Console Output

Started by upstream project "bdg-utils" build number 2177
originally caused by:
 Started by timer
Running as SYSTEM
[EnvInject] - Loading node environment variables.
Building remotely on ubuntu-testing (ubuntu ubuntu-testing-gpu) in workspace /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/jenkins4926066594516824061.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/2.12/SPARK_VERSION/3.0.0/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/utilsTestMvn3BoPH2s

# 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/utilsTestMvn3BoPH2s: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 ${BASH_SOURCE[0]} 
+++ dirname /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts/..
VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g'
++ grep '<version>' /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/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 3.0.0 ]]

# is the scala version set?
if ! [[ ${SCALA_VERSION} ]];
then
    echo "SCALA_VERSION environment variable is not set."
    echo "Please set this variable before running."
    exit 1
fi
+ [[ -n 2.12 ]]

# 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 3.0.0 and Hadoop 2.7.5 and Scala 2.12'
Testing bdg-utils version 0.4.0-SNAPSHOT on Spark 3.0.0 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 [  0.168 s]
[INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code SUCCESS [  0.017 s]
[INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator SUCCESS [  0.002 s]
[INFO] utils-io-spark3_2.12: I/O utils .................... SUCCESS [  0.003 s]
[INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models SUCCESS [  0.002 s]
[INFO] utils-cli-spark3_2.12: utilities for building command line applications SUCCESS [  0.002 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 [  0.002 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.350 s
[INFO] Finished at: 2021-03-16T07:49:08-07:00
[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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-misc/target/2.12.8/classes at 1615906153245
[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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-misc/target/2.12.8/test-classes at 1615906157481
[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 123 milliseconds.
Run starting. Expected test count is: 11
SparkFunSuiteSuite:
2021-03-16 07:49:23 WARN  Utils:69 - Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
2021-03-16 07:49:23 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-03-16 07:49:24 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, 514 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
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Progress (1): 8.2/11 kB
Progress (1): 11 kB    
                   
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-mllib_2.12/3.0.1/spark-mllib_2.12-3.0.1.pom (11 kB at 27 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-streaming_2.12/3.0.1/spark-streaming_2.12-3.0.1.pom
Progress (1): 2.7/10 kB
Progress (1): 5.5/10 kB
Progress (1): 8.2/10 kB
Progress (1): 10 kB    
                   
