Console Output

Started by upstream project "ADAM-prb" build number 3155
originally caused by:
 GitHub pull request #2301 of commit fc9b1cfe074c22ee1930de17001f02d287b5728c, no merge conflicts.
Running as SYSTEM
[EnvInject] - Loading node environment variables.
Building remotely on research-jenkins-worker-09 (ubuntu ubuntu-gpu research-09 ubuntu-avx2) in workspace /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu
The recommended git tool is: NONE
No credentials specified
Wiping out workspace first.
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/adam.git
 > git init /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu # timeout=10
Using reference repository: /home/jenkins/gitcaches/adam.reference
Fetching upstream changes from https://github.com/bigdatagenomics/adam.git
 > git --version # timeout=10
 > git --version # 'git version 2.7.4'
 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/*:refs/remotes/origin/* # timeout=15
 > git config remote.origin.url https://github.com/bigdatagenomics/adam.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/adam.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/adam.git
 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=15
Checking out Revision fc9b1cfe074c22ee1930de17001f02d287b5728c (detached)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f fc9b1cfe074c22ee1930de17001f02d287b5728c # timeout=10
Commit message: "Update Spark dependency version to 3.0.2."
First time build. Skipping changelog.
[ubuntu] $ /bin/bash /tmp/jenkins4719326821061716522.sh
+ set -e
+ unset SPARK_TESTING
+ export JAVA_HOME=/usr/java/latest
+ JAVA_HOME=/usr/java/latest
+ export CONDA_BIN=/home/anaconda/bin/
+ CONDA_BIN=/home/anaconda/bin/
+ export PATH=/usr/java/latest/bin/:/home/anaconda/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/java/latest/bin/:/home/anaconda/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/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/jenkins-test

# make a tempdir for writing maven cruft to
ADAM_MVN_TMP_DIR=$(mktemp -d -t adamTestMvnXXXXXXX)
mktemp -d -t adamTestMvnXXXXXXX
++ mktemp -d -t adamTestMvnXXXXXXX
+ ADAM_MVN_TMP_DIR=/tmp/adamTestMvnCuR0aNF

# 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=${ADAM_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/adamTestMvnCuR0aNF:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/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/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/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 ${BASH_SOURCE[0]} 
+++ dirname /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/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/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.34.0-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 3.2.1 ]]

# 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 3.0.2 ]]

set -e
+ set -e

# print versions
echo "Testing ADAM version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing ADAM version 0.34.0-SNAPSHOT on Spark 3.0.2 and Hadoop 3.2.1'
Testing ADAM version 0.34.0-SNAPSHOT on Spark 3.0.2 and Hadoop 3.2.1

# if those pass, build the distribution package
mvn -U \
    -P distribution \
    package \
    -Dhadoop.version=${HADOOP_VERSION} \
    -DargLine=${ADAM_MVN_TMP_DIR}
+ mvn -U -P distribution package -Dhadoop.version=3.2.1 -DargLine=/tmp/adamTestMvnCuR0aNF
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ADAM_2.12                                                          [pom]
[INFO] ADAM_2.12: Shader workaround                                       [jar]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils                           [jar]
[INFO] ADAM_2.12: Core                                                    [jar]
[INFO] ADAM_2.12: APIs for Java, Python                                   [jar]
[INFO] ADAM_2.12: CLI                                                     [jar]
[INFO] ADAM_2.12: Assembly                                                [jar]
[INFO] ADAM_2.12: Distribution                                            [pom]
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-parent-spark3_2.12 >-------------
[INFO] Building ADAM_2.12 0.34.0-SNAPSHOT                                 [1/8]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark3_2.12 ---
[INFO] Modified 0 of 243 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-shade-spark3_2.12 >-------------
[INFO] Building ADAM_2.12: Shader workaround 0.34.0-SNAPSHOT              [2/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark3_2.12 ---
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/src/main/java:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/2.12.10/classes at 1613873636598
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/2.12.10/classes
[INFO] 
[INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark3_2.12 ---
[INFO] Discovered 1 component descriptors(s)
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark3_2.12 ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-shade-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/adam-shade-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/adam-shade-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-shade-spark3_2.12 ---
[INFO] 
Loading source files for package org.bdgenomics.adam.shade...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/ParquetAvroWorkaroundShader.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-frame.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-summary.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-tree.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/constant-values.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/class-use/ParquetAvroWorkaroundShader.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-use.html...
Building index for all the packages and classes...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/overview-tree.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/index-all.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/allclasses-frame.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/allclasses-noframe.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/index.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/apidocs/help-doc.html...
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/adam-shade-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-shade-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-shade-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark3_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-shade/target/adam-shade-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-codegen-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.34.0-SNAPSHOT  [3/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark3_2.12 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark3_2.12 ---
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/target/2.12.10/classes at 1613873643418
[WARNING] warning: there were 5 deprecation warnings (since 2.12.0); re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-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) @ adam-codegen-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark3_2.12 ---
Discovery starting.
Discovery completed in 74 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 114 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] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-codegen-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/target/adam-codegen-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/target/adam-codegen-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-codegen-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark3_2.12 ---
model contains 11 documentable templates
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/target/adam-codegen-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-core-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: Core 0.34.0-SNAPSHOT                           [4/8]
[INFO] --------------------------------[ jar ]---------------------------------
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-catalyst_2.12/3.0.2/spark-catalyst_2.12-3.0.2.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-network-common_2.12/3.0.2/spark-network-common_2.12-3.0.2.jar (2.4 MB at 11 MB/s)
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-sql_2.12/3.0.2/spark-sql_2.12-3.0.2.jar (7.2 MB at 17 MB/s)
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-catalyst_2.12/3.0.2/spark-catalyst_2.12-3.0.2.jar (9.4 MB at 17 MB/s)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala added.
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark3_2.12 ---
[INFO] Modified 2 of 204 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark3_2.12 ---
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/java:-1: info: compiling
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 140 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/2.12.10/classes at 1613873658929
[WARNING] warning: there were 24 deprecation warnings
[WARNING] warning: there were 31 deprecation warnings (since 0.21.0)
[WARNING] warning: there was one deprecation warning (since 1.0.6)
[WARNING] warning: there was one deprecation warning (since 2.11.0)
[WARNING] warning: there were 174 deprecation warnings (since 2.12.0)
[WARNING] warning: there was one deprecation warning (since 2.12.7)
[WARNING] warning: there were 232 deprecation warnings in total; re-run with -deprecation for details
[WARNING] warning: there were 5 feature warnings; re-run with -feature for details
[WARNING] 8 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 20 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 6 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/2.12.10/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 152 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark3_2.12 ---
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala:-1: info: compiling
[INFO] Compiling 70 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/2.12.10/test-classes at 1613873680681
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]       .build()
[WARNING]             ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val new_cigar = NormalizationUtils.leftAlignIndel(read)
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(RichAlignment(read).samtoolsCigar.getReadLength === new_cigar.getReadLength)
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:171: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val newSAMRecord = newSAMReader.iterator().dropWhile(r => r.getReadName != readName)
[WARNING]                                             ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:274: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:311: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:335: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val fragment = Fragment.newBuilder().setAlignments(List(record)).build()
[WARNING]                                                            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:54: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:89: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       val samIter = asScalaIterator(newSAMReader.iterator())
[WARNING]                     ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in class SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path)))
[WARNING]                                                       ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:63: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                  ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:69: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T"), Allele.create("G")))
[WARNING]                  ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:75: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<NON_REF>", false)))
[WARNING]                  ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<CN0>", false)))
[WARNING]                  ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:143: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       GenotypeBuilder.create("NA12878", vcb.getAlleles(), genotypeAttributes))
[WARNING]                                                           ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:154: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.ALT)))
[WARNING]                   ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:184: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamVariant.variant.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                  ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:219: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamGT.getVariantCallingAnnotations.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                                  ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:234: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(htsjdkVC.getAlternateAlleles.sameElements(List(Allele.create("T"))))
[WARNING]                     ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:245: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2, 4, 6).map(i => i: java.lang.Integer))
[WARNING]                                                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:246: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:279: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:280: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:298: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:299: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:320: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     for ((allele, idx) <- vc.getAlternateAlleles.zipWithIndex) {
[WARNING]                              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:328: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("T"), Allele.create("G")))
[WARNING]                                                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:347: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT)))
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:349: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:354: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT)))
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:356: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:380: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("A", true), Allele.create("A", true)))
[WARNING]                                                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:393: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.REF)))
[WARNING]                   ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:396: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getNonReferenceLikelihoods
[WARNING]                   ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:421: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 1)
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:433: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 2)
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:543: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       genotypeAttributes)))((bldr, fn) => {
[WARNING]       ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]                                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]                                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]                                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:714: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(0) === 10)
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:715: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(1) === 12)
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:716: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(2) === 14)
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:717: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(3) === 16)
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:762: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER")
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:776: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER1")
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:777: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(1) === "FAILED_FILTER2")
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:778: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(2) === "FAILED_FILTER3")
[WARNING]            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:930: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(d => d: java.lang.Double))
[WARNING]             ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:954: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]           .map(i => i: java.lang.Integer))
[WARNING]               ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:962: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(i => i: java.lang.Integer))
[WARNING]             ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1089: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq"))
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq", "lowdp"))
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1195: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 1)
[WARNING]              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1205: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 2)
[WARNING]              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1262: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         vcb.filters(Set("FAILED1", "FAILED2", "FAILED3"))
[WARNING]                        ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1267: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val failedSet = v.getFiltersFailed.toSet
[WARNING]                       ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1285: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name"))
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1295: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name1", "name2"))
[WARNING]                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1364: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED"))
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1378: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED1", "FAILED2"))
[WARNING]                            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1493: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10).map(i => i: java.lang.Integer)
[WARNING]              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1501: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                      ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1516: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f).map(i => i: java.lang.Float)
[WARNING]                ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1523: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("+Inf")
[WARNING]                                              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1530: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("-Inf")
[WARNING]                                              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1538: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f, 0.01f, 0.001f).map(i => i: java.lang.Float)
[WARNING]                               ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1552: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M")
[WARNING]                                              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1559: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M", "100M", "90M10D")
[WARNING]                                              ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1575: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1584: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1601: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1610: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1627: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1636: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2436: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("ONE_INT", "42")))
[WARNING]                                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2459: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_INTS", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2482: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_FLOATS", "5.0,10.1,15.2,20.3")))
[WARNING]                                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2505: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("A_INT", "10,15,20")))
[WARNING]                                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2528: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_INT", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2551: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_STRING", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2574: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("STRING_G", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/fragment/FragmentDatasetSuite.scala:327: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       fragment.getAlignments.toSeq
[WARNING]                ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/AlignmentDatasetSuite.scala:988: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Seq("tee", "/dev/null"),
[WARNING]          ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/AlignmentDatasetSuite.scala:989: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       (List.empty[String]: java.util.List[String]),
[WARNING]                  ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/AlignmentDatasetSuite.scala:990: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       (Map.empty[String, String]: java.util.Map[String, String]),
[WARNING]                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/BinQualitiesSuite.scala:181: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(List(read))
[WARNING]                          ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/BinQualitiesSuite.scala:189: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     testQuals(newFragment.getAlignments.head.getQualityScores)
[WARNING]                           ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:83: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(TargetOrdering.contains(targets.head, read))
[WARNING]                                                  ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:191: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]         if (read.getStart < 105) {
[WARNING]             ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:194: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.start === read.getStart)
[WARNING]                                                   ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:195: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.end === read.getEnd)
[WARNING]                                                 ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:196: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]           assert(check_indel(targets.head, read))
[WARNING]                                            ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/variant/GenotypeDatasetSuite.scala:697: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.end === 16157602L)
[WARNING]                  ^
[WARNING] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/test/scala/org/bdgenomics/adam/ds/variant/GenotypeDatasetSuite.scala:698: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                          ^
[WARNING] 168 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 22 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-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) @ adam-core-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark3_2.12 ---
Discovery starting.
Discovery completed in 1 second, 502 milliseconds.
Run starting. Expected test count is: 1178
VariantDatasetSuite:
2021-02-20 18:15:05 WARN  Utils:69 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
2021-02-20 18:15:05 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-02-20 18:15:05 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- union two variant genomic datasets together
- round trip to parquet
2021-02-20 18:15:14 WARN  package:69 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.sql.debug.maxToStringFields'.
- save and reload from partitioned parquet
- use broadcast join to pull down variants mapped to targets
- use right outer broadcast join to pull down variants mapped to targets
- use shuffle join to pull down variants mapped to targets
- use right outer shuffle join to pull down variants mapped to targets
- use left outer shuffle join to pull down variants mapped to targets
- use full outer shuffle join to pull down variants mapped to targets
- use shuffle join with group by to pull down variants mapped to targets
- use right outer shuffle join with group by to pull down variants mapped to targets
- convert back to variant contexts
- load parquet to sql, save, re-read from avro
2021-02-20 18:15:26 WARN  DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored.
- transform variants to slice genomic dataset
- transform variants to coverage genomic dataset
- transform variants to feature genomic dataset
- transform variants to fragment genomic dataset
- transform variants to read genomic dataset
- transform variants to genotype genomic dataset
- transform variants to variant context genomic dataset
- filter RDD bound variants to filters passed
- filter dataset bound variants to filters passed
- filter RDD bound variants by quality
- filter dataset bound variants by quality
- filter RDD bound variants by read depth
- filter dataset bound variants by read depth
- filter RDD bound variants by reference read depth
- filter dataset bound variants by reference read depth
- filter RDD bound single nucleotide variants
- filter dataset bound single nucleotide variants
- filter RDD bound multiple nucleotide variants
- filter dataset bound multiple nucleotide variants
- filter RDD bound indel variants
- filter dataset bound indel variants
- filter RDD bound variants to single nucleotide variants
- filter dataset bound variants to single nucleotide variants
- filter RDD bound variants to multiple nucleotide variants
- filter dataset bound variants to multiple nucleotide variants
- filter RDD bound variants to indel variants
- filter dataset bound variants to indel variants
- transform dataset via java API
SingleReadBucketSuite:
- convert unmapped pair to fragment
- convert proper pair to fragment
- convert read pair to fragment with first of pair chimeric read
GFF3HeaderWriterSuite:
- write gff3 header pragma
InnerTreeRegionJoinSuite:
- Ensure same reference regions get passed together
- Overlapping reference regions
- Multiple reference regions do not throw exception
TwoBitFileSuite:
- correctly read sequence from .2bit file
- correctly return masked sequences from .2bit file
- correctly return Ns from .2bit file
- correctly calculates sequence dictionary
SliceDatasetSuite:
- create a new slice genomic dataset
- create a new slice genomic dataset with sequence dictionary
- merge slices into a sequence genomic dataset
- save as parquet
- round trip as parquet
- save as fasta
- save as single file fasta
- convert slices to reads
- convert slices to sequences
VariantContextDatasetSuite:
- load a gvcf with a missing info field set to .
- union two variant context genomic datasets together
- can write, then read in .vcf file
- can write as a single file via simple saveAsVcf method, then read in .vcf file
- can write as a single file via full saveAsVcf method, then read in .vcf file
- transform a vcf file with bad header
- read a vcf file with multi-allelic variants to split
- support VCFs with +Inf/-Inf float values
- support VCFs with `nan` instead of `NaN` float values
- don't lose any variants when piping as VCF
- pipe works with empty partitions
- don't lose any non-default VCF header lines or attributes when piping as VCF
- save a file sorted by contig index
- save a lexicographically sorted file
- save a multiallelic gvcf !!! IGNORED !!!
- test metadata
- save sharded bgzip vcf
- save bgzip vcf as single file
- can't save file with non-vcf extension
- transform variant contexts to slice genomic dataset
- transform variant contexts to coverage genomic dataset
- transform variant contexts to feature genomic dataset
- transform variant contexts to fragment genomic dataset
- transform variant contexts to read genomic dataset
- transform variant contexts to genotype genomic dataset
- transform variant contexts to variant genomic dataset
- save and reload from partitioned parquet
- transform dataset via java API
SequenceDatasetSuite:
- create a new sequence genomic dataset
- create a new sequence genomic dataset with sequence dictionary
- save as parquet
- round trip as parquet
- save as fasta
- save as single file fasta
- convert sequences to reads
- convert sequences to slices
- slice sequences to a maximum length
- slice sequences shorter than maximum length
- filter sequences by overlapping region
- filter sequences failing to overlap region
- filter sequences by overlapping regions
- filter sequences failing to overlap regions
- slice sequences overlapping a smaller region
- slice sequences overlapping a larger region
- slice sequences failing to overlap a region
- slice sequences overlapping smaller regions
- slice sequences overlapping larger regions
- slice sequences failing to overlap regions
NonoverlappingRegionsSuite:
- alternating returns an alternating seq of items
- Single region returns itself
- Two adjacent regions will be merged
- Nonoverlapping regions will all be returned
- Many overlapping regions will all be merged
- ADAMRecords return proper references
ReferencePositionSuite:
- create reference position from mapped read
- create reference position from variant
- create reference position from genotype
- create reference position from variant starting at vcf 0
- create reference position from genotype starting at vcf 0
FeatureDatasetSuite:
- round trip GTF format
- save GTF as GFF3 format
- save GTF as BED format
- save GTF as IntervalList format
- save GTF as NarrowPeak format
- save GFF3 as GTF format
- save GFF3 as BED format
- save GFF3 as IntervalList format
- save GFF3 as NarrowPeak format
- round trip GFF3 format
- ignore FASTA sequence in GFF3 file
- save BED as GTF format
- save BED as GFF3 format
- save BED as IntervalList format
- save BED as NarrowPeak format
- round trip BED6 format
- keeps sample metadata
- round trip BED12 format
- save to UCSC BED format
- save IntervalList as GTF format
- save IntervalList as GFF3 format
- save IntervalList as BED format
- save IntervalList as IntervalList format
- save IntervalList as NarrowPeak format
- round trip IntervalList format
- save NarrowPeak as GTF format
- save NarrowPeak as GFF3 format
- save NarrowPeak as BED format
- save NarrowPeak as IntervalList format
- save NarrowPeak as NarrowPeak format
- round trip NarrowPeak format
- sort by reference
- sort by reference and feature fields
- sort gene features by reference and gene structure
- sort transcript features by reference and gene structure
- sort exon features by reference and gene structure
- sort intron features by reference and gene structure
- correctly flatmaps CoverageDataset from FeatureDataset
- use broadcast join to pull down features mapped to targets
- use right outer broadcast join to pull down features mapped to targets
- use shuffle join to pull down features mapped to targets
- use right outer shuffle join to pull down features mapped to targets
- use left outer shuffle join to pull down features mapped to targets
- use full outer shuffle join to pull down features mapped to targets
- use shuffle join with group by to pull down features mapped to targets
- use right outer shuffle join with group by to pull down features mapped to targets
- union two feature rdds together
- obtain sequence dictionary contig lengths from header in IntervalList format
- don't lose any features when piping as BED format
- don't lose any features when piping as GTF format
- don't lose any features when piping as GFF3 format
- don't lose any features when piping as NarrowPeak format
- load parquet to sql, save, re-read from avro
- load partitioned parquet to sql, save, re-read from avro
2021-02-20 18:16:14 WARN  DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored.
- transform features to slice genomic dataset
- transform features to coverage genomic dataset
- transform features to fragment genomic dataset
- transform features to read genomic dataset
- transform features to genotype genomic dataset
- transform features to variant genomic dataset
- transform features to variant context genomic dataset
- filter RDD bound features to reference name
- filter dataset bound features to reference name
- filter RDD bound features by feature type
- filter dataset bound features by feature type
- filter RDD bound features by feature types
- filter dataset bound features by feature types
- filter RDD bound features by gene
- filter dataset bound features by gene
- filter RDD bound features by genes
- filter dataset bound features by genes
- filter RDD bound features by transcript
- filter dataset bound features by transcript
- filter RDD bound features by transcripts
- filter dataset bound features by transcripts
- filter RDD bound features by exon
- filter dataset bound features by exon
- filter RDD bound features by exons
- filter dataset bound features by exons
- filter RDD bound features by score
- filter dataset bound features by score
- filter RDD bound features by parent
- filter dataset bound features by parent
- filter RDD bound features by parents
- filter dataset bound features by parents
- filter RDD bound features by attribute
- filter dataset bound features by attribute
- transform dataset via java API
MDTaggingSuite:
- test adding MDTags over boundary
- test adding MDTags; reads span full contig
- test adding MDTags; reads start inside first fragment
- test adding MDTags; reads end inside last fragment
- test adding MDTags; reads start inside first fragment and end inside last fragment
- test adding MDTags; reads start and end in middle fragements
2021-02-20 18:16:25 WARN  BlockManager:69 - Putting block rdd_5_3 failed due to exception java.lang.Exception: Reference chr2 not found in reference map with keys: chr1.
2021-02-20 18:16:25 WARN  BlockManager:69 - Block rdd_5_3 could not be removed as it was not found on disk or in memory
2021-02-20 18:16:25 ERROR Executor:94 - Exception in task 3.0 in stage 2.0 (TID 11)
java.lang.Exception: Reference chr2 not found in reference map with keys: chr1
	at org.bdgenomics.adam.util.ReferenceMap.$anonfun$extract$1(ReferenceMap.scala:64)
	at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119)
	at org.bdgenomics.adam.util.ReferenceMap.extract(ReferenceMap.scala:63)
	at org.bdgenomics.adam.ds.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76)
	at scala.Option$WithFilter.map(Option.scala:230)
	at org.bdgenomics.adam.ds.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71)
	at scala.collection.Iterator$$anon$10.next(Iterator.scala:459)
	at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222)
	at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299)
	at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1371)
	at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1298)
	at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1362)
	at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1186)
	at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:360)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:311)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:127)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:462)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:465)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
2021-02-20 18:16:25 WARN  TaskSetManager:69 - Lost task 3.0 in stage 2.0 (TID 11, 192.168.10.31, executor driver): java.lang.Exception: Reference chr2 not found in reference map with keys: chr1
	at org.bdgenomics.adam.util.ReferenceMap.$anonfun$extract$1(ReferenceMap.scala:64)
	at scala.collection.immutable.Map$Map1.getOrElse(Map.scala:119)
	at org.bdgenomics.adam.util.ReferenceMap.extract(ReferenceMap.scala:63)
	at org.bdgenomics.adam.ds.read.MDTagging.$anonfun$addMDTagsBroadcast$3(MDTagging.scala:76)
	at scala.Option$WithFilter.map(Option.scala:230)
	at org.bdgenomics.adam.ds.read.MDTagging.$anonfun$addMDTagsBroadcast$1(MDTagging.scala:71)
	at scala.collection.Iterator$$anon$10.next(Iterator.scala:459)
	at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:222)
	at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:299)
	at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1371)
	at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1298)
	at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1362)
	at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1186)
	at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:360)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:311)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:127)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:462)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:465)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

