Started by upstream project "bdg-utils" build number 2175 originally caused by: Started by timer Running as SYSTEM [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-07 (research-07 ubuntu) in workspace /home/jenkins/workspace/bdg-utils/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/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 Avoid second fetch Checking out Revision 084aa218b2f2a812e0cce62902c2b3169c9d901b (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 084aa218b2f2a812e0cce62902c2b3169c9d901b # timeout=10 Commit message: "Default build to Spark 3.0.1 and Scala 2.12." > git rev-list --no-walk 084aa218b2f2a812e0cce62902c2b3169c9d901b # timeout=10 [EnvInject] - Executing scripts and injecting environment variables after the SCM step. [EnvInject] - Injecting as environment variables the properties content JAVA_HOME=/usr/lib/jvm/java-8-oracle [EnvInject] - Variables injected successfully. [ubuntu] $ /bin/bash /tmp/jenkins4652469403187050901.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 + /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to UTILS_MVN_TMP_DIR=$(mktemp -d -t utilsTestMvnXXXXXXX) mktemp -d -t utilsTestMvnXXXXXXX ++ mktemp -d -t utilsTestMvnXXXXXXX + UTILS_MVN_TMP_DIR=/tmp/utilsTestMvnWWVYuvA # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/utilsTestMvnWWVYuvA: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 ${BASH_SOURCE[0]} +++ dirname /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/bdg-utils/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/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 [ 0.180 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 [ 0.004 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 [ 0.003 s] [INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree SUCCESS [ 0.003 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.383 s [INFO] Finished at: 2021-03-10T22:26:45-08:00 [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/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/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/2.12.8/classes at 1615444010747 [INFO] prepare-compile in 0 s [INFO] compile in 3 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/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/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/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 1615444014996 [INFO] prepare-compile in 0 s [INFO] compile in 5 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 134 milliseconds. Run starting. Expected test count is: 11 SparkFunSuiteSuite: 2021-03-10 22:27:01 WARN Utils:69 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2021-03-10 22:27:01 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2021-03-10 22:27:02 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 3 seconds, 291 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 ]--------------------------------- [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/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/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/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/2.12.8/classes at 1615444025667 [INFO] prepare-compile in 0 s [INFO] compile in 4 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/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/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/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/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 1615444031247 [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: 2021-03-10 22:27:17 WARN Utils:69 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2021-03-10 22:27:17 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2021-03-10 22:27:17 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 4 seconds, 747 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/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/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/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/2.12.8/classes at 1615444042791 [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/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/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/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 1615444047539 [INFO] prepare-compile in 0 s [INFO] compile in 3 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 114 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 244 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/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/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/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/2.12.8/classes at 1615444053433 [INFO] prepare-compile in 0 s [INFO] compile in 4 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/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/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/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/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 1615444058875 [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 122 milliseconds. Run starting. Expected test count is: 6 ZScoreNormalizationSuite: 2021-03-10 22:27:44 WARN Utils:69 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2021-03-10 22:27:44 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2021-03-10 22:27:45 WARN NativeCodeLoader:60 - 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 2021-03-10 22:27:49 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2021-03-10 22:27:49 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS - fit a poisson to several thousand points Run completed in 6 seconds, 388 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/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/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/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/target/2.12.8/classes at 1615444071445 [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/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/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/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/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/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/target/2.12.8/classes at 1615444076447 [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/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/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 90 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 136 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/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/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/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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/2.12.8/classes at 1615444081045 [INFO] prepare-compile in 0 s [INFO] compile in 5 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/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/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/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/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 