Console Output

Started by upstream project "bdg-utils-prb" build number 169
originally caused by:
 GitHub pull request #169 of commit defb164657156a1b6be644ad065b71825bd7e8d5, no merge conflicts.
Running as SYSTEM
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-staging-worker-02 (ubuntu ubuntu-gpu ubuntu-avx2 staging-02 staging) in workspace /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu
The recommended git tool is: NONE
No credentials specified
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/utils.git
 > git init /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/utils.git
 > git --version # timeout=10
 > git --version # 'git version 2.7.4'
 > git fetch --tags --progress https://github.com/bigdatagenomics/utils.git +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/bigdatagenomics/utils.git # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/bigdatagenomics/utils.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/utils.git
 > git fetch --tags --progress https://github.com/bigdatagenomics/utils.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=10
Checking out Revision 69b614a3cc501ac9a2376ce3450f5da30e051127 (refs/remotes/origin/pr/169/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 69b614a3cc501ac9a2376ce3450f5da30e051127 # timeout=10
Commit message: "Merge defb164657156a1b6be644ad065b71825bd7e8d5 into ca8592e2f43113d33e8b1245cf579df2a15c0a76"
First time build. Skipping changelog.
[EnvInject] - Executing scripts and injecting environment variables after the SCM step.
[EnvInject] - Injecting as environment variables the properties content 
JAVA_HOME=/usr/lib/jvm/java-8-oracle

[EnvInject] - Variables injected successfully.
[ubuntu] $ /bin/bash /tmp/jenkins6715467809723290378.sh
+ set -e
+ export JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ ./scripts/jenkins-test

# make a tempdir for writing maven cruft to
UTILS_MVN_TMP_DIR=$(mktemp -d -t utilsTestMvnXXXXXXX)
mktemp -d -t utilsTestMvnXXXXXXX
++ mktemp -d -t utilsTestMvnXXXXXXX
+ UTILS_MVN_TMP_DIR=/tmp/utilsTestMvnf2HC12D

# 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/utilsTestMvnf2HC12D:g' '{}' ';'
find . -name "*.bak" -exec rm {} \;
+ find . -name '*.bak' -exec rm '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8"
+ export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
+ MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )
 cd $( dirname ${BASH_SOURCE[0]} ) && pwd 
 dirname ${BASH_SOURCE[0]} 
+++ dirname ./scripts/jenkins-test
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/scripts/..
VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g'
++ grep '<version>' /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/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 2.12 ]]

# 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 2.12'
Testing bdg-utils version 0.4.0-SNAPSHOT on Spark 2.4.6 and Hadoop 2.7.5 and Scala 2.12

# 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 [  0.247 s]
[INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code SUCCESS [  0.026 s]
[INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator SUCCESS [  0.004 s]
[INFO] utils-io-spark3_2.12: I/O utils .................... SUCCESS [  0.005 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 [  0.004 s]
[INFO] utils-serialization-spark3_2.12: tools for serializing data SUCCESS [  0.004 s]
[INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree SUCCESS [  0.003 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.458 s
[INFO] Finished at: 2021-01-27T12:32:09-08:00
[INFO] ------------------------------------------------------------------------

# if those pass, build the distribution package and the integration tests
mvn -U test
+ mvn -U test
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] utils                                                              [pom]
[INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code           [jar]
[INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator [jar]
[INFO] utils-io-spark3_2.12: I/O utils                                    [jar]
[INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models [jar]
[INFO] utils-cli-spark3_2.12: utilities for building command line applications [jar]
[INFO] utils-serialization-spark3_2.12: tools for serializing data        [jar]
[INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree  [jar]
[INFO] 
[INFO] -----------< org.bdgenomics.utils:utils-parent-spark3_2.12 >------------
[INFO] Building utils 0.4.0-SNAPSHOT                                      [1/8]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-parent-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-parent-spark3_2.12 ---
[INFO] Modified 0 of 40 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] ------------< org.bdgenomics.utils:utils-misc-spark3_2.12 >-------------
[INFO] Building utils-misc-spark3_2.12: Miscellaneous Spark utility code 0.4.0-SNAPSHOT [2/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-misc-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-misc-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-misc-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-misc-spark3_2.12 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-misc-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-misc-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/2.12.8/classes at 1611779535678
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-misc-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-misc-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-misc-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-misc-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/src/test/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-misc/target/2.12.8/test-classes at 1611779541232
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-misc-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-misc-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-misc-spark3_2.12 ---
Discovery starting.
Discovery completed in 157 milliseconds.
Run starting. Expected test count is: 11
SparkFunSuiteSuite:
2021-01-27 12:32:29 WARN  Utils:69 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2021-01-27 12:32:29 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-01-27 12:32:29 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- a simple test using spark
- copying a resource should pass equivalence testing
- load a resource file
MathUtilsSuite:
- check equality with floating point comparison
- check inequality with floating point comparison
- compute factorials
- test array aggregation in isolation
- use array aggregator with an rdd
- safe wrapped log should work
- softmax an array
- multiply an array by a scalar
Run completed in 4 seconds, 200 milliseconds.
Total number of tests run: 11
Suites: completed 3, aborted 0
Tests: succeeded 11, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] -----------< org.bdgenomics.utils:utils-minhash-spark3_2.12 >-----------
[INFO] Building utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator 0.4.0-SNAPSHOT [3/8]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/3.0.1/spark-mllib_2.12-3.0.1.pom
Progress (1): 2.7/11 kB
Progress (1): 5.5/11 kB
Progress (1): 8.2/11 kB
Progress (1): 11 kB    
                   