2021-02-20 18:16:25 ERROR TaskSetManager:73 - Task 3 in stage 2.0 failed 1 times; aborting job
- try realigning a read on a missing contig, stringency == STRICT
2021-02-20 18:16:25 WARN  MDTagging:190 - Caught exception when processing read chr2: java.lang.Exception: Reference chr2 not found in reference map with keys: chr1
- try realigning a read on a missing contig, stringency == LENIENT
ConsensusGeneratorFromReadsSuite:
- checking search for consensus list for artificial reads
InnerShuffleRegionJoinSuite:
- Overlapping reference regions
- Multiple reference regions do not throw exception
RecalibratorSuite:
- don't replace quality if quality was null
- if no covariates, return alignment
- skip recalibration if base is below quality threshold
- recalibrate changed bases above quality threshold
FlankSlicesSuite:
- don't put flanks on non-adjacent slices
- put flanks on adjacent slices
FragmentConverterSuite:
- build a fragment collector and convert to a read
- if a fragment isn't associated with a contig, don't get a fragment collector
- convert an rdd of discontinuous fragments, all from the same contig
- convert an rdd of contiguous fragments, all from the same contig
- convert an rdd of varied fragments from multiple contigs
FileMergerSuite:
- cannot write both empty gzip block and cram eof
- buffer size must be non-negative
RichAlignmentSuite:
- Unclipped Start
- Unclipped End
- tags contains optional fields
- read overlap unmapped read
- read overlap reference position
- read overlap same position different contig
InterleavedFastqInputFormatSuite:
- interleaved FASTQ hadoop reader: interleaved_fastq_sample1.ifq->interleaved_fastq_sample1.ifq.output
- interleaved FASTQ hadoop reader: interleaved_fastq_sample2.ifq->interleaved_fastq_sample2.ifq.output
- interleaved FASTQ hadoop reader: interleaved_fastq_sample3.ifq->interleaved_fastq_sample3.ifq.output
- interleaved FASTQ hadoop reader: interleaved_fastq_sample4.ifq->interleaved_fastq_sample4.ifq.output
- interleaved FASTQ hadoop reader: interleaved_fastq_sample5.ifq->interleaved_fastq_sample5.ifq.output
ModPartitionerSuite:
- report number of partitions correctly
- partition a number that is lower than the number of partitions and positive
- partition a number that is greater than the number of partitions and positive
- partition a number that is lower than the number of partitions and negative
- partition a number that is greater than the number of partitions and negative
- fire an exception if input is not an integer
ReferenceRegionSuite:
- cannot create an empty predicate
- parse empty string throws IllegalArgumentException
- parse contigName only string into reference regions
- parse to end strings into reference regions
- parse string into reference regions
- contains(: ReferenceRegion)
- contains(: ReferencePosition)
- merge
- overlaps and covers
- overlapsBy and coversBy
- distance(: ReferenceRegion)
- distance(: ReferencePosition)
- unstrandedDistance
- subtract fails on non-overlapping and non-covering regions
- subtract
- create region from unmapped read fails
- create region from read with null alignment positions fails
- create stranded region from unmapped read fails
- create stranded region from read with null alignment positions fails
- create stranded region from read with null alignment strand fails
- create stranded region from read on forward strand
- create stranded region from read on reverse strand
- create region from mapped read contains read start and end
- validate that adjacent regions can be merged
- validate that non-adjacent regions cannot be merged
- validate that nearby regions can be merged
- validate that non-nearby regions cannot be merged
- compute convex hull of two sets
- region name is sanitized when creating region from read
- intersection fails on non-overlapping regions
- intersection fails when minOverlap is not met
- compute intersection
- overlap tests for oriented reference region
- check the width of a reference region
- make a reference region for a variant or genotype
- make a reference region for a variant or genotype starting at VCF 0
- uniformly pad a reference region
- uniformly pad a reference region into negative coordinate space, ensure non negative start
- unevenly pad a reference region
- unevenly pad a reference region into negative coordinate space, ensure non negative start
- can build an open ended reference region
- can build an open ended reference region with strand
- can build a reference region with an open start position
- can build a reference region with an open start position with strand
- can build a reference region that covers the entirety of a contig
- can build a reference region that covers the entirety of a contig with strand
- convert a genotype and then get the reference region
- create region from feature with null alignment positions fails
- create stranded region from feature with null alignment positions fails
- create stranded region from feature with null alignment strand fails
- create stranded region from feature on forward strand
- create stranded region from feature on reverse strand
BinQualitiesSuite:
- make a quality score bin
- can't have a quality score bin with negative score
- can't have a quality score bin with high score below low
- can't have a quality score bin with high score above 255
- can't have a quality score bin with score outside
- make a quality score bin from a string
- quality score bin must have exactly 3 elements
- quality score bin must be integers
- must define at least one bin
- build multiple bins
- rewrite quality scores for a read
- rewriting quality scores fails if bins overlap
- rewriting quality scores fails if base is out of bounds
- skip read if qualities are null
- rewrite a read
SingleFastqInputFormatSuite:
- FASTQ hadoop reader: fastq_sample1.fq->single_fastq_sample1.fq.output
- FASTQ hadoop reader: fastq_sample2.fq->single_fastq_sample2.fq.output
- FASTQ hadoop reader: fastq_sample3.fq->single_fastq_sample3.fq.output
- FASTQ hadoop reader: fastq_sample4.fq->single_fastq_sample4.fq.output
RealignIndelsSuite:
- map reads to targets
- checking mapping to targets for artificial reads
- checking alternative consensus for artificial reads
- checking extraction of reference from reads
- checking realigned reads for artificial input
- checking realigned reads for artificial input with reference file
- checking realigned reads for artificial input using knowns
- checking realigned reads for artificial input using knowns and reads
- skip realigning reads if target is highly covered
- skip realignment if target is an insufficient LOD improvement
- realign reads to an insertion
- test mismatch quality scoring
- test mismatch quality scoring for no mismatches
- test mismatch quality scoring for offset
- test mismatch quality scoring with early exit
- test mismatch quality scoring after unpacking read
- we shouldn't try to realign a region with no target
- we shouldn't try to realign reads with no indel evidence
- test OP and OC tags
- realign a read with an insertion that goes off the end of the read
- if realigning a target doesn't improve the LOD, don't drop reads
- extract seq/qual from a read with no clipped bases
- extract seq/qual from a read with clipped bases at start
- extract seq/qual from a read with clipped bases at end
- if unclip is selected, don't drop base when extracting from a read with clipped bases
- get cigar and coordinates for read that spans indel, no clipped bases
- get cigar and coordinates for read that spans deletion, clipped bases at start
- get cigar and coordinates for read that falls wholly before insertion
- get cigar and coordinates for read that falls wholly after insertion
- get cigar and coordinates for read that falls wholly after deletion
- get cigar and coordinates for read that partially spans insertion, no clipped bases
- get cigar and coordinates for read that partially spans insertion, clipped bases at end
- get cigar and coordinates for read that partially spans insertion, clipped bases both ends
ConsensusSuite:
- test the insertion of a consensus insertion into a reference
- test the insertion of a consensus deletion into a reference
- inserting empty consensus returns the reference
AttributeUtilsSuite:
- parseTags returns a reasonable set of tagStrings
- parseTags works with NumericSequence tagType
- empty string is parsed as zero tagStrings
- incorrectly formatted tag throws an exception
- string tag with a ':' in it is correctly parsed
- oq string tag with many ':' in it is correctly parsed
- oq string tag with a ',' in it is correctly parsed
- if a tag is an array but doesn't define it's format, throw
ReadDatasetSuite:
- create a new read genomic dataset
- create a new read genomic dataset with sequence dictionary
- save as parquet
- round trip as parquet
- save as fastq
- save as single file fastq
- filter read genomic dataset by reference region
- broadcast region join reads and features
- shuffle region join reads and features
- convert reads to alignments
- convert reads to sequences
- convert reads to slices
TranscriptEffectConverterSuite:
- parse empty transcript effect
- parse empty transcript effect strict validation stringency
- parse invalid transcript effect
- parse invalid transcript effect strict validation stringency
- parse transcript effect
- parse empty list VCF ANN attribute
- parse empty list VCF ANN attribute strict validation stringency
- parse empty string VCF ANN attribute
- parse empty string VCF ANN attribute strict validation stringency
- parse invalid VCF ANN attribute
- parse invalid VCF ANN attribute strict validation stringency
- parse VCF ANN attribute with one transcript effect
- parse VCF ANN attribute with multiple transcript effects
- parse VCF ANN attribute with Ensembl VEP position attribute
- convert to transcript effect from null VCF ANN attribute in variant context
- convert to transcript effect from empty list VCF ANN attribute in variant context
- convert to transcript effect from empty list VCF ANN attribute in variant context strict validation stringency
- convert to transcript effect from empty string VCF ANN attribute in variant context
- convert to transcript effect from empty string VCF ANN attribute in variant context strict validation stringency
- convert to transcript effect from invalid VCF ANN attribute in variant context
- convert to transcript effect from invalid VCF ANN attribute in variant context strict validation stringency
2021-02-20 18:16:35 WARN  TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number".
- convert to transcript effect from VCF ANN attribute with invalid number in variant context lenient validation stringency
2021-02-20 18:16:35 WARN  TranscriptEffectConverter$:190 - Could not convert VCF INFO reserved key ANN value to TranscriptEffect, caught java.lang.NumberFormatException: For input string: "not a number".
- convert to transcript effect from VCF ANN attribute with invalid fraction in variant context lenient validation stringency
- convert to transcript effect from VCF ANN attribute with invalid number in variant context strict validation stringency
- convert to transcript effect from VCF ANN attribute with invalid fraction in variant context strict validation stringency
- convert to transcript effect from VCF ANN attribute in variant context different alt allele
- convert to transcript effect from VCF ANN attribute in variant context same alt allele
- convert to transcript effect from VCF ANN attribute in variant context multiple effects same alt allele
- convert transcript effect to VCF ANN attribute value
- convert transcript effect with null fields to VCF ANN attribute value
2021-02-20 18:16:35 WARN  TranscriptEffectConverter$:190 - Incorrect fractional value ?/2, missing numerator
- convert transcript effect with incorrect fractional value to VCF ANN attribute value
NormalizationUtilsSuite:
- cannot move an indel left if there are no bases to it's left
- move a simple indel to farthest position left until bases run out
- move a simple indel to farthest position left, past length of indel
- cannot move a left normalized indel in a short tandem repeat
- move an indel in a short tandem repeat
- move an indel in a short tandem repeat of more than 2 bases, where shift is not an integer multiple of repeated sequence length
- moving a simple read with single deletion that cannot shift
- shift an indel left by 0 in a cigar
- shift an indel left by 1 in a cigar
- do not left align a complex read which is already left aligned
ReadGroupDictionarySuite:
- simple conversion to and from sam read group
- sample name must be set
- simple equality checks
- get samples from read group dictionary
- empty read group is empty
- merging a dictionary with itself should work
- round trip a record with all attributes set
GenomicPositionPartitionerSuite:
- partitions the UNMAPPED ReferencePosition into the top partition
- if we do not have a contig for a record, we throw an IAE
- partitioning into N pieces on M total sequence length, where N > M, results in M partitions
- correctly partitions a single dummy sequence into two pieces
- correctly counts cumulative lengths
- correctly partitions positions across two dummy sequences
- test that we can range partition ADAMRecords
- test that we can range partition ADAMRecords indexed by sample
- test that simple partitioning works okay on a reasonable set of ADAMRecords
- test indexed ReferencePosition partitioning works on a set of indexed ADAMRecords
AlphabetSuite:
- test size of a case-sensitive alphabet
- test apply of a case-sensitive alphabet
- test reverse complement of a case-sensitive alphabet
- test exact reverse complement of a case-sensitive alphabet
- test size of a case-insensitive alphabet
- test apply of a case-insensitive alphabet
- test reverse complement of a case-insensitive alphabet
- test exact reverse complement of a case-insensitive alphabet
- DNA alphabet
- map unknown bases to N
CoverageDatasetSuite:
- correctly saves coverage
- can read a bed file to coverage
- correctly filters coverage with predicate
- keeps sample metadata
- can read a bed file with multiple samples to coverage
- correctly flatmaps coverage without aggregated bins
- correctly flatmaps coverage with aggregated bins
- collapses coverage records in one partition
- approximately collapses coverage records in multiple partitions
2021-02-20 18:16:42 WARN  DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored.
- transform coverage to slice genomic dataset
- transform coverage to feature genomic dataset
- transform coverage to fragment genomic dataset
- transform coverage to read genomic dataset
- transform coverage to genotype genomic dataset
- transform coverage to variant genomic dataset
- transform coverage to variant context genomic dataset
- copy coverage rdd
- copy coverage dataset
- copy coverage rdd without sequence dictionary
- copy coverage dataset without sequence dictionary
- transform dataset via java API
RightOuterTreeRegionJoinSuite:
- Ensure same reference regions get passed together
- Overlapping reference regions
FragmentDatasetSuite:
- don't lose any reads when piping interleaved fastq to sam
- don't lose any reads when piping tab5 to sam
- don't lose any reads when piping tab6 to sam
- use broadcast join to pull down fragments mapped to targets
- use right outer broadcast join to pull down fragments mapped to targets
- use shuffle join to pull down fragments mapped to targets
- use right outer shuffle join to pull down fragments mapped to targets
- use left outer shuffle join to pull down fragments mapped to targets
- use full outer shuffle join to pull down fragments mapped to targets
- use shuffle join with group by to pull down fragments mapped to targets
- use right outer shuffle join with group by to pull down fragments mapped to targets
- bin quality scores in fragments
- union two genomic datasets of fragments together
- load parquet to sql, save, re-read from avro
- transform fragments to slice genomic dataset
- transform fragments to coverage genomic dataset
- transform fragments to feature genomic dataset
- transform fragments to read genomic dataset
- transform fragments to genotype genomic dataset
- transform fragments to variant genomic dataset
- transform fragments to variant context genomic dataset
- paired read names with index sequences in read names can group into fragments
- interleaved paired read names with index sequences in read names can group into fragments
- interleaved paired read names with index sequences in read names as fragments
- transform dataset via java API
- dataset and rdd conversion to alignments are equivalent
VariantContextConverterSuite:
- Convert htsjdk site-only SNV to ADAM
- Convert somatic htsjdk site-only SNV to ADAM
- Convert htsjdk site-only CNV to ADAM
- Convert htsjdk SNV w/ genotypes w/ phase information to ADAM
- Convert htsjdk SNV with different variant filters to ADAM
- Convert htsjdk SNV with different genotype filters to ADAM
- Convert ADAM site-only SNV to htsjdk
- Convert ADAM SNV w/ genotypes to htsjdk
- Convert ADAM SNV w/ genotypes but bad SB to htsjdk with strict validation
2021-02-20 18:17:02 WARN  VariantContextConverter:190 - Applying annotation extraction function org.bdgenomics.adam.converters.VariantContextConverter$$Lambda$724/1077873186@31f3ba42 to {"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null} failed with java.lang.IllegalArgumentException: requirement failed: Illegal strand bias components length. Must be empty or 4. In:
- Convert ADAM SNV w/ genotypes but bad SB to htsjdk with lenient validation
{"variant": {"referenceName": "1", "start": 0, "end": 1, "names": [], "splitFromMultiAllelic": false, "referenceAllele": "A", "alternateAllele": "T", "quality": null, "filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "annotation": null}, "referenceName": null, "start": null, "end": null, "variantCallingAnnotations": {"filtersApplied": null, "filtersPassed": null, "filtersFailed": [], "downsampled": null, "baseQRankSum": null, "fisherStrandBiasPValue": 3.0, "rmsMapQ": 0.0, "mapq0Reads": 5, "mqRankSum": null, "readPositionRankSum": null, "genotypePriors": [], "genotypePosteriors": [], "vqslod": null, "culprit": null, "attributes": {}}, "sampleId": "NA12878", "sampleDescription": null, "processingDescription": null, "alleles": ["REF", "ALT"], "expectedAlleleDosage": null, "referenceReadDepth": null, "alternateReadDepth": null, "readDepth": null, "minReadDepth": null, "genotypeQuality": null, "genotypeLikelihoods": [], "nonReferenceLikelihoods": [], "strandBiasComponents": [0, 2], "splitFromMultiAllelic": false, "phased": false, "phaseSetId": null, "phaseQuality": null}.
- Convert htsjdk multi-allelic sites-only SNVs to ADAM
- Convert htsjdk multi-allelic SNVs to ADAM and back to htsjdk
- Convert gVCF reference records to ADAM
- Convert htsjdk variant context with no IDs to ADAM
- Convert htsjdk variant context with one ID to ADAM
- Convert htsjdk variant context with multiple IDs to ADAM
- Convert ADAM variant context with no names to htsjdk
- Convert ADAM variant context with one name to htsjdk
- Convert ADAM variant context with multiple names to htsjdk
- Convert ADAM variant context with null filters applied to htsjdk
- Convert ADAM variant context with no filters applied to htsjdk
