Started by upstream project "bdg-utils-prb" build number 169 originally caused by: GitHub pull request #169 of commit defb164657156a1b6be644ad065b71825bd7e8d5, no merge conflicts. Running as SYSTEM [EnvInject] - Loading node environment variables. Building remotely on amp-jenkins-staging-worker-02 (ubuntu ubuntu-gpu ubuntu-avx2 staging-02 staging) in workspace /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu The recommended git tool is: NONE No credentials specified Cloning the remote Git repository Cloning repository https://github.com/bigdatagenomics/utils.git > git init /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/utils.git > git --version # timeout=10 > git --version # 'git version 2.7.4' > git fetch --tags --progress https://github.com/bigdatagenomics/utils.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/utils.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/utils.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/utils.git > git fetch --tags --progress https://github.com/bigdatagenomics/utils.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=10 Checking out Revision 69b614a3cc501ac9a2376ce3450f5da30e051127 (refs/remotes/origin/pr/169/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 69b614a3cc501ac9a2376ce3450f5da30e051127 # timeout=10 Commit message: "Merge defb164657156a1b6be644ad065b71825bd7e8d5 into ca8592e2f43113d33e8b1245cf579df2a15c0a76" 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/jenkins5732411937202894285.sh + set -e + export JAVA_HOME=/usr/lib/jvm/java-8-oracle + JAVA_HOME=/usr/lib/jvm/java-8-oracle + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + ./scripts/jenkins-test # make a tempdir for writing maven cruft to UTILS_MVN_TMP_DIR=$(mktemp -d -t utilsTestMvnXXXXXXX) mktemp -d -t utilsTestMvnXXXXXXX ++ mktemp -d -t utilsTestMvnXXXXXXX + UTILS_MVN_TMP_DIR=/tmp/utilsTestMvnFeFiugB # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/utilsTestMvnFeFiugB:g' '{}' ';' find . -name "*.bak" -exec rm {} \; + find . -name '*.bak' -exec rm '{}' ';' # variable declarations export PATH=${JAVA_HOME}/bin/:${PATH} + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8" + export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' + MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd ) cd $( dirname ${BASH_SOURCE[0]} ) && pwd dirname ${BASH_SOURCE[0]} +++ dirname ./scripts/jenkins-test ++ cd ./scripts ++ pwd + DIR=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/.. VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g') grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g' ++ grep '<version>' /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.4.0-SNAPSHOT # is the hadoop version set? if ! [[ ${HADOOP_VERSION} ]]; then echo "HADOOP_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.7.5 ]] # is the spark version set? if ! [[ ${SPARK_VERSION} ]]; then echo "SPARK_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.4.6 ]] # is the scala version set? if ! [[ ${SCALA_VERSION} ]]; then echo "SCALA_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.11 ]] # print versions echo "Testing bdg-utils version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION} and Scala ${SCALA_VERSION}" + echo 'Testing bdg-utils version 0.4.0-SNAPSHOT on Spark 2.4.6 and Hadoop 2.7.5 and Scala 2.11' Testing bdg-utils version 0.4.0-SNAPSHOT on Spark 2.4.6 and Hadoop 2.7.5 and Scala 2.11 # clean before building mvn clean + mvn clean Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] utils [pom] [INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code [jar] [INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator [jar] [INFO] utils-io-spark3_2.12: I/O utils [jar] [INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models [jar] [INFO] utils-cli-spark3_2.12: utilities for building command line applications [jar] [INFO] utils-serialization-spark3_2.12: tools for serializing data [jar] [INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree [jar] [INFO] [INFO] -----------< org.bdgenomics.utils:utils-parent-spark3_2.12 >------------ [INFO] Building utils 0.4.0-SNAPSHOT [1/8] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-parent-spark3_2.12 --- [INFO] [INFO] ------------< org.bdgenomics.utils:utils-misc-spark3_2.12 >------------- [INFO] Building utils-misc-spark3_2.12: Miscellaneous Spark utility code 0.4.0-SNAPSHOT [2/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-misc-spark3_2.12 --- [INFO] [INFO] -----------< org.bdgenomics.utils:utils-minhash-spark3_2.12 >----------- [INFO] Building utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator 0.4.0-SNAPSHOT [3/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-minhash-spark3_2.12 --- [INFO] [INFO] -------------< org.bdgenomics.utils:utils-io-spark3_2.12 >-------------- [INFO] Building utils-io-spark3_2.12: I/O utils 0.4.0-SNAPSHOT [4/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-io-spark3_2.12 --- [INFO] [INFO] ---------< org.bdgenomics.utils:utils-statistics-spark3_2.12 >---------- [INFO] Building utils-statistics-spark3_2.12: Spark code for fitting statistical models 0.4.0-SNAPSHOT [5/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-statistics-spark3_2.12 --- [INFO] [INFO] -------------< org.bdgenomics.utils:utils-cli-spark3_2.12 >------------- [INFO] Building utils-cli-spark3_2.12: utilities for building command line applications 0.4.0-SNAPSHOT [6/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-cli-spark3_2.12 --- [INFO] [INFO] --------< org.bdgenomics.utils:utils-serialization-spark3_2.12 >-------- [INFO] Building utils-serialization-spark3_2.12: tools for serializing data 0.4.0-SNAPSHOT [7/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-serialization-spark3_2.12 --- [INFO] [INFO] ---------< org.bdgenomics.utils:utils-intervalrdd-spark3_2.12 >--------- [INFO] Building utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree 0.4.0-SNAPSHOT [8/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ utils-intervalrdd-spark3_2.12 --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for utils 0.4.0-SNAPSHOT: [INFO] [INFO] utils .............................................. SUCCESS [ 0.197 s] [INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code SUCCESS [ 0.018 s] [INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 0.003 s] [INFO] utils-io-spark3_2.12: I/O utils .................... SUCCESS [ 0.003 s] [INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models SUCCESS [ 0.002 s] [INFO] utils-cli-spark3_2.12: utilities for building command line applications SUCCESS [ 0.003 s] [INFO] utils-serialization-spark3_2.12: tools for serializing data SUCCESS [ 0.002 s] [INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree SUCCESS [ 0.003 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.413 s [INFO] Finished at: 2021-01-27T12:32:09-08:00 [INFO] ------------------------------------------------------------------------ # if those pass, build the distribution package and the integration tests mvn -U test + mvn -U test Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] utils [pom] [INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code [jar] [INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator [jar] [INFO] utils-io-spark3_2.12: I/O utils [jar] [INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models [jar] [INFO] utils-cli-spark3_2.12: utilities for building command line applications [jar] [INFO] utils-serialization-spark3_2.12: tools for serializing data [jar] [INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree [jar] [INFO] [INFO] -----------< org.bdgenomics.utils:utils-parent-spark3_2.12 >------------ [INFO] Building utils 0.4.0-SNAPSHOT [1/8] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-parent-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-parent-spark3_2.12 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-parent-spark3_2.12 --- [INFO] Modified 0 of 40 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-parent-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-parent-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] ------------< org.bdgenomics.utils:utils-misc-spark3_2.12 >------------- [INFO] Building utils-misc-spark3_2.12: Miscellaneous Spark utility code 0.4.0-SNAPSHOT [2/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-misc-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-misc-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-misc-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-misc-spark3_2.12 --- [INFO] Modified 0 of 5 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-misc-spark3_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-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/src/main/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/2.12.8/classes at 1611779535358 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-misc-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-misc-spark3_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-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/src/test/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/2.12.8/test-classes at 1611779541170 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-misc-spark3_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-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-misc-spark3_2.12 --- Discovery starting. Discovery completed in 149 milliseconds. Run starting. Expected test count is: 11 SparkFunSuiteSuite: 2021-01-27 12:32:28 WARN Utils:69 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1) 2021-01-27 12:32:28 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2021-01-27 12:32:29 WARN NativeCodeLoader:60 - 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, 650 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] -----------< org.bdgenomics.utils:utils-minhash-spark3_2.12 >----------- [INFO] Building utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator 0.4.0-SNAPSHOT [3/8] [INFO] --------------------------------[ jar ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/3.0.1/spark-mllib_2.12-3.0.1.pom Progress (1): 2.7/11 kB Progress (1): 5.5/11 kB Progress (1): 8.2/11 kB Progress (1): 11 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/3.0.1/spark-mllib_2.12-3.0.1.pom (11 kB at 27 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-streaming_2.12/3.0.1/spark-streaming_2.12-3.0.1.pom Progress (1): 2.7/10 kB Progress (1): 5.5/10 kB Progress (1): 8.2/10 kB Progress (1): 10 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-streaming_2.12/3.0.1/spark-streaming_2.12-3.0.1.pom (10 kB at 518 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-graphx_2.12/3.0.1/spark-graphx_2.12-3.0.1.pom Progress (1): 2.7/7.0 kB Progress (1): 5.5/7.0 kB Progress (1): 7.0 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-graphx_2.12/3.0.1/spark-graphx_2.12-3.0.1.pom (7.0 kB at 93 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib-local_2.12/3.0.1/spark-mllib-local_2.12-3.0.1.pom Progress (1): 2.7/4.4 kB Progress (1): 4.4 kB Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib-local_2.12/3.0.1/spark-mllib-local_2.12-3.0.1.pom (4.4 kB at 368 kB/s) Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/3.0.1/spark-mllib_2.12-3.0.1.jar Downloading from central: 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https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/3.0.1/spark-mllib_2.12-3.0.1.jar (5.9 MB at 5.6 MB/s) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-minhash-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-minhash-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-minhash-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-minhash-spark3_2.12 --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-minhash-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-minhash-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/main/scala:-1: info: compiling [INFO] Compiling 6 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/2.12.8/classes at 1611779556029 [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-minhash-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-minhash-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-minhash-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/test/scala:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/2.12.8/test-classes