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/3.0.1/spark-mllib_2.12-3.0.1.pom (11 kB at 20 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/3.0.1/spark-mllib_2.12-3.0.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-streaming_2.12/3.0.1/spark-streaming_2.12-3.0.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib-local_2.12/3.0.1/spark-mllib-local_2.12-3.0.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-graphx_2.12/3.0.1/spark-graphx_2.12-3.0.1.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib-local_2.12/3.0.1/spark-mllib-local_2.12-3.0.1.jar (0 B at 0 B/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-graphx_2.12/3.0.1/spark-graphx_2.12-3.0.1.jar (0 B at 0 B/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-streaming_2.12/3.0.1/spark-streaming_2.12-3.0.1.jar (0 B at 0 B/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/3.0.1/spark-mllib_2.12-3.0.1.jar (0 B at 0 B/s)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-minhash-spark3_2.12 ---
[INFO] 
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[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-minhash-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/main/scala added.
[INFO] 
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[INFO] Modified 0 of 8 .scala files
[INFO] 
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[INFO] Using 'UTF-8' encoding to copy filtered resources.
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[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-minhash-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/main/scala:-1: info: compiling
[INFO] Compiling 6 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/2.12.8/classes at 1611779556300
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
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[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-minhash-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/test/scala added.
[INFO] 
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[INFO] Using 'UTF-8' encoding to copy filtered resources.
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[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-minhash-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/src/test/scala:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-minhash/target/2.12.8/test-classes at 1611779562313
[INFO] prepare-compile in 0 s
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[INFO] 
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[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-minhash-spark3_2.12 ---
Discovery starting.
Discovery completed in 181 milliseconds.
Run starting. Expected test count is: 5
MinHashSuite:
2021-01-27 12:32:49 WARN  Utils:69 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2021-01-27 12:32:49 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-01-27 12:32:49 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- compute exact overlap for ten 1000 bp reads
- compute approximate overlap for ten 1000 bp reads across different band sizes
- should throw exception if we pick an illegal band count
MinHashSignatureSuite:
- compute the similarity of signatures
- compute buckets for a simple signature
Run completed in 6 seconds, 154 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] 
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[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/main/scala added.
[INFO] 
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[INFO] Modified 0 of 9 .scala files
[INFO] 
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[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-io-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/main/scala:-1: info: compiling
[INFO] Compiling 8 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/2.12.8/classes at 1611779575924
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
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[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-io-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-io-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-io-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-io/target/2.12.8/test-classes at 1611779581146
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
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[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark3_2.12 ---
Discovery starting.
Discovery completed in 165 milliseconds.
Run starting. Expected test count is: 7
LocalFileLocatorSuite:
- parentLocator retrieves the parent directory
- relativeLocator retrieves a subdirectory
- bytes accesses the named underlying file
ByteArrayLocatorSuite:
- byte access can be wrapped in a locator correctly
FileLocatorSuite:
- parseSlash can correctly parse a one-slash string
- parseSlash can correctly parse a two-slash string
- parseSlash can correctly parse a no-slash string
Run completed in 364 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] 
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[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-statistics-spark3_2.12 ---
[INFO] Modified 0 of 6 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-statistics-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/2.12.8/classes at 1611779587649
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-statistics-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-statistics-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-statistics-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-statistics-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/src/test/scala:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-statistics/target/2.12.8/test-classes at 1611779593757
[INFO] prepare-compile in 0 s
[INFO] compile in 5 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 155 milliseconds.
Run starting. Expected test count is: 6
PoissonMixtureModelSuite:
2021-01-27 12:33:20 WARN  Utils:69 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2021-01-27 12:33:20 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-01-27 12:33:20 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- run the m step on a trivial example
2021-01-27 12:33:25 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2021-01-27 12:33:25 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
- fit a poisson to several thousand points
ZScoreNormalizationSuite:
- compute mean of a set of samples
- compute variance of a set of samples
- variance should be 0 if all elements are the same
- check z-score for a varying rdd
Run completed in 7 seconds, 617 milliseconds.
Total number of tests run: 6
Suites: completed 3, aborted 0
Tests: succeeded 6, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] -------------< org.bdgenomics.utils:utils-cli-spark3_2.12 >-------------