- Convert ADAM variant context with passing filters to htsjdk
- Convert ADAM variant context with failing filters to htsjdk
- no phasing set going htsjdk->adam
- phased but no phase set info going htsjdk->adam
- set phase set and extract going htsjdk->adam
- no allelic depth going htsjdk->adam
- set allelic depth going htsjdk->adam
- no gt read depth going htsjdk->adam
- extract gt read depth going htsjdk->adam
- no min gt read depth going htsjdk->adam
- extract min gt read depth going htsjdk->adam
- no genotype quality going htsjdk->adam
- extract genotype quality going htsjdk->adam
- no phred likelihood going htsjdk->adam
- extract phred likelihoods going htsjdk->adam
- no strand bias info going htsjdk->adam
- extract strand bias info going htsjdk->adam
- no filters going htsjdk->adam
- filters passed going htsjdk->adam
- extract single filter going htsjdk->adam
- extract multiple filters going htsjdk->adam
- no fisher strand bias going htsjdk->adam
- extract fisher strand bias going htsjdk->adam
- no rms mapping quality going htsjdk->adam
- extract rms mapping quality going htsjdk->adam
- no mq0 going htsjdk->adam
- extract mq0 going htsjdk->adam
- no gt read depth going adam->htsjdk
- extract gt read depth going adam->htsjdk
- throw iae if missing one component of gt read depth going adam->htsjdk
- no depth going adam->htsjdk
- extract depth going adam->htsjdk
- no min depth going adam->htsjdk
- extract min depth going adam->htsjdk
- no quality going adam->htsjdk
- extract quality going adam->htsjdk
- no genotype likelihoods going adam->htsjdk
- extract genotype likelihoods going adam->htsjdk
- no strand bias going adam->htsjdk
- malformed strand bias going adam->htsjdk
- extract strand bias going adam->htsjdk
- no phasing info going adam->htsjdk
- unphased going adam->htsjdk
- phased but no ps/pq going adam->htsjdk
- phased but no pq going adam->htsjdk
- phased but no ps going adam->htsjdk
- phased going adam->htsjdk
- no filter info going adam->htsjdk
- if filters applied, must set passed/failed going adam->htsjdk
- filters passed going adam->htsjdk
- if filters failed, must set filters failed going adam->htsjdk
- single filter failed going adam->htsjdk
- multiple filters failed going adam->htsjdk
- no fisher strand bias going adam->htsjdk
- extract fisher strand bias going adam->htsjdk
- no rms mapping quality going adam->htsjdk
- extract rms mapping quality going adam->htsjdk
- no mapping quality 0 reads going adam->htsjdk
- extract mapping quality 0 reads going adam->htsjdk
- no names set going htsjdk->adam
- single name set going htsjdk->adam
- multiple names set going htsjdk->adam
- no quality going htsjdk->adam
- quality set going htsjdk->adam
- no filters applied going htsjdk->adam
- filters applied and passed going htsjdk->adam
- single filter applied and failed going htsjdk->adam
- multiple filters applied and failed going htsjdk->adam
- no names set adam->htsjdk
- set a single name adam->htsjdk
- set multiple names adam->htsjdk
- no qual set adam->htsjdk
- qual is set adam->htsjdk
- no filters applied adam->htsjdk
- null filters applied adam->htsjdk
- filters passed adam->htsjdk
- if filter failed, must have filters adam->htsjdk
- single filter failed adam->htsjdk
- multiple filters failed adam->htsjdk
- no ancestral allele set going htsjdk->adam
- ancestral allele set going htsjdk->adam
- no dbsnp membership set going htsjdk->adam
- dbsnp membership set going htsjdk->adam
- no hapmap2 membership set going htsjdk->adam
- hapmap2 membership set going htsjdk->adam
- no hapmap3 membership set going htsjdk->adam
- hapmap3 membership set going htsjdk->adam
- no validated set going htsjdk->adam
- validated set going htsjdk->adam
- no 1000G membership set going htsjdk->adam
- 1000G membership set going htsjdk->adam
- not somatic going htsjdk->adam
- somatic going htsjdk->adam
- no allele count going htsjdk->adam
- single allele count going htsjdk->adam
- multiple allele counts going htsjdk->adam
- no allele frequency going htsjdk->adam
- single allele frequency going htsjdk->adam
- single allele frequency is +Inf going htsjdk->adam
- single allele frequency is -Inf going htsjdk->adam
- multiple allele frequencies going htsjdk->adam
- no CIGAR going htsjdk->adam
- single CIGAR going htsjdk->adam
- multiple CIGARs going htsjdk->adam
- no read depth going htsjdk->adam
- single read depth going htsjdk->adam
- multiple read depths going htsjdk->adam
- no forward read depth going htsjdk->adam
- single forward read depth going htsjdk->adam
- multiple forward read depths going htsjdk->adam
- no reverse read depth going htsjdk->adam
- single reverse read depth going htsjdk->adam
- multiple reverse read depths going htsjdk->adam
- no ancestral allele set adam->htsjdk
- ancestral allele set adam->htsjdk
- no dbsnp membership set adam->htsjdk
- dbsnp membership set adam->htsjdk
- no hapmap2 membership set adam->htsjdk
- hapmap2 membership set adam->htsjdk
- no hapmap3 membership set adam->htsjdk
- hapmap3 membership set adam->htsjdk
- no validated set adam->htsjdk
- validated set adam->htsjdk
- no 1000G membership set adam->htsjdk
- 1000G membership set adam->htsjdk
- no allele count set adam->htsjdk
- allele count set adam->htsjdk
- no allele frequency set adam->htsjdk
- allele frequency set adam->htsjdk
- no cigar set adam->htsjdk
- cigar set adam->htsjdk
- no read depth set adam->htsjdk
- read depth set adam->htsjdk
- read depth without reference read depth
- reference read depth without read depth
- no forward read depth set adam->htsjdk
- forward read depth set adam->htsjdk
- reference forward read depth without forward read depth
- forward read depth without reference forward read depth
- no reverse read depth set adam->htsjdk
- reverse read depth set adam->htsjdk
- reference reverse read depth without reverse read depth
- reverse read depth without reference reverse read depth
- VCF INFO attribute Number=0 Type=Flag adam->htsjdk
- VCF INFO attribute Number=4 Type=Flag adam->htsjdk unsupported, strict !!! IGNORED !!!
- VCF INFO attribute Number=1 Type=Integer adam->htsjdk
- VCF INFO attribute Number=4 Type=Integer adam->htsjdk
- VCF INFO attribute Number=A Type=Integer adam->htsjdk
- VCF INFO attribute Number=R Type=Integer adam->htsjdk
- VCF INFO attribute Number=R Type=String adam->htsjdk
- VCF INFO attribute Number=G Type=String adam->htsjdk not supported
- VCF INFO attribute Number=0 Type=Flag htsjdk->adam
- VCF INFO attribute Number=1 Type=Integer htsjdk->adam
- VCF INFO attribute Number=4 Type=Integer htsjdk->adam
- VCF INFO attribute Number=4 Type=Float htsjdk->adam
- VCF INFO attribute Number=A Type=Integer htsjdk->adam
- VCF INFO attribute Number=R Type=Integer htsjdk->adam
- VCF INFO attribute Number=R Type=String htsjdk->adam
- VCF INFO attribute Number=G Type=String htsjdk->adam not supported
- VCF FORMAT attribute Number=0 Type=Flag adam->htsjdk not supported
- VCF FORMAT attribute Number=1 Type=Integer adam->htsjdk
- VCF FORMAT attribute Number=4 Type=Integer adam->htsjdk
- VCF FORMAT attribute Number=A Type=Integer adam->htsjdk
- VCF FORMAT attribute Number=R Type=Integer adam->htsjdk
- VCF FORMAT attribute Number=R Type=String adam->htsjdk
- VCF FORMAT attribute Number=0 Type=Flag htsjdk->adam is not supported
- VCF FORMAT attribute Number=1 Type=Integer htsjdk->adam
- VCF FORMAT attribute Number=4 Type=Integer htsjdk->adam
- VCF FORMAT attribute Number=4 Type=Float htsjdk->adam
- VCF FORMAT attribute Number=A Type=Integer htsjdk->adam
- VCF FORMAT attribute Number=R Type=Integer htsjdk->adam
- VCF FORMAT attribute Number=R Type=String htsjdk->adam
- VCF FORMAT attribute Number=G Type=String htsjdk->adam
- respect end position for symbolic alts
FastqRecordConverterSuite:
- test read name suffix and index of pair must match
- test parseReadInFastq, read suffix removal
- test parseReadInFastq, read metadata removal
- test parseReadInFastq, read quality shorter than read length, padded with B
- test parseReadInFastq, read quality longer than read length 
- test parseReadInFastq, no read quality
- testing FastqRecordConverter.convertPair with valid input
- testing FastqRecordConverter.convertPair with 7-line invalid input
- testing FastqRecordConverter.convertPair with invalid input: first read length and qual don't match
- testing FastqRecordConverter.convertPair with invalid input: second read length and qual don't match
- testing FastqRecordConverter.convertFragment with valid input
- testing FastqRecordConverter.convertFragment with another valid input having /1, /2 suffixes
- testing FastqRecordConverter.convertFragment with invalid input: different read names
- testing FastqRecordConverter.convertRead with valid input
- testing FastqRecordConverter.convertRead with valid input: setFirstOfPair set to true
- testing FastqRecordConverter.convertRead with valid input: setSecondOfPair set to true
- testing FastqRecordConverter.convertRead with valid input: setFirstOfPair and setSecondOfPair both true
- testing FastqRecordConverter.convertRead with valid input, no qual, strict
- testing FastqRecordConverter.convertRead with valid input, no qual, not strict
AttributeSuite:
- test SAMTagAndValue parsing
- Attributes can be correctly re-encoded as text SAM tags
DinucCovariateSuite:
- computing dinucleotide pairs for a single base sequence should return (N,N)
- compute dinucleotide pairs for a string of all valid bases
- compute dinucleotide pairs for a string with an N
- compute covariates for a read on the negative strand
- compute covariates for a read on the positive strand
RecalibrationTableSuite:
- look up quality scores in table
IndexedFastaFileSuite:
- correctly generates reference sequence dictionary from .dict file
- correctly gets sequence
- fails when fai index is not provided
2021-02-20 18:17:02 WARN  IndexedFastaFile:190 - Caught exception java.lang.NullPointerException when loading FASTA sequence dictionary. Using empty dictionary instead.
- passes when dict is not provided and ValidationStringency = LENIENT
SAMRecordConverterSuite:
- testing the fields in an Alignment obtained from a mapped samRecord conversion
- testing the fields in an Alignment obtained from an unmapped samRecord conversion
- '*' quality gets nulled out
- don't keep denormalized fields
ADAMContextSuite:
- ctr is accessible
- load from an empty directory
- sc.loadParquet should not fail on unmapped reads
- sc.loadParquet should not load a file without a type specified
- can read a small .SAM file
- can read a small .SAM file with a bad header with lenient validation
- loading a sam file with a bad header and strict stringency should fail
- can read a small .CRAM file
- can read a small .SAM with all attribute tag types
- can filter a .SAM file based on quality
- Can convert to phred
- Can convert from phred
- Can read a .gtf file
- Can read a .bed file
- Can read a BED 12 file
- Can read a .narrowPeak file
- Can read a .interval_list file
2021-02-20 18:17:05 WARN  VariantContextConverter:190 - Saw invalid info field java.lang.IllegalArgumentException: Multivalued flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag.">. Ignoring...
2021-02-20 18:17:05 WARN  VariantContextConverter:190 - Generating field extractor from header line INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag."> failed: java.lang.IllegalArgumentException: Multivalue flags are not supported for INFO lines: INFO=<ID=ABADFLAG,Number=.,Type=Flag,Description="A no good, very bad flag.">
- can read a small .vcf file with a validation issue
- can read a small .vcf file
2021-02-20 18:17:05 WARN  VCFInputFormat:218 - file:/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/2.12.10/test-classes/test.vcf.gz is not splittable, consider using block-compressed gzip (BGZF)
- can read a gzipped .vcf file
- can read a vcf file with an empty alt
- can read a BGZF gzipped .vcf file with .gz file extension
- can read a BGZF gzipped .vcf file with .bgz file extension
- can read a vcf file with a projection
- can read an uncompressed BCFv2.2 file !!! IGNORED !!!
- can read a BGZF compressed BCFv2.2 file !!! IGNORED !!!
- loadIndexedVcf with 1 ReferenceRegion
- loadIndexedVcf with multiple ReferenceRegions
- load block compressed interleaved fastq
- import records from interleaved FASTQ: 1
- import records from interleaved FASTQ: 2
- import records from interleaved FASTQ: 3
- import records from interleaved FASTQ: 4
- import block compressed single fastq
- import records from single ended FASTQ: 1
- import records from single ended FASTQ: 2
- import records from single ended FASTQ: 3
- import records from single ended FASTQ: 4
- filter on load using the filter2 API
- saveAsParquet with file path
- saveAsParquet with file path, block size, page size
- saveAsParquet with save args
- read a HLA fasta from GRCh38
- read a gzipped fasta file
- read a fasta file with comments, gaps, and translation stops
- loadIndexedBam with 1 ReferenceRegion
- loadIndexedBam with multiple ReferenceRegions
- loadIndexedBam with multiple ReferenceRegions and indexed bams
- loadIndexedBam with multiple ReferenceRegions and a directory of indexed bams
- loadIndexedBam should throw exception without an index file
- loadIndexedBam should work with indexed file with index naming format <filename>.bai
- loadIndexedBam glob should throw exception without an index file
- loadBam with a glob
- loadBam with a directory
- load vcf with a glob
- load vcf from a directory
- load gvcf which contains a multi-allelic row from a directory
- load and save gvcf which contains rows without likelihoods
- parse annotations for multi-allelic rows
- load parquet with globs
- bad glob should fail
- empty directory should fail
- can read a SnpEff-annotated .vcf file
- loadAlignments should not fail on single-end and paired-end fastq reads
- load queryname sorted sam as fragments
- load query grouped sam as fragments
- load paired fastq
- load paired fastq without cache
- load paired fastq as fragments
- load paired fastq as fragments without cache
- load HTSJDK sequence dictionary
- load Bedtools .genome file as sequence dictionary
- load Bedtools .genome.txt file as sequence dictionary
- load UCSC Genome Browser chromInfo.txt file as sequence dictionary
- load unrecognized file extension as sequence dictionary fails
- load BED features with Bedtools .genome file as sequence dictionary
- load BED features with Bedtools .genome file as sequence dictionary, no matching features
- convert program record
- load program record from sam file
- load alignments from data frame
- load features from data frame
- load fragments from data frame
- load genotypes from data frame with default header lines
- load genotypes from data frame with empty header lines
- load reads from data frame
- load sequences from data frame
- load slices from data frame
- load variant contexts from data frame with default header lines
- load variant contexts from data frame with empty header lines
- load variants from data frame with default header lines
- load variants from data frame with empty header lines
- load alignments with metadata from data frame
- load features with metadata from data frame
- load fragments with metadata from data frame
- load genotypes with metadata from data frame
- load variant contexts with metadata from data frame
- load variants with metadata from data frame
- read a fasta file with short sequences as sequences
- read a fasta file with long sequences as sequences
- read a fasta file with short sequences as slices
- read a fasta file with long sequences as slices
CycleCovariateSuite:
- compute covariates for an unpaired read on the negative strand
- compute covariates for a first-of-pair read on the negative strand
- compute covariates for a second-of-pair read on the negative strand
- compute covariates for an unpaired read on the positive strand
- compute covariates for a first-of-pair read on the positive strand
- compute covariates for a second-of-pair read on the positive strand
AlignmentConverterSuite:
- testing the fields in a converted ADAM Read
- converting a read with null quality is OK
- convert a read to fastq
- reverse complement reads when converting to fastq
- converting to fastq with unmapped reads where  read reverse complemented flag (Ox10) was NOT set
- converting to fastq with unmapped reads where reverse complemented flag (0x10) was set
- converting a fragment with no alignments should yield unaligned reads
- converting a fragment with alignments should restore the alignments
- read negative strand is propagated even when not mapped
ConsensusGeneratorFromKnownsSuite:
- no consensuses for empty target
- no consensuses for reads that don't overlap a target
- return a consensus for read overlapping a single target
RichCigarSuite:
- moving 2 bp from a deletion to a match operator
- moving 2 bp from a insertion to a match operator
- moving 1 base in a two element cigar
- move to start of read
- process right clipped cigar
- process left clipped cigar
- process cigar clipped on both ends
FileExtensionsSuite:
- ends in gzip extension
- is a vcf extension
PhredUtilsSuite:
- convert low phred score to log and back
- convert high phred score to log and back
- convert overflowing phred score to log and back and clip
- convert negative zero log probability to phred and clip
- round trip log probabilities
AlignmentDatasetSuite:
- sorting reads
- unmapped reads go at the end when sorting
- coverage does not fail on unmapped reads
- computes coverage
- computes coverage with multiple samples
- merges adjacent records with equal coverage values
- sorting reads by reference index
- round trip from ADAM to SAM and back to ADAM produces equivalent Read values
- round trip with single CRAM file produces equivalent Read values
- round trip with sharded CRAM file produces equivalent Read values
- SAM conversion sets read mapped flag properly
- load long FASTQ reads
- load FASTQ with no bases
- convert malformed FASTQ (no quality scores) => SAM => well-formed FASTQ => SAM
- round trip from ADAM to FASTQ and back to ADAM produces equivalent Read values
- round trip from ADAM to paired-FASTQ and back to ADAM produces equivalent Read values
- writing a small file with tags should produce the expected result
- writing a small sorted file as SAM should produce the expected result
- writing unordered sam from unordered sam
- writing ordered sam from unordered sam
- write single sam file back
- write single bam file back
- saveAsParquet with save args, sequence dictionary, and read group dictionary
- load parquet to sql, save, re-read from avro
- load from sam, save as partitioned parquet, and re-read from partitioned parquet
- save as SAM format
- save as sorted SAM format
- save as BAM format
- save as sorted BAM format
- save as FASTQ format
- save as ADAM parquet format
- saveAsSam SAM format
- saveAsSam SAM format single file
- saveAsSam sorted SAM format single file
- saveAsSam BAM format
- saveAsSam BAM format single file
- saveAsSam sorted BAM format single file
- saveAsFastq
- saveAsFastq as single file
- saveAsFastq with original base qualities
- saveAsFastq sorted by read name
- saveAsFastq sorted by read name with original base qualities
2021-02-20 18:19:02 WARN  RDDBoundAlignmentDataset:190 - Found 20 read names that don't occur exactly twice:
	1x:	20