at 1611779562034 [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-minhash-spark3_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-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-minhash-spark3_2.12 --- Discovery starting. Discovery completed in 150 milliseconds. Run starting. Expected test count is: 5 MinHashSuite: 2021-01-27 12:32:49 WARN Utils:69 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1) 2021-01-27 12:32:49 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2021-01-27 12:32:49 WARN NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - compute exact overlap for ten 1000 bp reads - compute approximate overlap for ten 1000 bp reads across different band sizes - should throw exception if we pick an illegal band count MinHashSignatureSuite: - compute the similarity of signatures - compute buckets for a simple signature Run completed in 5 seconds, 317 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] -------------< org.bdgenomics.utils:utils-io-spark3_2.12 >-------------- [INFO] Building utils-io-spark3_2.12: I/O utils 0.4.0-SNAPSHOT [4/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-io-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-io-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-io-spark3_2.12 --- [INFO] Modified 0 of 9 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-io-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-io-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/main/scala:-1: info: compiling [INFO] Compiling 8 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/2.12.8/classes at 1611779575122 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-io-spark3_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-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/test/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/2.12.8/test-classes at 1611779580149 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-spark3_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-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark3_2.12 --- Discovery starting. Discovery completed in 125 milliseconds. Run starting. Expected test count is: 7 LocalFileLocatorSuite: - parentLocator retrieves the parent directory - relativeLocator retrieves a subdirectory - bytes accesses the named underlying file ByteArrayLocatorSuite: - byte access can be wrapped in a locator correctly FileLocatorSuite: - parseSlash can correctly parse a one-slash string - parseSlash can correctly parse a two-slash string - parseSlash can correctly parse a no-slash string Run completed in 262 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] ---------< org.bdgenomics.utils:utils-statistics-spark3_2.12 >---------- [INFO] Building utils-statistics-spark3_2.12: Spark code for fitting statistical models 0.4.0-SNAPSHOT [5/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-statistics-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-statistics-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-statistics-spark3_2.12 --- [INFO] Modified 0 of 6 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-statistics-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/2.12.8/classes at 1611779586775 [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-statistics-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-statistics-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-statistics-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/test/scala:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/2.12.8/test-classes at 1611779592454 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-statistics-spark3_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-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-statistics-spark3_2.12 --- Discovery starting. Discovery completed in 125 milliseconds. Run starting. Expected test count is: 6 PoissonMixtureModelSuite: 2021-01-27 12:33:18 WARN Utils:69 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1) 2021-01-27 12:33:18 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2021-01-27 12:33:18 WARN NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - run the m step on a trivial example 2021-01-27 12:33:23 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2021-01-27 12:33:23 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS - fit a poisson to several thousand points ZScoreNormalizationSuite: - compute mean of a set of samples - compute variance of a set of samples - variance should be 0 if all elements are the same - check z-score for a varying rdd Run completed in 7 seconds, 144 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] -------------< org.bdgenomics.utils:utils-cli-spark3_2.12 >------------- [INFO] Building utils-cli-spark3_2.12: utilities for building command line applications 0.4.0-SNAPSHOT [6/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-cli-spark3_2.12 --- [INFO] Modified 0 of 3 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-cli-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-cli-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/src/main/scala:-1: info: compiling [INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/target/2.12.8/classes at 1611779605969 [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 3 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-cli-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-cli-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-cli-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-cli-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --------< org.bdgenomics.utils:utils-serialization-spark3_2.12 >-------- [INFO] Building utils-serialization-spark3_2.12: tools for serializing data 0.4.0-SNAPSHOT [7/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-serialization-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-serialization-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-serialization-spark3_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-serialization-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-serialization-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/src/main/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/target/2.12.8/classes at 1611779611065 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-serialization-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-serialization-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-serialization-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-serialization-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-serialization-spark3_2.12 --- Discovery starting. Discovery completed in 103 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 160 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] ---------< org.bdgenomics.utils:utils-intervalrdd-spark3_2.12 >--------- [INFO] Building utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree 0.4.0-SNAPSHOT [8/8] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-intervalrdd-spark3_2.12 --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-intervalrdd-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/main/scala:-1: info: compiling [INFO] Compiling 5 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/2.12.8/classes at 1611779616293 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-intervalrdd-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-intervalrdd-spark3_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/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-intervalrdd-spark3_2.12 --- [INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/test/scala:-1: info: compiling [INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/2.12.8/test-classes at 1611779622980 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-intervalrdd-spark3_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-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-intervalrdd-spark3_2.12 --- Discovery starting. Discovery completed in 190 milliseconds. Run starting. Expected test count is: 31 IntervalRDDSuite: 2021-01-27 12:33:51 WARN Utils:69 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1) 2021-01-27 12:33:51 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2021-01-27 12:33:51 WARN NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - create IntervalRDD from RDD of datatype string - merge new values into existing IntervalRDD - call put multiple times on data with same interval - test filterByInterval - verify no data is lost in conversion from rdd to intervalrdd - count data where chromosome partitions overlap - get data where chromosome partitions overlap - apply predicate to the RDD - testing collect - test before and after toRDD sizes are the same - testing mapValues - Attempt to access data from non existing key - Delete values from rdd - Repartitions IntervalRDD IntervalPartitionSuite: - create new partition - create partition from iterator - get values from iterator-created partition - correctly fetches data that is initially unsorted - put some for iterator of intervals and key-values - get some for iterator of intervals - selectively getting intervals - putting differing number of reads into different regions - putting then getting a region that overlaps 3 regions - applying a predicate - applying a map IntervalArraySuite: - succeeds in searching empty IntervalArray - build a IntervalArray with a single item and retrieve data - build a IntervalArray out of multiple datapoints and retrieve data - verify get with requireOverlap set to false on IntervalArray retrieves nearest data - verify IntervalArray fetches all valid ranges - inserts new elements into IntervalArray Run completed in 6 seconds, 498 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] Reactor Summary for utils 0.4.0-SNAPSHOT: [INFO] [INFO] utils .............................................. SUCCESS [ 2.350 s] [INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code SUCCESS [ 19.937 s] [INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 21.139 s] [INFO] utils-io-spark3_2.12: I/O utils .................... SUCCESS [ 11.653 s] [INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models SUCCESS [ 19.339 s] [INFO] utils-cli-spark3_2.12: utilities for building command line applications SUCCESS [ 5.319 s] [INFO] utils-serialization-spark3_2.12: tools for serializing data SUCCESS [ 4.985 s] [INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree SUCCESS [ 21.659 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:46 min [INFO] Finished at: 2021-01-27T12:33:57-08:00 [INFO] ------------------------------------------------------------------------ # make verbose again set -x -v + set -x -v # we are done with maven, so clean up the maven temp dir find ${UTILS_MVN_TMP_DIR} + find /tmp/utilsTestMvnFeFiugB /tmp/utilsTestMvnFeFiugB /tmp/utilsTestMvnFeFiugB/LocalFileLocatorSuite1475708133941365724test /tmp/utilsTestMvnFeFiugB/test.txt3698768067322580684.txt /tmp/utilsTestMvnFeFiugB/LocalFileLocatorSuite7915709769582208732test /tmp/utilsTestMvnFeFiugB/LocalFileLocatorSuite694989474996517380test rm -rf ${UTILS_MVN_TMP_DIR} + rm -rf /tmp/utilsTestMvnFeFiugB echo + echo echo "All the tests passed" + echo 'All the tests passed' All the tests passed echo + echo Recording test results [Checks API] No suitable checks publisher found. [Set GitHub commit status (universal)] SUCCESS on repos [GHRepository@11b8f41a[nodeId=MDEwOlJlcG9zaXRvcnkyNDQxOTgzNw==,description=General utility code used across BDG products. Apache 2 licensed.,homepage=,name=utils,fork=false,archived=false,size=629,milestones={},language=Scala,commits={},source=<null>,parent=<null>,isTemplate=<null>,url=https://api.github.com/repos/bigdatagenomics/utils,id=24419837,nodeId=<null>,createdAt=2014-09-24T15:07:01Z,updatedAt=2020-06-21T21:58:11Z]] (sha:69b614a) with context:bdg-utils-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.11,SPARK_VERSION=2.4.6,label=ubuntu Setting commit status on GitHub for https://github.com/bigdatagenomics/utils/commit/69b614a3cc501ac9a2376ce3450f5da30e051127 Finished: SUCCESS