1615444086956 [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 157 milliseconds. Run starting. Expected test count is: 31 IntervalRDDSuite: 2021-03-10 22:28:15 WARN Utils:69 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0) 2021-03-10 22:28:15 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2021-03-10 22:28:15 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 5 seconds, 906 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 [ 2.105 s] [INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code SUCCESS [ 15.843 s] [INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 17.440 s] [INFO] utils-io-spark3_2.12: I/O utils .................... SUCCESS [ 10.540 s] [INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models SUCCESS [ 18.112 s] [INFO] utils-cli-spark3_2.12: utilities for building command line applications SUCCESS [ 5.125 s] [INFO] utils-serialization-spark3_2.12: tools for serializing data SUCCESS [ 4.458 s] [INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree SUCCESS [ 20.254 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:34 min [INFO] Finished at: 2021-03-10T22:28:20-08:00 [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/utilsTestMvnWWVYuvA /tmp/utilsTestMvnWWVYuvA /tmp/utilsTestMvnWWVYuvA/LocalFileLocatorSuite3263284667926101706test /tmp/utilsTestMvnWWVYuvA/LocalFileLocatorSuite5469031149133052523test /tmp/utilsTestMvnWWVYuvA/test.txt1876969915904240653.txt /tmp/utilsTestMvnWWVYuvA/LocalFileLocatorSuite350600351939880312test rm -rf ${UTILS_MVN_TMP_DIR} + rm -rf /tmp/utilsTestMvnWWVYuvA echo + echo echo "All the tests passed" + echo 'All the tests passed' All the tests passed echo + echo + '[' 2.7.5 == 2.7.5 ']' + mvn --settings=/home/jenkins/workspace/settings.xml deploy -DskipTests -Pdistribution [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] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ utils-parent-spark3_2.12 >>> [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] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ utils-parent-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ utils-parent-spark3_2.12 --- [INFO] No source files found [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ utils-parent-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-parent-spark3_2.12/0.4.0-SNAPSHOT/utils-parent-spark3_2.12-0.4.0-SNAPSHOT.pom [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ utils-parent-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 625 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml (625 B at 1.2 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/0.4.0-SNAPSHOT/utils-parent-spark3_2.12-0.4.0-20210311.062825-127.pom Progress (1): 4.1/18 kB Progress (1): 8.2/18 kB Progress (1): 12/18 kB Progress (1): 16/18 kB Progress (1): 18 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/0.4.0-SNAPSHOT/utils-parent-spark3_2.12-0.4.0-20210311.062825-127.pom (18 kB at 33 kB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/maven-metadata.xml Progress (1): 364 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/maven-metadata.xml (364 B at 2.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 625 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml (625 B at 1.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/maven-metadata.xml Progress (1): 364 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-parent-spark3_2.12/maven-metadata.xml (364 B at 793 B/s) [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/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] Nothing to compile - all classes are up to date [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/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] Nothing to compile - all classes are up to date [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 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ utils-misc-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/utils-misc-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ utils-misc-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/utils-misc-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ utils-misc-spark3_2.12 >>> [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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ utils-misc-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ utils-misc-spark3_2.12 --- model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/utils-misc-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ utils-misc-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/utils-misc-spark3_2.12-0.4.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark3_2.12/0.4.0-SNAPSHOT/utils-misc-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark3_2.12/0.4.0-SNAPSHOT/utils-misc-spark3_2.12-0.4.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/utils-misc-spark3_2.12-0.4.0-SNAPSHOT-tests.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark3_2.12/0.4.0-SNAPSHOT/utils-misc-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/utils-misc-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark3_2.12/0.4.0-SNAPSHOT/utils-misc-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ 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https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-misc-spark3_2.12/maven-metadata.xml Progress (1): 362 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-misc-spark3_2.12/maven-metadata.xml (362 B at 591 B/s) [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-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/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/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] Nothing to compile - all classes are up to date [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/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/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] Nothing to compile - all classes are up to date [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 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ utils-minhash-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/utils-minhash-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ utils-minhash-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/utils-minhash-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ utils-minhash-spark3_2.12 >>> [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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ utils-minhash-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ utils-minhash-spark3_2.12 --- model contains 10 documentable templates /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/main/scala/org/bdgenomics/utils/minhash/MinHash.scala:72: warning: Could not find any member to link for "IllegalArgumentException". /** ^ one warning found [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/utils-minhash-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ utils-minhash-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/utils-minhash-spark3_2.12-0.4.