Samples:
	simread:1:237728409:true
	simread:1:195211965:false
	simread:1:163841413:false
	simread:1:231911906:false
	simread:1:26472783:false
	simread:1:165341382:true
	simread:1:240344442:true
	simread:1:50683371:false
	simread:1:240997787:true
	simread:1:14397233:false
	simread:1:207027738:true
	simread:1:20101800:true
	simread:1:101556378:false
	simread:1:37577445:false
	simread:1:189606653:true
	simread:1:5469106:true
	simread:1:186794283:true
	simread:1:89554252:false
	simread:1:153978724:false
	simread:1:169801933:true
- saveAsFastq paired FASTQ
2021-02-20 18:19:06 WARN  RDDBoundAlignmentDataset:190 - Found 20 read names that don't occur exactly twice:
	1x:	20

Samples:
	simread:1:237728409:true
	simread:1:195211965:false
	simread:1:163841413:false
	simread:1:231911906:false
	simread:1:26472783:false
	simread:1:165341382:true
	simread:1:240344442:true
	simread:1:50683371:false
	simread:1:240997787:true
	simread:1:14397233:false
	simread:1:207027738:true
	simread:1:20101800:true
	simread:1:101556378:false
	simread:1:37577445:false
	simread:1:189606653:true
	simread:1:5469106:true
	simread:1:186794283:true
	simread:1:89554252:false
	simread:1:153978724:false
	simread:1:169801933:true
- saveAsPairedFastq
2021-02-20 18:19:10 WARN  RDDBoundAlignmentDataset:190 - Found 20 read names that don't occur exactly twice:
	1x:	20