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-streaming_2.12/3.0.1/spark-streaming_2.12-3.0.1.pom (10 kB at 129 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-graphx_2.12/3.0.1/spark-graphx_2.12-3.0.1.pom
Progress (1): 2.7/7.0 kB
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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 (5.9 MB at 5.6 MB/s)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-minhash-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-minhash-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-minhash-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-minhash/target/2.12.8/classes at 1615906170066
[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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-minhash/target/2.12.8/test-classes at 1615906175431
[INFO] prepare-compile in 0 s
[INFO] compile in 4 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 155 milliseconds.
Run starting. Expected test count is: 5
MinHashSignatureSuite:
- compute the similarity of signatures
- compute buckets for a simple signature
MinHashSuite:
2021-03-16 07:49:41 WARN  Utils:69 - Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
2021-03-16 07:49:41 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-03-16 07:49:41 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
Run completed in 4 seconds, 865 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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-io/target/2.12.8/classes at 1615906186670
[INFO] prepare-compile in 0 s
[INFO] compile in 3 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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-io/target/2.12.8/test-classes at 1615906191022
[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 110 milliseconds.
Run starting. Expected test count is: 7
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
LocalFileLocatorSuite:
- parentLocator retrieves the parent directory
- relativeLocator retrieves a subdirectory
- bytes accesses the named underlying file
Run completed in 241 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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-statistics/target/2.12.8/classes at 1615906196669
[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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-statistics/target/2.12.8/test-classes at 1615906201873
[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 123 milliseconds.
Run starting. Expected test count is: 6
ZScoreNormalizationSuite:
2021-03-16 07:50:07 WARN  Utils:69 - Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
2021-03-16 07:50:07 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-03-16 07:50:07 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
2021-03-16 07:50:12 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2021-03-16 07:50:12 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, 614 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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-cli/target/2.12.8/classes at 1615906214453
[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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-serialization/target/2.12.8/classes at 1615906219011
[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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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 88 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 131 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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-intervalrdd/target/2.12.8/classes at 1615906223420
[INFO] prepare-compile in 0 s
[INFO] compile in 4 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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/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/2.12/SPARK_VERSION/3.0.0/label/ubuntu/utils-intervalrdd/target/2.12.8/test-classes at 1615906228830
[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 168 milliseconds.
Run starting. Expected test count is: 31
IntervalRDDSuite:
2021-03-16 07:50:36 WARN  Utils:69 - Your hostname, ubuntu-testing resolves to a loopback address: 127.0.1.1; using 192.168.10.30 instead (on interface eno1)
2021-03-16 07:50:36 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-03-16 07:50:36 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, 414 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 [  1.749 s]
[INFO] utils-misc-spark3_2.12: Miscellaneous Spark utility code SUCCESS [ 15.550 s]
[INFO] utils-minhash-spark3_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 18.875 s]
[INFO] utils-io-spark3_2.12: I/O utils .................... SUCCESS [  9.939 s]
[INFO] utils-statistics-spark3_2.12: Spark code for fitting statistical models SUCCESS [ 17.933 s]
[INFO] utils-cli-spark3_2.12: utilities for building command line applications SUCCESS [  4.709 s]
[INFO] utils-serialization-spark3_2.12: tools for serializing data SUCCESS [  4.279 s]
[INFO] utils-intervalrdd-spark3_2.12: IntervalRDD based on interval tree SUCCESS [ 19.716 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:32 min
[INFO] Finished at: 2021-03-16T07:50:42-07:00
[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/utilsTestMvn3BoPH2s
/tmp/utilsTestMvn3BoPH2s
/tmp/utilsTestMvn3BoPH2s/LocalFileLocatorSuite8337221425190277538test
/tmp/utilsTestMvn3BoPH2s/LocalFileLocatorSuite4083789949382688333test
/tmp/utilsTestMvn3BoPH2s/LocalFileLocatorSuite8692734226906342204test
/tmp/utilsTestMvn3BoPH2s/test.txt5465368908772951680.txt
rm -rf ${UTILS_MVN_TMP_DIR}
+ rm -rf /tmp/utilsTestMvn3BoPH2s

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
[ERROR] Error executing Maven.
[ERROR] The specified user settings file does not exist: /home/jenkins/workspace/settings.xml
Build step 'Execute shell' marked build as failure
Recording test results
[Checks API] No suitable checks publisher found.
Sending e-mails to: fnothaft@berkeley.edu
ERROR: Couldn't connect to host, port: 127.0.0.1, 25; timeout 60000
com.sun.mail.util.MailConnectException: Couldn't connect to host, port: 127.0.0.1, 25; timeout 60000;
  nested exception is:
	java.net.ConnectException: Connection refused (Connection refused)
	at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2210)
	at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:722)
	at javax.mail.Service.connect(Service.java:342)
	at javax.mail.Service.connect(Service.java:222)
	at javax.mail.Service.connect(Service.java:171)
	at javax.mail.Transport.send0(Transport.java:230)
	at javax.mail.Transport.send(Transport.java:100)
	at hudson.tasks.MailSender.run(MailSender.java:130)
	at hudson.tasks.Mailer.perform(Mailer.java:176)
	at hudson.tasks.Mailer.perform(Mailer.java:139)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:803)
	at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:752)
	at hudson.model.Build$BuildExecution.post2(Build.java:177)
	at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:697)
	at hudson.model.Run.execute(Run.java:1932)
	at hudson.matrix.MatrixRun.run(MatrixRun.java:153)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:429)
Caused by: java.net.ConnectException: Connection refused (Connection refused)
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:607)
	at com.sun.mail.util.SocketFetcher.createSocket(SocketFetcher.java:333)
	at com.sun.mail.util.SocketFetcher.getSocket(SocketFetcher.java:214)
	at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2160)
	... 18 more
Finished: FAILURE