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-minhash-spark3_2.12/0.4.0-SNAPSHOT/utils-minhash-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-minhash-spark3_2.12/0.4.0-SNAPSHOT/utils-minhash-spark3_2.12-0.4.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/utils-minhash-spark3_2.12-0.4.0-SNAPSHOT-tests.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-minhash-spark3_2.12/0.4.0-SNAPSHOT/utils-minhash-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] Installing 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https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-minhash-spark3_2.12/maven-metadata.xml (365 B at 643 B/s) [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/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/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] Nothing to compile - all classes are up to date [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/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] Nothing to compile - all classes are up to date [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 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ utils-io-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/utils-io-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ utils-io-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/utils-io-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ utils-io-spark3_2.12 >>> [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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ utils-io-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ utils-io-spark3_2.12 --- model contains 14 documentable templates [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/utils-io-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ utils-io-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/utils-io-spark3_2.12-0.4.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark3_2.12/0.4.0-SNAPSHOT/utils-io-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark3_2.12/0.4.0-SNAPSHOT/utils-io-spark3_2.12-0.4.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/utils-io-spark3_2.12-0.4.0-SNAPSHOT-tests.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark3_2.12/0.4.0-SNAPSHOT/utils-io-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/utils-io-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark3_2.12/0.4.0-SNAPSHOT/utils-io-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ utils-io-spark3_2.12 --- 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from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-io-spark3_2.12/maven-metadata.xml Progress (1): 360 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-io-spark3_2.12/maven-metadata.xml (360 B at 2.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-io-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-io-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 2.7 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-io-spark3_2.12/maven-metadata.xml Progress (1): 360 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-io-spark3_2.12/maven-metadata.xml (360 B at 794 B/s) [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/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/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] Nothing to compile - all classes are up to date [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/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/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] Nothing to compile - all classes are up to date [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 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ utils-statistics-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ utils-statistics-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ utils-statistics-spark3_2.12 >>> [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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ utils-statistics-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ utils-statistics-spark3_2.12 --- model contains 11 documentable templates [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ utils-statistics-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT-tests.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/utils-statistics-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ utils-statistics-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 8.3 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/utils-statistics-spark3_2.12-0.4.0-20210311.062923-127.jar Progress (1): 4.1/26 kB Progress (1): 8.2/26 kB Progress (1): 12/26 kB Progress (1): 16/26 kB Progress (1): 20/26 kB Progress (1): 25/26 kB Progress (1): 26 kB Uploaded to sonatype-nexus-snapshots: 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Progress (1): 1.2/1.2 MB Progress (1): 1.2 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/utils-statistics-spark3_2.12-0.4.0-20210311.062923-127-javadoc.jar (1.2 MB at 1.6 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/maven-metadata.xml Progress (1): 368 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/maven-metadata.xml (368 B at 2.6 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 2.2 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/maven-metadata.xml Progress (1): 368 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-statistics-spark3_2.12/maven-metadata.xml (368 B at 815 B/s) [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/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/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] Nothing to compile - all classes are up to date [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/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/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] --- maven-jar-plugin:3.2.0:jar (default-jar) @ utils-cli-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/target/utils-cli-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ utils-cli-spark3_2.12 >>> [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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ utils-cli-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ utils-cli-spark3_2.12 --- model contains 17 documentable templates [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/target/utils-cli-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ utils-cli-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/target/utils-cli-spark3_2.12-0.4.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark3_2.12/0.4.0-SNAPSHOT/utils-cli-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark3_2.12/0.4.0-SNAPSHOT/utils-cli-spark3_2.12-0.4.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/target/utils-cli-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark3_2.12/0.4.0-SNAPSHOT/utils-cli-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ utils-cli-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-cli-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.0 kB Downloaded from sonatype-nexus-snapshots: 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(1): 1.2 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-cli-spark3_2.12/0.4.0-SNAPSHOT/utils-cli-spark3_2.12-0.4.0-20210311.062933-126-javadoc.jar (1.2 MB at 1.6 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-cli-spark3_2.12/maven-metadata.xml Progress (1): 361 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-cli-spark3_2.12/maven-metadata.xml (361 B at 2.