Samples:
	simread:1:237728409:true
	simread:1:195211965:false
	simread:1:163841413:false
	simread:1:231911906:false
	simread:1:26472783:false
	simread:1:165341382:true
	simread:1:240344442:true
	simread:1:50683371:false
	simread:1:240997787:true
	simread:1:14397233:false
	simread:1:207027738:true
	simread:1:20101800:true
	simread:1:101556378:false
	simread:1:37577445:false
	simread:1:189606653:true
	simread:1:5469106:true
	simread:1:186794283:true
	simread:1:89554252:false
	simread:1:153978724:false
	simread:1:169801933:true
- saveAsPairedFastq as single files
- don't lose any reads when piping as SAM
2021-02-20 18:19:23 WARN  OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds.
2021-02-20 18:19:23 WARN  OutFormatterRunner:190 - Piped command List(sleep, 10) timed out after 5 seconds.
- lose all records when a command times out
- lose no records without a timeout
2021-02-20 18:19:46 WARN  OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnCuR0aNF/spark-3537dc5b-ac3f-47f9-8484-9e3251091125/userFiles-f0ddb97e-e9a9-4582-a53e-93ef1f69d2fc/timeout.py) timed out after 5 seconds.
2021-02-20 18:19:46 WARN  OutFormatterRunner:190 - Piped command List(python, /tmp/adamTestMvnCuR0aNF/spark-3537dc5b-ac3f-47f9-8484-9e3251091125/userFiles-f0ddb97e-e9a9-4582-a53e-93ef1f69d2fc/timeout.py) timed out after 5 seconds.
- lose some records when a command times out
- don't lose any reads when piping as SAM using java pipe
- don't lose any reads when piping as BAM
- don't lose any reads when piping fastq to sam
- can properly set environment variables inside of a pipe
- read vcf from alignment pipe !!! IGNORED !!!
- use broadcast join to pull down reads mapped to targets
- use broadcast join against to pull down reads mapped to targets
- use right outer broadcast join to pull down reads mapped to targets
- use right outer broadcast join against to pull down reads mapped to targets
- use shuffle join with feature spanning partitions
- use shuffle join to pull down reads mapped to targets
- use shuffle join with flankSize to pull down reads mapped close to targets
- use right outer shuffle join to pull down reads mapped to targets
- use left outer shuffle join to pull down reads mapped to targets
- use full outer shuffle join to pull down reads mapped to targets
- use shuffle join with group by to pull down reads mapped to targets
- use right outer shuffle join with group by to pull down reads mapped to targets
- cannot provide empty quality score bins
- cannot provide bins with a gap
- cannot provide overlapping bins
- binning quality scores in reads succeeds even if reads have no quality scores
- bin quality scores in reads
- union two read files together
- test k-mer counter
- test dataset based k-mer counter
- transform reads to slice genomic dataset
- transform reads to coverage genomic dataset
- transform reads to feature genomic dataset
- transform reads to fragment genomic dataset
- transform reads to genotype genomic dataset
loading /tmp/adamTestMvnCuR0aNF/TempSuite3006204927654708936.adam as parquet into RDD...
loading /tmp/adamTestMvnCuR0aNF/TempSuite3092714170091450716.adam as parquet into RDD...
- transform reads to variant genomic dataset
- cannot have a null processing step ID
- convert a processing description to htsjdk
- GenomicDataset.sort does not fail on unmapped reads
- GenomicDataset.sortLexicographically does not fail on unmapped reads
- left normalize indels
2021-02-20 18:20:56 WARN  DAGScheduler:69 - Broadcasting large task binary with size 1134.1 KiB
- running base recalibration with downsampling doesn't drop reads
- filter RDD bound alignments by MAPQ
- filter dataset bound alignments by MAPQ
- filter RDD bound unaligned alignments
- filter dataset bound unaligned alignments
- filter RDD bound unpaired alignments
- filter dataset bound unpaired alignments
- filter RDD bound duplicate alignments
- filter dataset bound duplicate alignments
- filter RDD bound alignments to primary alignments
- filter dataset bound alignments to primary alignments
- filter RDD bound alignments to read group
- filter dataset bound alignments to read group
- filter RDD bound alignments to read groups
- filter dataset bound alignments to read groups
- filter RDD bound alignments to sample
- filter dataset bound alignments to sample
- filter RDD bound alignments to samples
- filter dataset bound alignments to samples
- sort by read name
- transform dataset via java API
- convert alignments to reads
SortedGenomicDatasetSuite:
- testing that partition and sort provide correct outputs
- testing copartition maintains or adds sort
- testing that we don't drop any data on the right side even though it doesn't map to a partition on the left
- testing that sorted shuffleRegionJoin matches unsorted
- testing that sorted fullOuterShuffleRegionJoin matches unsorted
- testing that sorted rightOuterShuffleRegionJoin matches unsorted
- testing that sorted leftOuterShuffleRegionJoin matches unsorted
- testing that we can persist the sorted knowledge
SmithWatermanSuite:
- gather max position from simple scoring matrix
- gather max position from irregular scoring matrix
- gather max position from irregular scoring matrix with deletions
- score simple alignment with constant gap
- score irregular scoring matrix
- score irregular scoring matrix with indel
- can unroll cigars correctly
- execute simple trackback
- execute trackback with indel
- run end to end smith waterman for simple reads
- run end to end smith waterman for short sequences with indel
- run end to end smith waterman for longer sequences with snp
- run end to end smith waterman for longer sequences with short indel
- run end to end smith waterman for shorter sequence in longer sequence
- run end to end smith waterman for shorter sequence in longer sequence, with indel
- smithWaterman - simple alignment
IndelRealignmentTargetSuite:
- checking simple realignment target
- creating simple target from read with deletion
- creating simple target from read with insertion
- joining simple realignment targets on same chr
- joining simple realignment targets on different chr throws exception
- creating targets from three intersecting reads, same indel
- creating targets from three intersecting reads, two different indel
- creating targets from two disjoint reads
- creating targets for artificial reads: one-by-one
- creating targets for artificial reads: all-at-once (merged)
- creating indel targets for mason reads
- additional indel targets taken from consensus generator
MdTagSuite:
- null md tag
- zero length md tag
- md tag with non-digit initial value
- md tag invalid base
- md tag, pure insertion
- md tag, pure insertion, test 2
- md tag pure insertion equality
- md tag equality and hashcode
- valid md tags
- get start of read with no mismatches or deletions
- get start of read with no mismatches, but with a deletion at the start
- get start of read with mismatches at the start
- get end of read with no mismatches or deletions
- check that mdtag and rich record return same end
- get end of read with no mismatches, but a deletion at end
- CIGAR with N operator
- CIGAR with multiple N operators
- CIGAR with P operators
- Get correct matches for mdtag with insertion
- Get correct matches for mdtag with mismatches and insertion
- Get correct matches for mdtag with insertion between mismatches
- Get correct matches for mdtag with intron between mismatches
- Get correct matches for mdtag with intron and deletion between mismatches
- Throw exception when number of deleted bases in mdtag disagrees with CIGAR
- Get correct matches for mdtag with mismatch, insertion and deletion
- Get correct matches for mdtag with mismatches, insertion and deletion
- Get correct matches for MDTag with mismatches and deletions
- Get correct matches base from MDTag and CIGAR with N
- get end of read with mismatches and a deletion at end
- get correct string out of mdtag with no mismatches
- get correct string out of mdtag with mismatches at start
- get correct string out of mdtag with deletion at end
- get correct string out of mdtag with mismatches at end
- get correct string out of complex mdtag
- check complex mdtag
- get gapped reference
- move a cigar alignment by two for a read
- rewrite alignment to all matches
- rewrite alignment to two mismatches followed by all matches
- rewrite alignment to include a deletion but otherwise all matches
- rewrite alignment to include an insertion at the start of the read but otherwise all matches
- create new md tag from read vs. reference, perfect match
- create new md tag from read vs. reference, perfect alignment match, 1 mismatch
- create new md tag from read vs. reference, alignment with deletion
- create new md tag from read vs. reference, alignment with insert
- handle '=' and 'X' operators
- CIGAR/MD tag mismatch should cause errors
ParallelFileMergerSuite:
- cannot write both empty gzip block and cram eof
- buffer size must be non-negative
- get the size of several files
- block size must be positive and non-zero when trying to merge files
- must provide files to merge
- if two files are both below the block size, they should merge into one shard
- merge two files where one is greater than the block size
- merge a sharded sam file
- merge a sharded bam file
- merge a sharded cram file
- can't turn a negative index into a path
- generate a path from an index
IndelTableSuite:
- check for indels in a region with known indels
- check for indels in a contig that doesn't exist
- check for indels in a region without known indels
- build indel table from rdd of variants
FlagStatSuite:
- Standard FlagStat test
SnpTableSuite:
- create an empty snp table
- create a snp table from variants on multiple contigs
- create a snp table from a larger set of variants
- perform lookups on multi-contig snp table
- perform lookups on larger snp table
GenomicDatasetSuite:
- processing a command that is the spark root directory should return an absolute path
- processing a command that is just a single word should do nothing
- processing a command should handle arguments that include spaces
- processing a command that is a single substitution should succeed
- processing a command that is multiple words should split the string
- process a command that is multiple words with a replacement
- process a command that is multiple words with multiple replacements
RepairPartitionsSuite:
- don't pull from the first partition
- properly handle pulling from an empty iterator
- gets a single read from the partition if there are no other reads in the pair
- gets all the reads from a pair from the start of a partition
- properly handle dropping from an empty iterator
- don't drop from the first partition
- drop a single read from the partition if there are no other reads in the pair
- drops all the reads from a pair from the start of a partition
- only append to the first partition
- drop a single read from the partition and append read when in the middle
- drop reads from the start and don't append when in the last partition
- can't have more records than number of partitions
- unroll array for broadcast
- move pairs around an rdd
SequenceDictionarySuite:
- Convert from sam sequence record and back
- Convert from SAM sequence dictionary file (with extra fields)
- merge into existing dictionary
- Convert from SAM sequence dictionary and back
- Can retrieve sequence by name
- SequenceDictionary's with same single element are equal
- SequenceDictionary's with same two elements are equals
- SequenceDictionary's with different elements are unequal
- SequenceDictionaries with same elements in different order are compatible
- isCompatible tests equality on overlap
- The addition + works correctly
- The append operation ++ works correctly
- ContainsRefName works correctly for different string types
- Apply on name works correctly for different String types
- convert from sam sequence record and back
- convert from sam sequence dictionary and back
- conversion to sam sequence dictionary has correct sort order
- load sequence dictionary from VCF file
- empty sequence dictionary must be empty
- test filter to reference name
- test filter to reference names
- test filter to reference name by function
BaseQualityRecalibrationSuite:
2021-02-20 18:21:48 WARN  DAGScheduler:69 - Broadcasting large task binary with size 1134.1 KiB
- BQSR Test Input #1 w/ VCF Sites without caching
2021-02-20 18:21:54 WARN  DAGScheduler:69 - Broadcasting large task binary with size 1134.1 KiB
- BQSR Test Input #1 w/ VCF Sites with caching
2021-02-20 18:22:00 WARN  DAGScheduler:69 - Broadcasting large task binary with size 1134.1 KiB
- BQSR Test Input #1 w/ VCF Sites with serialized caching
CoverageSuite:
- Convert to coverage from valid Feature
- Convert to coverage from valid Feature with sampleId
- Convert to coverage from Feature with null/empty contigName fails with correct error
- Convert to coverage from Feature with no start/end position fails with correct error
- Convert to coverage from Feature with no score fails with correct error
GenotypeDatasetSuite:
- union two genotype genomic datasets together
- round trip to parquet
- round trip to partitioned parquet
- use broadcast join to pull down genotypes mapped to targets
- use right outer broadcast join to pull down genotypes mapped to targets
- use shuffle join to pull down genotypes mapped to targets
- use right outer shuffle join to pull down genotypes mapped to targets
- use left outer shuffle join to pull down genotypes mapped to targets
- use full outer shuffle join to pull down genotypes mapped to targets
- use shuffle join with group by to pull down genotypes mapped to targets
- use right outer shuffle join with group by to pull down genotypes mapped to targets
- convert back to variant contexts
- load parquet to sql, save, re-read from avro
2021-02-20 18:22:30 WARN  DatasetBoundSliceDataset:190 - Saving directly as Parquet from SQL. Options other than compression codec are ignored.
- transform genotypes to slice genomic dataset
- transform genotypes to coverage genomic dataset
- transform genotypes to feature genomic dataset
- transform genotypes to fragment genomic dataset
- transform genotypes to read genomic dataset
- transform genotypes to variant genomic dataset
- transform genotypes to variant context genomic dataset
- loading genotypes then converting to variants yields same output as loading variants
- filter RDD bound genotypes to genotype filters passed
- filter dataset bound genotypes to genotype filters passed
- filter RDD bound genotypes by genotype quality
- filter dataset bound genotypes by genotype quality
- filter RDD bound genotypes by read depth
- filter dataset bound genotypes by read depth
- filter RDD bound genotypes by alternate read depth
- filter dataset bound genotypes by alternate read depth
- filter RDD bound genotypes by reference read depth
- filter dataset bound genotypes by reference read depth
- filter RDD bound genotypes by sample
- filter dataset bound genotypes by sample
- filter RDD bound genotypes by samples
- filter dataset bound genotypes by samples
- filter RDD bound no call genotypes
- filter dataset no call genotypes
- round trip gVCF END attribute without nested variant annotations rdd bound
- round trip gVCF END attribute without nested variant annotations dataset bound
- round trip gVCF END attribute with nested variant annotations rdd bound
- round trip gVCF END attribute with nested variant annotations dataset bound
- transform dataset via java API
MarkDuplicatesSuite:
- single read
- reads at different positions
- reads at the same position
- reads at the same position with clipping
- reads on reverse strand
- unmapped reads
- read pairs
- read pairs with fragments
- quality scores
- read pairs that cross chromosomes
- single fragment
- fragments at different positions
- fragments at the same position
- fragments at the same position with clipping
- fragments on reverse strand
- unmapped fragments
- read pairs as fragments
- read pairs with fragments as fragments
- chimeric fragments
- inverse pairs
- supplemental reads
TreeRegionJoinSuite:
- run a join between data on a single contig
Run completed in 8 minutes, 30 seconds.
Total number of tests run: 1178
Suites: completed 68, aborted 0
Tests: succeeded 1178, failed 0, canceled 0, ignored 5, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-core-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark3_2.12 ---
[INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:3.1.0:javadoc' has not been previously called for the module: 'org.bdgenomics.adam:adam-codegen-spark3_2.12:jar:0.34.0-SNAPSHOT'. Trying to invoke it...
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/target/apidocs
[ERROR] Error fetching link: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-codegen/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.apache.parquet.avro...
Loading source files for package org.bdgenomics.adam.io...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/overview-frame.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/constant-values.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/overview-tree.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/index-all.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/allclasses-frame.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/allclasses-noframe.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/index.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/overview-summary.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/apidocs/help-doc.html...
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala added.
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-core-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark3_2.12 ---
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverters.scala:274: warning: discarding unmoored doc comment
    /**
    ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/read/AlignmentDataset.scala:844: warning: Octal escape literals are deprecated, use \u0001 instead.
      binaryCodec.writeBytes("BAM\001".getBytes())
                                 ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment
    /**
    ^
warning: there were 5 feature warnings; re-run with -feature for details
model contains 283 documentable templates
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException".
/**
^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:474: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:444: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:429: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:354: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDataset.scala:747: warning: Variable x undefined in comment for method pipe in trait GenomicDataset
   * Files are substituted in to the command with a $x syntax. E.g., to invoke
                                                     ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDataset.scala:748: warning: Variable 0 undefined in comment for method pipe in trait GenomicDataset
   * a command that uses the first file from the files Seq, use $0. To access
                                                                 ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDataset.scala:749: warning: Variable root undefined in comment for method pipe in trait GenomicDataset
   * the path to the directory where the files are copied, use $root.
                                                                ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala:3464: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala:1859: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala:1839: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala:1810: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:377: warning: Could not find any member to link for "RuntimeException".
    /**
    ^
24 warnings found
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-core-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-apis-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: APIs for Java, Python 0.34.0-SNAPSHOT          [5/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark3_2.12 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark3_2.12 ---
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/target/2.12.10/classes at 1613874246043
[WARNING] warning: there was one deprecation warning (since 2.12.0); re-run with -deprecation for details
[WARNING] warning: there were two feature warnings; re-run with -feature for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-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) @ adam-apis-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark3_2.12 ---
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/src/test/java:-1: info: compiling
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 9 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/target/2.12.10/test-classes at 1613874252199
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 8 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/target/2.12.10/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark3_2.12 ---
Discovery starting.
Discovery completed in 191 milliseconds.
Run starting. Expected test count is: 10
JavaADAMContextSuite:
2021-02-20 18:24:17 WARN  Utils:69 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
2021-02-20 18:24:17 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-02-20 18:24:17 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- can read and write a small .SAM file
- loadIndexedBam with multiple ReferenceRegions
- can read and write a small .SAM file as fragments
- can read and write a small .bed file as features
- can read and write a small .bed file as coverage
- can read and write a small .vcf as genotypes
- can read and write a small .vcf as variants
- can read a two bit file
2021-02-20 18:24:27 WARN  RDDBoundSequenceDataset:190 - asSingleFile = true ignored when saving as Parquet.
- can read and write .fa as sequences
2021-02-20 18:24:28 WARN  RDDBoundSliceDataset:190 - asSingleFile = true ignored when saving as Parquet.
- can read and write .fa as slices
Run completed in 11 seconds, 811 milliseconds.
Total number of tests run: 10
Suites: completed 2, aborted 0
Tests: succeeded 10, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/target/adam-apis-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/target/adam-apis-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark3_2.12 ---
warning: there were two feature warnings; re-run with -feature for details
model contains 192 documentable templates
one warning found
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/target/adam-apis-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/target/adam-apis-spark3_2.12-0.34.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] --------------< org.bdgenomics.adam:adam-cli-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: CLI 0.34.0-SNAPSHOT                            [6/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark3_2.12 ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark3_2.12 ---
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 19 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/2.12.10/classes at 1613874279821
[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 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/2.12.10/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 15 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark3_2.12 ---
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 12 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/2.12.10/test-classes at 1613874287325
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-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) @ adam-cli-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark3_2.12 ---
Discovery starting.
Discovery completed in 194 milliseconds.
Run starting. Expected test count is: 44
TransformFeaturesSuite:
2021-02-20 18:24:54 WARN  Utils:69 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
2021-02-20 18:24:54 WARN  Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address
2021-02-20 18:24:54 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- can convert a simple BED file
TransformVariantsSuite:
- save a file sorted by contig index
- save a lexicographically sorted file
ViewSuite:
- -f 0 -F 0 is a no-op
- no -f or -F args is a no-op
- -f 4: only unmapped reads
- -F 4: only mapped reads
- -f 4 -F 8: unmapped reads with mapped mates
- -f 12: unmapped reads with unmapped mates
- -g 12: reads that are unmapped or whose mate is unmapped
- -F 12: mapped reads with mapped mates
- -g 36: unmapped reads or reads with mate on negative strand
- -F 36: unmapped reads or reads with mate on negative strand
TransformFragmentsSuite:
- load queryname sorted sam and save as parquet
- cannot sort if not saving as sam
2021-02-20 18:25:07 WARN  TransformFragments:190 - If loading and saving as alignments, consider using TransformAlignments instead
- load reads as sam and save them sorted
- bin quality scores on reads
TransformGenotypesSuite:
- save a file sorted by contig index
- save a lexicographically sorted file
- transform VCF without nested annotations
- transform VCF with nested annotations
AboutSuite:
- template variables have been replaced
- templated values are not empty
CoverageSuite:
- correctly calculates coverage from small sam file
MergeShardsSuite:
- merge shards from unordered sam to unordered sam
- unordered sam to ordered sam
- merge sharded bam
- merge sharded cram
TransformAlignmentsSuite:
- unordered sam to unordered sam
- unordered sam to ordered sam
- unordered sam, to adam, to sam
- unordered sam, to adam, to ordered sam
- put quality scores into bins
- run region predicate
ADAMMainSuite:
- default command groups is non empty
- module provides default command groups
- inject default command groups when called via main
- command groups is empty when called via apply
- single command group
- add new command group to default command groups
- module restores default command groups when called via apply
- custom module with single command group
- custom module with new command group added to default command groups
Adam2FastqSuite:
2021-02-20 18:25:17 WARN  RDDBoundAlignmentDataset:190 - Found 16 read names that don't occur exactly twice:
	1x:	16

