting. Expected test count is: 5 MinHashSuite: 2020-02-10 14:18:12 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) 2020-02-10 14:18:12 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:18:13 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - compute exact overlap for ten 1000 bp reads - compute approximate overlap for ten 1000 bp reads across different band sizes - should throw exception if we pick an illegal band count MinHashSignatureSuite: - compute the similarity of signatures - compute buckets for a simple signature Run completed in 6 seconds, 107 milliseconds. Total number of tests run: 5 Suites: completed 3, aborted 0 Tests: succeeded 5, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-minhash-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-minhash-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-metrics-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-metrics-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-metrics-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-metrics-spark2_2.12 --- [INFO] Modified 0 of 39 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-metrics-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-metrics-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala:-1: info: compiling [INFO] Compiling 22 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/2.12.8/classes at 1581373099260 [WARNING] warning: non-variable type argument com.netflix.servo.monitor.Monitor[_] in type pattern scala.runtime.NonLocalReturnControl[com.netflix.servo.monitor.Monitor[_]] is unchecked since it is eliminated by erasure [WARNING] warning: there were 5 deprecation warnings (since 2.0.0) [WARNING] warning: there were two deprecation warnings (since 2.12.0) [WARNING] warning: there were 7 deprecation warnings in total; re-run with -deprecation for details [WARNING] warning: there were three feature warnings; re-run with -feature for details [WARNING] 5 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 12 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-metrics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-metrics-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-metrics-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-metrics-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala:-1: info: compiling [INFO] Compiling 17 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/target/2.12.8/test-classes at 1581373111517 [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedOrderedRDDFunctionsSuite.scala:44: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val timerNames = timerMap.keys().map(_.timerName).toSet [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedPairRDDFunctionsSuite.scala:58: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val timers = Metrics.Recorder.value.get.accumulable.value.timerMap.filter(entry => [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:86: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assertOnNameAndCountInTimingsTable(dataRows.get(1), "map at InstrumentedRDDSuite.scala", 1) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:87: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assertOnNameAndCountInTimingsTable(dataRows.get(2), "function call", 10) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:88: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assertOnNameAndCountInTimingsTable(dataRows.get(3), "timer 1", 10) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/InstrumentedRDDSuite.scala:89: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] assertOnNameAndCountInTimingsTable(dataRows.get(4), "timer 2", 10) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsListenerSuite.scala:32: warning: method accumulator in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] val accumulator = sc.accumulator(0) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsListenerSuite.scala:32: warning: object IntAccumulatorParam in object AccumulatorParam is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] val accumulator = sc.accumulator(0) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsListenerSuite.scala:32: warning: object AccumulatorParam in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] val accumulator = sc.accumulator(0) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:30: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:30: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:39: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:39: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:56: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:56: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:70: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:70: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:84: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:84: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:95: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/MetricsRecorderSuite.scala:95: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] val accumulable = mock[Accumulable[ServoTimers, RecordedTiming]] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimerSuite.scala:94: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] timer.getMonitors.foreach(monitor => { [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:30: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] var accumulable: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers()) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:30: warning: method accumulable in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] var accumulable: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers()) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:70: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] var accumulable: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers()) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:70: warning: method accumulable in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] var accumulable: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers()) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:108: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] var accumulable1: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers()) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:108: warning: method accumulable in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] var accumulable1: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers()) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:114: warning: class Accumulable in package spark is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] var accumulable2: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers()) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParamSuite.scala:114: warning: method accumulable in class SparkContext is deprecated (since 2.0.0): use AccumulatorV2 [WARNING] var accumulable2: Accumulable[ServoTimers, RecordedTiming] = sc.accumulable(new ServoTimers()) [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TimerSuite.scala:34: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead [WARNING] val recorder = mock[MetricsRecorder] [WARNING] ^ [WARNING] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala/org/bdgenomics/utils/instrumentation/TimerSuite.scala:41: warning: value MockitoSugar in package mock is deprecated: Please use org.scalatest.mockito.MockitoSugar instead [WARNING] val recorder = mock[MetricsRecorder] [WARNING] ^ [WARNING] 32 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 11 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-metrics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-metrics-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-metrics-spark2_2.12 --- Discovery starting. Discovery completed in 303 milliseconds. Run starting. Expected test count is: 43 InstrumentedRDDSuite: 2020-02-10 14:18:44 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) 2020-02-10 14:18:44 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:18:44 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, 786 milliseconds. Total number of tests run: 43 Suites: completed 16, aborted 0 Tests: succeeded 43, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-metrics-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-metrics-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-metrics-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-metrics-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-metrics-spark2_2.12 --- [INFO] Modified 0 of 39 