[INFO] Building utils-cli-spark3_2.12: utilities for building command line applications 0.4.0-SNAPSHOT [6/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/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] 
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[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-cli-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/target/2.12.8/classes at 1611779608173
[WARNING] warning: there was one deprecation warning
[WARNING] warning: there was one deprecation warning (since 2.12.0)
[WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details
[WARNING] three warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-cli-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-cli/src/test/scala added.
[INFO] 
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[INFO] 
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[INFO] No sources to compile
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[INFO] No sources to compile
[INFO] 
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[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] 
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[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/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] 
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[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-serialization-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/target/2.12.8/classes at 1611779613783
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-serialization-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-serialization/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-serialization-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/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] 
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[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 106 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 153 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] ---------< org.bdgenomics.utils:utils-intervalrdd-spark3_2.12 >---------
[INFO] Building utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree 0.4.0-SNAPSHOT [8/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-intervalrdd-spark3_2.12 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ utils-intervalrdd-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/main/scala:-1: info: compiling
[INFO] Compiling 5 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/2.12.8/classes at 1611779619449
[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-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-intervalrdd-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ utils-intervalrdd-spark3_2.12 ---
[INFO] /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/src/test/scala:-1: info: compiling
[INFO] Compiling 3 source files to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.6/label/ubuntu/utils-intervalrdd/target/2.12.8/test-classes at 1611779625909
[INFO] prepare-compile in 0 s
[INFO] compile in 7 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 170 milliseconds.
Run starting. Expected test count is: 31
IntervalRDDSuite:
2021-01-27 12:33:54 WARN  Utils:69 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2021-01-27 12:33:54 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-01-27 12:33:54 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- create IntervalRDD from RDD of datatype string
- merge new values into existing IntervalRDD
- call put multiple times on data with same interval
- test filterByInterval
- verify no data is lost in conversion from rdd to intervalrdd
- count data where chromosome partitions overlap
- get data where chromosome partitions overlap
- apply predicate to the RDD
- testing collect
- test before and after toRDD sizes are the same
- testing mapValues
- Attempt to access data from non existing key
- Delete values from rdd
- Repartitions IntervalRDD
IntervalPartitionSuite:
- create new partition
- create partition from iterator
- get values from iterator-created partition
- correctly fetches data that is initially unsorted
- put some for iterator of intervals and key-values
- get some for iterator of intervals
- selectively getting intervals
- putting differing number of reads into different regions
- putting then getting a region that overlaps 3 regions
- applying a predicate
- applying a map
IntervalArraySuite:
- succeeds in searching empty IntervalArray
- build a IntervalArray with a single item and retrieve data
- build a IntervalArray out of multiple datapoints and retrieve data
- verify get with requireOverlap set to false on IntervalArray retrieves nearest data
- verify IntervalArray fetches all valid ranges
- inserts new elements into IntervalArray
Run completed in 6 seconds, 513 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 [  2.670 s]
[INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code SUCCESS [ 19.886 s]
[INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 22.173 s]
[INFO] utils-io-spark3_2.12: I/O utils .................... SUCCESS [ 11.501 s]
[INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models SUCCESS [ 20.808 s]
[INFO] utils-cli-spark3_2.12: utilities for building command line applications SUCCESS [  5.675 s]
[INFO] utils-serialization-spark3_2.12: tools for serializing data SUCCESS [  5.315 s]
[INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree SUCCESS [ 22.158 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:50 min
[INFO] Finished at: 2021-01-27T12:34:00-08:00
[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/utilsTestMvnf2HC12D
/tmp/utilsTestMvnf2HC12D
/tmp/utilsTestMvnf2HC12D/LocalFileLocatorSuite7686759132253363366test
/tmp/utilsTestMvnf2HC12D/LocalFileLocatorSuite7689451642284051107test
/tmp/utilsTestMvnf2HC12D/test.txt7220038519501577246.txt
/tmp/utilsTestMvnf2HC12D/LocalFileLocatorSuite20925656377790166test
rm -rf ${UTILS_MVN_TMP_DIR}
+ rm -rf /tmp/utilsTestMvnf2HC12D

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

Recording test results
[Checks API] No suitable checks publisher found.
[Set GitHub commit status (universal)] SUCCESS on repos [GHRepository@2a7c48f0[nodeId=MDEwOlJlcG9zaXRvcnkyNDQxOTgzNw==,description=General utility code used across BDG products. Apache 2 licensed.,homepage=,name=utils,fork=false,archived=false,size=629,milestones={},language=Scala,commits={},source=<null>,parent=<null>,isTemplate=<null>,url=https://api.github.com/repos/bigdatagenomics/utils,id=24419837,nodeId=<null>,createdAt=2014-09-24T15:07:01Z,updatedAt=2020-06-21T21:58:11Z]] (sha:69b614a) with context:bdg-utils-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=2.4.6,label=ubuntu
Setting commit status on GitHub for https://github.com/bigdatagenomics/utils/commit/69b614a3cc501ac9a2376ce3450f5da30e051127
Finished: SUCCESS