Samples:
	SRR062634.16445865
	SRR062634.9119161
	SRR062634.17190076
	SRR062634.17969132
	SRR062634.7301099
	SRR062634.2087100
	SRR062634.20911784
	SRR062634.16769670
	SRR062634.18958430
	SRR062634.12099057
	SRR062634.12606172
	SRR062634.14985224
	SRR062634.10448889
	SRR062634.4789722
	SRR062634.3203184
	SRR062634.17698657
- convert SAM to paired FASTQ
Run completed in 24 seconds, 540 milliseconds.
Total number of tests run: 44
Suites: completed 12, aborted 0
Tests: succeeded 44, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-cli-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/adam-cli-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/adam-cli-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark3_2.12 ---
[INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:3.1.0:javadoc' has not been previously called for the module: 'org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.34.0-SNAPSHOT'. Trying to invoke it...
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/target/apidocs
[ERROR] Error fetching link: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-apis/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.adam.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/constant-values.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/overview-tree.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/index-all.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/allclasses-frame.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/index.html...
Generating /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/adam-cli-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark3_2.12 ---
model contains 55 documentable templates
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-cli/target/adam-cli-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -----------< org.bdgenomics.adam:adam-assembly-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Assembly 0.34.0-SNAPSHOT                       [7/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark3_2.12 ---
[INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark3_2.12 ---
[INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/target/2.12.10/classes at 1613874334085
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-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) @ adam-assembly-spark3_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-assembly-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark3_2.12 ---
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark3_2.12 ---
[INFO] Request to add '/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark3_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark3_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark3_2.12 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark3_2.12:jar:0.34.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.10 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.30 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
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[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark3_2.12:jar:0.34.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
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[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
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[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
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[INFO] Including org.bdgenomics.adam:adam-codegen-spark3_2.12:jar:0.34.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.34.0-SNAPSHOT in the shaded jar.
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[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
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[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT-shaded.jar
[INFO] 
[INFO] ---------< org.bdgenomics.adam:adam-distribution-spark3_2.12 >----------
[INFO] Building ADAM_2.12: Distribution 0.34.0-SNAPSHOT                   [8/8]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-distribution-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-distribution-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-distribution-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-distribution-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-distribution-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-distribution-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:3.2.0:single (default) @ adam-distribution-spark3_2.12 ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-distribution/target/adam-distribution-spark3_2.12-0.34.0-SNAPSHOT-bin.tar.gz
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[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
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[INFO] Building zip: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/adam-distribution/target/adam-distribution-spark3_2.12-0.34.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.12 0.34.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  6.032 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  7.075 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  8.697 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [09:53 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 32.751 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 55.475 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 14.660 s]
[INFO] ADAM_2.12: Distribution ............................ SUCCESS [ 30.454 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  12:28 min
[INFO] Finished at: 2021-02-20T18:26:18-08:00
[INFO] ------------------------------------------------------------------------