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-metrics-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-metrics-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-metrics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-metrics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-metrics-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-metrics-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-metrics-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-metrics/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-metrics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-metrics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-metrics-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-metrics-spark2_2.12 --- Discovery starting. Discovery completed in 274 milliseconds. Run starting. Expected test count is: 43 InstrumentedRDDSuite: 2020-02-10 14:18:55 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) 2020-02-10 14:18:55 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:18:55 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, 701 milliseconds. Total number of tests run: 43 Suites: completed 16, aborted 0 Tests: succeeded 43, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-metrics-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-metrics-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-io-spark2_2.12: I/O utils 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-io-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-io-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-io-spark2_2.12 --- [INFO] Modified 0 of 9 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-io-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-io-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/scala:-1: info: compiling [INFO] Compiling 8 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/2.12.8/classes at 1581373143719 [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-io-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-io-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-io-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/test/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/2.12.8/test-classes at 1581373148878 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-io-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark2_2.12 --- Discovery starting. Discovery completed in 175 milliseconds. Run starting. Expected test count is: 7 LocalFileLocatorSuite: - parentLocator retrieves the parent directory - relativeLocator retrieves a subdirectory - bytes accesses the named underlying file 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 ByteArrayLocatorSuite: - byte access can be wrapped in a locator correctly Run completed in 412 milliseconds. Total number of tests run: 7 Suites: completed 4, aborted 0 Tests: succeeded 7, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-io-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-io-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-io-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-io-spark2_2.12 --- [INFO] Modified 0 of 9 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-io-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-io-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-io-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-io-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-io-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-io-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-io-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-io-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark2_2.12 --- Discovery starting. Discovery completed in 154 milliseconds. Run starting. Expected test count is: 7 LocalFileLocatorSuite: - parentLocator retrieves the parent directory - relativeLocator retrieves a subdirectory - bytes accesses the named underlying file 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 ByteArrayLocatorSuite: - byte access can be wrapped in a locator correctly Run completed in 398 milliseconds. Total number of tests run: 7 Suites: completed 4, aborted 0 Tests: succeeded 7, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-io-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-io-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-statistics-spark2_2.12: Spark code for fitting statistical models 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-statistics-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-statistics-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-statistics-spark2_2.12 --- [INFO] Modified 0 of 6 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-statistics-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/2.12.8/classes at 1581373157508 [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_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-statistics-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-statistics-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-statistics-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/scala:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/2.12.8/test-classes at 1581373163917 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-statistics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-statistics-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-statistics-spark2_2.12 --- Discovery starting. Discovery completed in 154 milliseconds. Run starting. Expected test count is: 6 ZScoreNormalizationSuite: 2020-02-10 14:19:31 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) 2020-02-10 14:19:31 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:19:32 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - 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 PoissonMixtureModelSuite: - run the m step on a trivial example 2020-02-10 14:19:36 WARN KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2020-02-10 14:19:37 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2020-02-10 14:19:37 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS 2020-02-10 14:19:38 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 Run completed in 7 seconds, 916 milliseconds. Total number of tests run: 6 Suites: completed 3, aborted 0 Tests: succeeded 6, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-statistics-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-statistics-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-statistics-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-statistics-spark2_2.12 --- [INFO] Modified 0 of 6 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-statistics-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-statistics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-statistics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-statistics-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-statistics-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-statistics-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-statistics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-statistics-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-statistics-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-statistics-spark2_2.12 --- Discovery starting. Discovery completed in 139 milliseconds. Run starting. Expected test count is: 6 ZScoreNormalizationSuite: 2020-02-10 14:19:41 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) 2020-02-10 14:19:41 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:19:41 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - 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 PoissonMixtureModelSuite: - run the m step on a trivial example 2020-02-10 14:19:46 WARN KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2020-02-10 14:19:46 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2020-02-10 14:19:46 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS 2020-02-10 14:19:47 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 Run completed in 7 seconds, 788 milliseconds. Total number of tests run: 6 Suites: completed 3, aborted 0 Tests: succeeded 6, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-statistics-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-statistics-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-cli-spark2_2.12: utilities for building command line applications 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-cli-spark2_2.12 --- [INFO] Modified 0 of 3 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-cli-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/scala:-1: info: compiling [INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target/2.12.8/classes at 1581373188800 [WARNING] warning: there was one deprecation warning [WARNING] warning: there was one