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-cli-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.0 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-cli-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml (1.0 kB at 2.2 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-cli-spark3_2.12/maven-metadata.xml Progress (1): 361 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-cli-spark3_2.12/maven-metadata.xml (361 B at 786 B/s) [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/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/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] Nothing to compile - all classes are up to date [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/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/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 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ utils-serialization-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/target/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ utils-serialization-spark3_2.12 --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/target/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ utils-serialization-spark3_2.12 >>> [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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ utils-serialization-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ utils-serialization-spark3_2.12 --- model contains 7 documentable templates [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/target/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ utils-serialization-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/target/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-serialization-spark3_2.12/0.4.0-SNAPSHOT/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-serialization-spark3_2.12/0.4.0-SNAPSHOT/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/target/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT-tests.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-serialization-spark3_2.12/0.4.0-SNAPSHOT/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/target/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-serialization-spark3_2.12/0.4.0-SNAPSHOT/utils-serialization-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ utils-serialization-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-serialization-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-serialization-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 8.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-serialization-spark3_2.12/0.4.0-SNAPSHOT/utils-serialization-spark3_2.12-0.4.0-20210311.062941-127.jar Progress (1): 4.1/4.6 kB Progress (1): 4.6 kB Uploaded to sonatype-nexus-snapshots: 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Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-serialization-spark3_2.12/maven-metadata.xml Progress (1): 371 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-serialization-spark3_2.12/maven-metadata.xml (371 B at 817 B/s) [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/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/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] Nothing to compile - all classes are up to date [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/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/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] Nothing to compile - all classes are up to date [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 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ utils-intervalrdd-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ utils-intervalrdd-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ utils-intervalrdd-spark3_2.12 >>> [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/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ utils-intervalrdd-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ utils-intervalrdd-spark3_2.12 --- model contains 17 documentable templates [INFO] Building jar: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ utils-intervalrdd-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT-tests.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT-tests.jar [INFO] Installing /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/utils-intervalrdd-spark3_2.12-0.4.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ utils-intervalrdd-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 8.3 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/utils-intervalrdd-spark3_2.12-0.4.0-20210311.062953-127.jar Progress (1): 4.1/50 kB Progress (1): 8.2/50 kB Progress (1): 12/50 kB Progress (1): 16/50 kB Progress (1): 20/50 kB Progress (1): 25/50 kB Progress (1): 29/50 kB Progress (1): 33/50 kB Progress (1): 37/50 kB Progress (1): 41/50 kB Progress (1): 45/50 kB Progress 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MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.2/1.2 MB Progress (1): 1.2/1.2 MB Progress (1): 1.2/1.2 MB Progress (1): 1.2/1.2 MB Progress (1): 1.2/1.2 MB Progress (1): 1.2/1.2 MB Progress (1): 1.2/1.2 MB Progress (1): 1.2 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/utils-intervalrdd-spark3_2.12-0.4.0-20210311.062953-127-javadoc.jar (1.2 MB at 1.7 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/maven-metadata.xml Progress (1): 369 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/maven-metadata.xml (369 B at 2.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.4.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 2.7 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/maven-metadata.xml Progress (1): 369 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/maven-metadata.xml (369 B at 820 B/s) [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for utils 0.4.0-SNAPSHOT: [INFO] [INFO] utils .............................................. SUCCESS [ 4.869 s] [INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code SUCCESS [ 19.024 s] [INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 19.483 s] [INFO] utils-io-spark3_2.12: I/O utils .................... SUCCESS [ 10.246 s] [INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models SUCCESS [ 10.911 s] [INFO] utils-cli-spark3_2.12: utilities for building command line applications SUCCESS [ 9.614 s] [INFO] utils-serialization-spark3_2.12: tools for serializing data SUCCESS [ 8.742 s] [INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree SUCCESS [ 11.552 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:34 min [INFO] Finished at: 2021-03-10T22:29:56-08:00 [INFO] ------------------------------------------------------------------------ [WARNING] The requested profile "distribution" could not be activated because it does not exist. Recording test results [Checks API] No suitable checks publisher found. Finished: SUCCESS