# make sure that the distribution package contains an assembly jar
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzvf adam-distribution/target/adam-distribution*-bin.tar.gz | \
    grep adam-assembly | \
    grep jar | \
    grep -v -e sources -e javadoc 
+ tar tzvf adam-distribution/target/adam-distribution-spark3_2.12-0.34.0-SNAPSHOT-bin.tar.gz
+ grep adam-assembly
+ grep jar
+ grep -v -e sources -e javadoc
-rw-r--r-- jenkins/jenkins 45506553 2021-02-20 18:25 adam-distribution-spark3_2.12-0.34.0-SNAPSHOT/repo/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${ADAM_MVN_TMP_DIR}
+ find /tmp/adamTestMvnCuR0aNF
/tmp/adamTestMvnCuR0aNF
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/.part-00001-d3ce2220-f1da-4df8-a2f9-317274c8fc2c-c000.snappy.parquet.crc
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/part-00001-d3ce2220-f1da-4df8-a2f9-317274c8fc2c-c000.snappy.parquet
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/part-00002-d3ce2220-f1da-4df8-a2f9-317274c8fc2c-c000.snappy.parquet
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/.part-00000-d3ce2220-f1da-4df8-a2f9-317274c8fc2c-c000.snappy.parquet.crc
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/._SUCCESS.crc
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/.part-00002-d3ce2220-f1da-4df8-a2f9-317274c8fc2c-c000.snappy.parquet.crc
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/._processingSteps.avro.crc
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/._references.avro.crc
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/_SUCCESS
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/._readGroups.avro.crc
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/part-00000-d3ce2220-f1da-4df8-a2f9-317274c8fc2c-c000.snappy.parquet
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/_references.avro
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/_processingSteps.avro
/tmp/adamTestMvnCuR0aNF/TempSuite5918541597762226047.adam/_readGroups.avro
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/._SUCCESS.crc
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/._metadata.crc
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/._header.crc
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/._references.avro.crc
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/_SUCCESS
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/_metadata
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/_common_metadata
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/_references.avro
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/_header
/tmp/adamTestMvnCuR0aNF/TempSuite8197890354633201776.adam/._common_metadata.crc
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/.part-00001-5e8d112c-80db-4bd6-aa02-d83aac652375-c000.snappy.parquet.crc
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/.part-00002-5e8d112c-80db-4bd6-aa02-d83aac652375-c000.snappy.parquet.crc
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/._SUCCESS.crc
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/part-00000-5e8d112c-80db-4bd6-aa02-d83aac652375-c000.snappy.parquet
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/.part-00000-5e8d112c-80db-4bd6-aa02-d83aac652375-c000.snappy.parquet.crc
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/._references.avro.crc
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/_SUCCESS
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/part-00002-5e8d112c-80db-4bd6-aa02-d83aac652375-c000.snappy.parquet
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/part-00001-5e8d112c-80db-4bd6-aa02-d83aac652375-c000.snappy.parquet
/tmp/adamTestMvnCuR0aNF/TempSuite9062671237860397509.adam/_references.avro
/tmp/adamTestMvnCuR0aNF/596011715244991852
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/._SUCCESS.crc
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/._metadata.crc
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/._processingSteps.avro.crc
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/._references.avro.crc
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/_SUCCESS
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/_metadata
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/._readGroups.avro.crc
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/_common_metadata
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/_references.avro
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/_processingSteps.avro
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/_readGroups.avro
/tmp/adamTestMvnCuR0aNF/596011715244991852/binned.adam/._common_metadata.crc
/tmp/adamTestMvnCuR0aNF/TempSuite494991377238735231.bed
/tmp/adamTestMvnCuR0aNF/TempSuite494991377238735231.bed/._SUCCESS.crc
/tmp/adamTestMvnCuR0aNF/TempSuite494991377238735231.bed/.part-00000.crc
/tmp/adamTestMvnCuR0aNF/TempSuite494991377238735231.bed/part-00000
/tmp/adamTestMvnCuR0aNF/TempSuite494991377238735231.bed/_SUCCESS
/tmp/adamTestMvnCuR0aNF/TempSuite1650566991721859825
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/part-r-00000.gz.parquet
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/._SUCCESS.crc
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/.part-r-00000.gz.parquet.crc
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/._metadata.crc
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/._header.crc
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/._references.avro.crc
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/_SUCCESS
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/_metadata
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/_samples.avro
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/_common_metadata
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/._samples.avro.crc
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/_references.avro
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/_header
/tmp/adamTestMvnCuR0aNF/TempSuite6108609805489720647.adam/._common_metadata.crc
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/tmp/adamTestMvnCuR0aNF/FeatureDatasetFunctionsSuite8476308574070660556
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/tmp/adamTestMvnCuR0aNF/TempSuite4585659589823915292.adam/_readGroups.avro
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/tmp/adamTestMvnCuR0aNF/TempSuite399694817801468038.bed/part-00000
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/tmp/adamTestMvnCuR0aNF/TempSuite7317330856891112018.bam
/tmp/adamTestMvnCuR0aNF/TempSuite7317330856891112018.bam/._SUCCESS.crc
/tmp/adamTestMvnCuR0aNF/TempSuite7317330856891112018.bam/_SUCCESS
/tmp/adamTestMvnCuR0aNF/TempSuite7317330856891112018.bam/.part-r-00000.bam.crc
/tmp/adamTestMvnCuR0aNF/TempSuite7317330856891112018.bam/part-r-00000.bam
rm -rf ${ADAM_MVN_TMP_DIR}
+ rm -rf /tmp/adamTestMvnCuR0aNF

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${ADAM_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/adamTestMvnCuR0aNF:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# run integration tests

# make a temp directory
ADAM_TMP_DIR=$(mktemp -d -t adamTestXXXXXXX)
mktemp -d -t adamTestXXXXXXX
++ mktemp -d -t adamTestXXXXXXX
+ ADAM_TMP_DIR=/tmp/adamTestvILfhHm

# Just to be paranoid.. use a directory internal to the ADAM_TMP_DIR
ADAM_TMP_DIR=$ADAM_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded
+ ADAM_TMP_DIR=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded
mkdir $ADAM_TMP_DIR
+ mkdir /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded

# set the TMPDIR envar, which is used by python to choose where to make temp directories
export TMPDIR=${ADAM_TMP_DIR}
+ export TMPDIR=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded

pushd $PROJECT_ROOT
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu

# Copy the jar into our temp space for testing
cp -r . $ADAM_TMP_DIR
+ cp -r . /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu

pushd $ADAM_TMP_DIR
+ pushd /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu

# what hadoop version are we on? format string for downloading spark assembly
if [[ $HADOOP_VERSION =~ ^3\.2 ]]; then
    HADOOP=hadoop3.2
else
    echo "Unknown Hadoop version."
    exit 1
fi
+ [[ 3.2.1 =~ ^3\.2 ]]
+ HADOOP=hadoop3.2

# set spark artifact string for downloading assembly
SPARK=spark-${SPARK_VERSION}
+ SPARK=spark-3.0.2
    
# download prepackaged spark assembly
curl \
    -v \
    -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
    -o ${SPARK}-bin-${HADOOP}.tgz
+ curl -v -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-3.0.2/spark-3.0.2-bin-hadoop3.2.tgz' -o spark-3.0.2-bin-hadoop3.2.tgz
*   Trying 95.216.26.30...
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0* Connected to www.apache.org (95.216.26.30) port 443 (#0)
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
*   CAfile: /home/jenkins/anaconda2/ssl/cacert.pem
  CApath: none
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [108 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [4639 bytes data]
* TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [333 bytes data]
* TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
* TLSv1.2 (OUT), TLS change cipher, Client hello (1):
} [1 bytes data]
* TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
* TLSv1.2 (IN), TLS change cipher, Client hello (1):
{ [1 bytes data]
* TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server accepted to use http/1.1
* Server certificate:
*  subject: OU=Domain Control Validated; OU=PositiveSSL Wildcard; CN=*.apache.org
*  start date: Jul  1 00:00:00 2019 GMT
*  expire date: Jun 30 23:59:59 2021 GMT
*  subjectAltName: host "www.apache.org" matched cert's "*.apache.org"
*  issuer: C=GB; ST=Greater Manchester; L=Salford; O=Sectigo Limited; CN=Sectigo RSA Domain Validation Secure Server CA
*  SSL certificate verify ok.
} [5 bytes data]
> GET /dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-3.0.2/spark-3.0.2-bin-hadoop3.2.tgz HTTP/1.1
> Host: www.apache.org
> User-Agent: curl/7.49.0
> Accept: */*
> 
{ [5 bytes data]
< HTTP/1.1 302 Found
< Date: Sun, 21 Feb 2021 02:26:20 GMT
< Server: Apache
< Cache-Control: private, max-age=3600
< Location: https://mirrors.ocf.berkeley.edu/apache/spark/spark-3.0.2/spark-3.0.2-bin-hadoop3.2.tgz
< Expires: Sun, 21 Feb 2021 03:26:20 GMT
< Content-Length: 0
< 

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
* Connection #0 to host www.apache.org left intact
* Issue another request to this URL: 'https://mirrors.ocf.berkeley.edu/apache/spark/spark-3.0.2/spark-3.0.2-bin-hadoop3.2.tgz'
*   Trying 169.229.226.30...
* Connected to mirrors.ocf.berkeley.edu (169.229.226.30) port 443 (#1)
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
*   CAfile: /home/jenkins/anaconda2/ssl/cacert.pem
  CApath: none
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [113 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [2844 bytes data]
* TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [589 bytes data]
* TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
* TLSv1.2 (OUT), TLS change cipher, Client hello (1):
} [1 bytes data]
* TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
* TLSv1.2 (IN), TLS change cipher, Client hello (1):
{ [1 bytes data]
* TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
* SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
* ALPN, server accepted to use http/1.1
* Server certificate:
*  subject: CN=fallingrocks.ocf.berkeley.edu
*  start date: Jan 16 06:25:56 2021 GMT
*  expire date: Apr 16 06:25:56 2021 GMT
*  subjectAltName: host "mirrors.ocf.berkeley.edu" matched cert's "mirrors.ocf.berkeley.edu"
*  issuer: C=US; O=Let's Encrypt; CN=R3
*  SSL certificate verify ok.
} [5 bytes data]
> GET /apache/spark/spark-3.0.2/spark-3.0.2-bin-hadoop3.2.tgz HTTP/1.1
> Host: mirrors.ocf.berkeley.edu
> User-Agent: curl/7.49.0
> Accept: */*
> 

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0{ [5 bytes data]
< HTTP/1.1 200 OK
< Date: Sun, 21 Feb 2021 02:26:20 GMT
< Server: Apache/2.4
< Last-Modified: Tue, 16 Feb 2021 06:33:55 GMT
< ETag: "d636a7e-5bb6e495b0017"
< Accept-Ranges: bytes
< Content-Length: 224619134
< Content-Type: application/x-gzip
< 
{ [5 bytes data]

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* Connection #1 to host mirrors.ocf.berkeley.edu left intact