deprecation warning (since 2.12.0) [WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-cli-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-cli-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-cli-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-cli-spark2_2.12 --- [INFO] Modified 0 of 3 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-cli-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-cli-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-cli-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-cli-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-cli-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-serialization-spark2_2.12: tools for serializing data 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-serialization-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-serialization-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-serialization-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-serialization-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-serialization-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target/2.12.8/classes at 1581373194485 [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-serialization-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-serialization-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-serialization-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-serialization-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-serialization-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-serialization-spark2_2.12 --- Discovery starting. Discovery completed in 112 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 168 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-serialization-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-serialization-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-serialization-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-serialization-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-serialization-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-serialization-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-serialization-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-serialization-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-serialization-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-serialization-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-serialization-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-serialization-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-serialization-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-serialization-spark2_2.12 --- Discovery starting. Discovery completed in 111 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 172 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-serialization-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-serialization-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-intervalrdd-spark2_2.12 --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-intervalrdd-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/scala:-1: info: compiling [INFO] Compiling 5 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/2.12.8/classes at 1581373202972 [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-intervalrdd-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-intervalrdd-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-intervalrdd-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-intervalrdd-spark2_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/scala:-1: info: compiling [INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/2.12.8/test-classes at 1581373210303 [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-intervalrdd-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-intervalrdd-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-intervalrdd-spark2_2.12 --- Discovery starting. Discovery completed in 272 milliseconds. Run starting. Expected test count is: 31 IntervalRDDSuite: 2020-02-10 14:20:20 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) 2020-02-10 14:20:20 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:20:21 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 8 seconds, 403 milliseconds. Total number of tests run: 31 Suites: completed 4, aborted 0 Tests: succeeded 31, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-intervalrdd-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-intervalrdd-spark2_2.12 --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-intervalrdd-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-intervalrdd-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-intervalrdd-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-intervalrdd-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-intervalrdd-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-intervalrdd-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-intervalrdd-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-intervalrdd-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-intervalrdd-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-intervalrdd-spark2_2.12 --- Discovery starting. Discovery completed in 250 milliseconds. Run starting. Expected test count is: 31 IntervalRDDSuite: 2020-02-10 14:20:31 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) 2020-02-10 14:20:31 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-02-10 14:20:31 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 8 seconds, 205 milliseconds. Total number of tests run: 31 Suites: completed 4, aborted 0 Tests: succeeded 31, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-intervalrdd-spark2_2.12 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-intervalrdd-spark2_2.12 --- [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] Skipping SCoverage report generation [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building utils 0.2.16-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ utils-parent-spark2_2.12 --- [INFO] Starting Coveralls job for jenkins (158 / https://amplab.cs.berkeley.edu/jenkins/job/bdg-utils-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=2.4.0,label=ubuntu/158/) [INFO] Using repository token <secret> [INFO] Git commit 76c6cd4 in pr/148/merge [INFO] Writing Coveralls data to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/target/coveralls.json... [INFO] Processing coverage report from /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/target/cobertura.xml [INFO] Successfully wrote Coveralls data in 63ms [INFO] Gathered code coverage metrics for 0 source files with 0 lines of code: [INFO] - 0 relevant lines [INFO] - 0 covered lines [INFO] - 0 missed lines [INFO] Submitting Coveralls data to API [INFO] Successfully submitted Coveralls data in 693ms for Job #158.1 [INFO] https://coveralls.io/jobs/58808300 [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 [ 1.392 s] [INFO] utils-misc-spark2_2.12: Miscellaneous Spark utility code SUCCESS [ 32.855 s] [INFO] utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 32.304 s] [INFO] utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs SUCCESS [ 44.951 s] [INFO] utils-io-spark2_2.12: I/O utils .................... SUCCESS [ 13.792 s] [INFO] utils-statistics-spark2_2.12: Spark code for fitting statistical models SUCCESS [ 31.262 s] [INFO] utils-cli-spark2_2.12: utilities for building command line applications SUCCESS [ 5.049 s] [INFO] utils-serialization-spark2_2.12: tools for serializing data SUCCESS [ 9.089 s] [INFO] utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree SUCCESS [ 36.656 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 03:32 min [INFO] Finished at: 2020-02-10T14:20:40-08:00 [INFO] Final Memory: 61M/1450M [INFO] ------------------------------------------------------------------------ # we are done with maven, so clean up the maven temp dir find ${UTILS_MVN_TMP_DIR} + find /tmp/utilsTestMvnCBL5Wn6 /tmp/utilsTestMvnCBL5Wn6 /tmp/utilsTestMvnCBL5Wn6/LocalFileLocatorSuite476678941775538919test /tmp/utilsTestMvnCBL5Wn6/test.txt3971900274956829341.txt /tmp/utilsTestMvnCBL5Wn6/LocalFileLocatorSuite4809619300846366321test /tmp/utilsTestMvnCBL5Wn6/test.txt2550358440208398951.txt /tmp/utilsTestMvnCBL5Wn6/LocalFileLocatorSuite1986506674886864950test /tmp/utilsTestMvnCBL5Wn6/LocalFileLocatorSuite4354592173214132711test /tmp/utilsTestMvnCBL5Wn6/LocalFileLocatorSuite6656979543577599307test /tmp/utilsTestMvnCBL5Wn6/LocalFileLocatorSuite6696548939470699444test rm -rf ${UTILS_MVN_TMP_DIR} + rm -rf /tmp/utilsTestMvnCBL5Wn6 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/76c6cd4309c3a4f9711e2fd089347912b1fab981 Finished: SUCCESS