tar xzvf ${SPARK}-bin-${HADOOP}.tgz
+ tar xzvf spark-3.0.2-bin-hadoop3.2.tgz
spark-3.0.2-bin-hadoop3.2/
spark-3.0.2-bin-hadoop3.2/R/
spark-3.0.2-bin-hadoop3.2/R/lib/
spark-3.0.2-bin-hadoop3.2/R/lib/sparkr.zip
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/worker/
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/worker/worker.R
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/worker/daemon.R
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/tests/
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/tests/testthat/
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/tests/testthat/test_basic.R
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/profile/
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/profile/shell.R
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/profile/general.R
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/R/
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/R/SparkR
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/R/SparkR.rdx
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/R/SparkR.rdb
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/Meta/
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/Meta/features.rds
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/Meta/package.rds
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/Meta/nsInfo.rds
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/Meta/Rd.rds
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/Meta/links.rds
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/Meta/hsearch.rds
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/DESCRIPTION
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/NAMESPACE
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/html/
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/html/R.css
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/html/00Index.html
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/help/
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/help/aliases.rds
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/help/AnIndex
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/help/SparkR.rdx
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/help/SparkR.rdb
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/help/paths.rds
spark-3.0.2-bin-hadoop3.2/R/lib/SparkR/INDEX
spark-3.0.2-bin-hadoop3.2/sbin/
spark-3.0.2-bin-hadoop3.2/sbin/stop-slaves.sh
spark-3.0.2-bin-hadoop3.2/sbin/stop-slave.sh
spark-3.0.2-bin-hadoop3.2/sbin/stop-all.sh
spark-3.0.2-bin-hadoop3.2/sbin/start-slaves.sh
spark-3.0.2-bin-hadoop3.2/sbin/start-slave.sh
spark-3.0.2-bin-hadoop3.2/sbin/start-all.sh
spark-3.0.2-bin-hadoop3.2/sbin/spark-daemons.sh
spark-3.0.2-bin-hadoop3.2/sbin/spark-daemon.sh
spark-3.0.2-bin-hadoop3.2/sbin/spark-config.sh
spark-3.0.2-bin-hadoop3.2/sbin/slaves.sh
spark-3.0.2-bin-hadoop3.2/sbin/stop-thriftserver.sh
spark-3.0.2-bin-hadoop3.2/sbin/stop-mesos-shuffle-service.sh
spark-3.0.2-bin-hadoop3.2/sbin/stop-mesos-dispatcher.sh
spark-3.0.2-bin-hadoop3.2/sbin/stop-master.sh
spark-3.0.2-bin-hadoop3.2/sbin/stop-history-server.sh
spark-3.0.2-bin-hadoop3.2/sbin/start-thriftserver.sh
spark-3.0.2-bin-hadoop3.2/sbin/start-mesos-shuffle-service.sh
spark-3.0.2-bin-hadoop3.2/sbin/start-mesos-dispatcher.sh
spark-3.0.2-bin-hadoop3.2/sbin/start-master.sh
spark-3.0.2-bin-hadoop3.2/sbin/start-history-server.sh
spark-3.0.2-bin-hadoop3.2/python/
spark-3.0.2-bin-hadoop3.2/python/pyspark/
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_utils.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_udf.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_types.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_streaming.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_session.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_serde.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_readwriter.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_pandas_udf_window.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_pandas_udf_typehints.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_pandas_udf_scalar.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_pandas_udf_grouped_agg.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_pandas_udf.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_pandas_map.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_pandas_grouped_map.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_pandas_cogrouped_map.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_group.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_functions.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_datasources.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_dataframe.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_context.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_conf.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_column.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_catalog.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/tests/test_arrow.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/utils.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/types.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/typehints.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/serializers.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/map_ops.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/group_ops.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/functions.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/conversion.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/pandas/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/avro/
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/avro/functions.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/avro/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/window.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/utils.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/udf.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/types.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/streaming.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/session.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/readwriter.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/group.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/functions.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/dataframe.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/conf.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/column.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/catalog.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/rddsampler.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/util.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/tree.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/regression.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/recommendation.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/random.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/fpm.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/feature.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/evaluation.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/common.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/clustering.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/classification.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/tests/
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/tests/test_util.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/tests/test_streaming_algorithms.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/tests/test_stat.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/tests/test_linalg.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/tests/test_feature.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/tests/test_algorithms.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/tests/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/stat/
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/stat/distribution.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/stat/_statistics.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/stat/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/stat/KernelDensity.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/stat/test.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/linalg/
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/linalg/distributed.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/mllib/linalg/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_tuning.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_training_summary.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_stat.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_pipeline.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_persistence.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_param.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_linalg.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_image.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_feature.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_evaluation.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_base.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_algorithms.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_util.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tests/test_wrapper.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/param/
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/param/shared.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/param/_shared_params_code_gen.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/param/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/linalg/
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/linalg/__init__.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/wrapper.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/util.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tuning.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/tree.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/stat.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/regression.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/recommendation.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/pipeline.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/image.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/functions.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/fpm.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/feature.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/evaluation.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/common.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/clustering.py
spark-3.0.2-bin-hadoop3.2/python/pyspark/ml/classification.py
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spark-3.0.2-bin-hadoop3.2/licenses/LICENSE-scala.txt
spark-3.0.2-bin-hadoop3.2/licenses/LICENSE-sbt-launch-lib.txt
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spark-3.0.2-bin-hadoop3.2/LICENSE
spark-3.0.2-bin-hadoop3.2/examples/
spark-3.0.2-bin-hadoop3.2/examples/src/
spark-3.0.2-bin-hadoop3.2/examples/src/main/
spark-3.0.2-bin-hadoop3.2/examples/src/main/scripts/
spark-3.0.2-bin-hadoop3.2/examples/src/main/scripts/getGpusResources.sh
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/correlation_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/chisq_selector_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/chi_square_test_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/bucketizer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/bucketed_random_projection_lsh_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/bisecting_k_means_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/binarizer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/als_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/aft_survival_regression.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/word2vec_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/vector_slicer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/vector_size_hint_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/vector_indexer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/vector_assembler_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/tokenizer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/tf_idf_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/summarizer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/string_indexer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/stopwords_remover_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/standard_scaler_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/sql_transformer.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/robust_scaler_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/rformula_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/random_forest_regressor_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/random_forest_classifier_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/quantile_discretizer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/polynomial_expansion_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/pipeline_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/train_validation_split.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/prefixspan_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/power_iteration_clustering_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/imputer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/fpgrowth_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/pca_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/onehot_encoder_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/one_vs_rest_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/normalizer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/naive_bayes_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/n_gram_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/multilayer_perceptron_classification.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/multiclass_logistic_regression_with_elastic_net.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/min_max_scaler_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/min_hash_lsh_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/max_abs_scaler_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/logistic_regression_with_elastic_net.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/logistic_regression_summary_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/linearsvc.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/linear_regression_with_elastic_net.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/lda_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/kmeans_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/isotonic_regression_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/interaction_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/index_to_string_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/gradient_boosted_tree_regressor_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/gradient_boosted_tree_classifier_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/generalized_linear_regression_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/gaussian_mixture_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/fm_regressor_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/fm_classifier_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/feature_hasher_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/estimator_transformer_param_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/elementwise_product_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/decision_tree_regression_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/decision_tree_classification_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/dct_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/dataframe_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/cross_validator.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/ml/count_vectorizer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/logistic_regression.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/kmeans.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/avro_inputformat.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/als.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/wordcount.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/transitive_closure.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/status_api_demo.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sort.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/pi.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/parquet_inputformat.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/pagerank.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/streaming/
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/streaming/stateful_network_wordcount.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/streaming/sql_network_wordcount.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/streaming/recoverable_network_wordcount.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/streaming/network_wordjoinsentiments.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/streaming/network_wordcount.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/streaming/hdfs_wordcount.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/streaming/queue_stream.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sql/
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sql/hive.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sql/datasource.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sql/basic.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sql/arrow.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sql/streaming/
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sql/streaming/structured_network_wordcount_windowed.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sql/streaming/structured_network_wordcount.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/sql/streaming/structured_kafka_wordcount.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/word2vec_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/word2vec.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/tf_idf_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/summary_statistics_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/streaming_linear_regression_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/streaming_k_means_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/stratified_sampling_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/standard_scaler_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/sampled_rdds.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/recommendation_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/random_rdd_generation.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/random_forest_regression_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/random_forest_classification_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/power_iteration_clustering_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/normalizer_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/naive_bayes_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/logistic_regression_with_lbfgs_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/logistic_regression.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/linear_regression_with_sgd_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/latent_dirichlet_allocation_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/kmeans.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/kernel_density_estimation_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/k_means_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/isotonic_regression_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/hypothesis_testing_kolmogorov_smirnov_test_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/hypothesis_testing_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/gradient_boosting_regression_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/gradient_boosting_classification_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/gaussian_mixture_model.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/gaussian_mixture_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/elementwise_product_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/decision_tree_regression_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/decision_tree_classification_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/correlations_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/correlations.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/bisecting_k_means_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/binary_classification_metrics_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/svm_with_sgd_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/svd_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/regression_metrics_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/ranking_metrics_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/pca_rowmatrix_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/multi_label_metrics_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/multi_class_metrics_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/python/mllib/fpgrowth_example.py
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/JavaStatefulNetworkWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/JavaSqlNetworkWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/JavaRecord.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/JavaQueueStream.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/JavaNetworkWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/JavaDirectKerberizedKafkaWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/JavaDirectKafkaWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/JavaCustomReceiver.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/streaming/JavaRecoverableNetworkWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/streaming/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredSessionization.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredNetworkWordCountWindowed.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredNetworkWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredKerberizedKafkaWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredKafkaWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/hive/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/hive/JavaSparkHiveExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/JavaUserDefinedUntypedAggregation.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/JavaUserDefinedTypedAggregation.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/JavaUserDefinedScalar.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/JavaSparkSQLExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/sql/JavaSQLDataSourceExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaSummaryStatisticsExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaStreamingTestExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaStratifiedSamplingExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaSimpleFPGrowth.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaSVMWithSGDExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaSVDExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaRecommendationExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaRankingMetricsExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaRandomForestRegressionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaRandomForestClassificationExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaPrefixSpanExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaPowerIterationClusteringExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaPCAExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaNaiveBayesExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaMulticlassClassificationMetricsExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaMultiLabelClassificationMetricsExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaLogisticRegressionWithLBFGSExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaLatentDirichletAllocationExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaLBFGSExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaKernelDensityEstimationExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaKMeansExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaIsotonicRegressionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaHypothesisTestingKolmogorovSmirnovTestExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaHypothesisTestingExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaGradientBoostingRegressionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaGradientBoostingClassificationExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaGaussianMixtureExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaElementwiseProductExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaDecisionTreeRegressionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaDecisionTreeClassificationExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaCorrelationsExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaChiSqSelectorExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaBisectingKMeansExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaBinaryClassificationMetricsExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaAssociationRulesExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/mllib/JavaALS.java
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spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaWord2VecExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorSlicerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorSizeHintExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorIndexerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorAssemblerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaTfIdfExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaSummarizerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaStringIndexerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaStopWordsRemoverExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaStandardScalerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaSQLTransformerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaRobustScalerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaRandomForestRegressorExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaRandomForestClassifierExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaRFormulaExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaQuantileDiscretizerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaPrefixSpanExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaPowerIterationClusteringExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaPolynomialExpansionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaPipelineExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaPCAExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaOneVsRestExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaOneHotEncoderExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaNormalizerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaNaiveBayesExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaNGramExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaMultilayerPerceptronClassifierExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaMulticlassLogisticRegressionWithElasticNetExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaModelSelectionViaTrainValidationSplitExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaModelSelectionViaCrossValidationExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaMinMaxScalerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaMinHashLSHExample.java
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spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionWithElasticNetExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionSummaryExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaLinearSVCExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaLinearRegressionWithElasticNetExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaLabeledDocument.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaLDAExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaKMeansExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaIsotonicRegressionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaInteractionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaIndexToStringExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaImputerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeRegressorExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeClassifierExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaGeneralizedLinearRegressionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaGaussianMixtureExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaFeatureHasherExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaFPGrowthExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaFMRegressorExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaFMClassifierExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaEstimatorTransformerParamExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaElementwiseProductExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaDocument.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaDecisionTreeRegressionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaDecisionTreeClassificationExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaDCTExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaCountVectorizerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaCorrelationExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaChiSquareTestExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaChiSqSelectorExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaBucketizerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaBucketedRandomProjectionLSHExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaBisectingKMeansExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaBinarizerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaALSExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/ml/JavaTokenizerExample.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/JavaWordCount.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/JavaTC.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/JavaStatusTrackerDemo.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/JavaSparkPi.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/JavaPageRank.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/JavaLogQuery.java
spark-3.0.2-bin-hadoop3.2/examples/src/main/java/org/apache/spark/examples/JavaHdfsLR.java
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/SparkKMeans.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/LocalKMeans.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/RecoverableNetworkWordCount.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewStream.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewGenerator.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/StreamingExamples.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/StatefulNetworkWordCount.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/SqlNetworkWordCount.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/RawNetworkGrep.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/QueueStream.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/NetworkWordCount.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/HdfsWordCount.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/DirectKerberizedKafkaWordCount.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/DirectKafkaWordCount.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/streaming/CustomReceiver.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/SparkSQLExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/SQLDataSourceExample.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredSessionization.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCountWindowed.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCount.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredKerberizedKafkaWordCount.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredKafkaWordCount.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/hive/SparkHiveExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedUntypedAggregation.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedTypedAggregation.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedScalar.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/SimpleTypedAggregator.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/sql/RDDRelation.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/pythonconverters/
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/pythonconverters/AvroConverters.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/RankingMetricsExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/Word2VecExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnySVD.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnyPCA.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/TFIDFExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/SummaryStatisticsExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLogisticRegression.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLinearRegressionExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingKMeansExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/StratifiedSamplingExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/StandardScalerExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/SparseNaiveBayes.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/SimpleFPGrowth.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/SampledRDDs.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/SVMWithSGDExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/SVDExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/RecommendationExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/RandomRDDGeneration.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestRegressionExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestClassificationExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/PrefixSpanExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/PowerIterationClusteringExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/PMMLModelExportExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnSourceVectorExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnRowMatrixExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/NormalizerExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/NaiveBayesExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/MultivariateSummarizer.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/MulticlassMetricsExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/MultiLabelMetricsExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/MovieLensALS.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/LogisticRegressionWithLBFGSExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/LatentDirichletAllocationExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/LDAExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/LBFGSExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/KernelDensityEstimationExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/KMeansExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/IsotonicRegressionExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/HypothesisTestingKolmogorovSmirnovTestExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/HypothesisTestingExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostingRegressionExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostingClassificationExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostedTreesRunner.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/CosineSimilarity.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/ChiSqSelectorExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/BisectingKMeansExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/mllib/BinaryClassificationMetricsExample.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/NGramExample.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/ModelSelectionViaTrainValidationSplitExample.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/GeneralizedLinearRegressionExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/GaussianMixtureExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/GBTExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/FeatureHasherExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/FPGrowthExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/FMRegressorExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/FMClassifierExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/EstimatorTransformerParamExample.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeRegressionExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeClassificationExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/DataFrameExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/DCTExample.scala
spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/CountVectorizerExample.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/scala/org/apache/spark/examples/ml/ChiSquareTestExample.scala
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spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/svmLinear.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/survreg.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/randomForest.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/prefixSpan.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/powerIterationClustering.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/naiveBayes.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/mlp.R
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spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/gaussianMixture.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/fpm.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/decisionTree.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/bisectingKmeans.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/ml/als.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/dataframe.R
spark-3.0.2-bin-hadoop3.2/examples/src/main/r/data-manipulation.R
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spark-3.0.2-bin-hadoop3.2/jars/spark-tags_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-tags_2.12-3.0.2-tests.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-streaming_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-sql_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-sketch_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-repl_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-network-shuffle_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-network-common_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-mllib_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-mllib-local_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-mesos_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-launcher_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-kvstore_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-kubernetes_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-hive_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-hive-thriftserver_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-graphx_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-core_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/spark-catalyst_2.12-3.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/snappy-java-1.1.8.2.jar
spark-3.0.2-bin-hadoop3.2/jars/snakeyaml-1.24.jar
spark-3.0.2-bin-hadoop3.2/jars/slf4j-log4j12-1.7.30.jar
spark-3.0.2-bin-hadoop3.2/jars/slf4j-api-1.7.30.jar
spark-3.0.2-bin-hadoop3.2/jars/shims-0.7.45.jar
spark-3.0.2-bin-hadoop3.2/jars/shapeless_2.12-2.3.3.jar
spark-3.0.2-bin-hadoop3.2/jars/scala-xml_2.12-1.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/scala-reflect-2.12.10.jar
spark-3.0.2-bin-hadoop3.2/jars/scala-parser-combinators_2.12-1.1.2.jar
spark-3.0.2-bin-hadoop3.2/jars/scala-library-2.12.10.jar
spark-3.0.2-bin-hadoop3.2/jars/scala-compiler-2.12.10.jar
spark-3.0.2-bin-hadoop3.2/jars/scala-collection-compat_2.12-2.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/re2j-1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/pyrolite-4.30.jar
spark-3.0.2-bin-hadoop3.2/jars/py4j-0.10.9.jar
spark-3.0.2-bin-hadoop3.2/jars/protobuf-java-2.5.0.jar
spark-3.0.2-bin-hadoop3.2/jars/parquet-jackson-1.10.1.jar
spark-3.0.2-bin-hadoop3.2/jars/parquet-hadoop-1.10.1.jar
spark-3.0.2-bin-hadoop3.2/jars/parquet-format-2.4.0.jar
spark-3.0.2-bin-hadoop3.2/jars/parquet-encoding-1.10.1.jar
spark-3.0.2-bin-hadoop3.2/jars/parquet-common-1.10.1.jar
spark-3.0.2-bin-hadoop3.2/jars/parquet-column-1.10.1.jar
spark-3.0.2-bin-hadoop3.2/jars/paranamer-2.8.jar
spark-3.0.2-bin-hadoop3.2/jars/osgi-resource-locator-1.0.3.jar
spark-3.0.2-bin-hadoop3.2/jars/oro-2.0.8.jar
spark-3.0.2-bin-hadoop3.2/jars/orc-shims-1.5.10.jar
spark-3.0.2-bin-hadoop3.2/jars/orc-mapreduce-1.5.10.jar
spark-3.0.2-bin-hadoop3.2/jars/orc-core-1.5.10.jar
spark-3.0.2-bin-hadoop3.2/jars/opencsv-2.3.jar
spark-3.0.2-bin-hadoop3.2/jars/okio-1.15.0.jar
spark-3.0.2-bin-hadoop3.2/jars/okhttp-3.12.6.jar
spark-3.0.2-bin-hadoop3.2/jars/okhttp-2.7.5.jar
spark-3.0.2-bin-hadoop3.2/jars/objenesis-2.5.1.jar
spark-3.0.2-bin-hadoop3.2/jars/nimbus-jose-jwt-4.41.1.jar
spark-3.0.2-bin-hadoop3.2/jars/netty-all-4.1.47.Final.jar
spark-3.0.2-bin-hadoop3.2/jars/minlog-1.3.0.jar
spark-3.0.2-bin-hadoop3.2/jars/metrics-jvm-4.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/metrics-json-4.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/metrics-jmx-4.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/metrics-graphite-4.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/metrics-core-4.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/mesos-1.4.0-shaded-protobuf.jar
spark-3.0.2-bin-hadoop3.2/jars/macro-compat_2.12-1.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/machinist_2.12-0.6.8.jar
spark-3.0.2-bin-hadoop3.2/jars/lz4-java-1.7.1.jar
spark-3.0.2-bin-hadoop3.2/jars/logging-interceptor-3.12.6.jar
spark-3.0.2-bin-hadoop3.2/jars/log4j-1.2.17.jar
spark-3.0.2-bin-hadoop3.2/jars/libthrift-0.12.0.jar
spark-3.0.2-bin-hadoop3.2/jars/libfb303-0.9.3.jar
spark-3.0.2-bin-hadoop3.2/jars/leveldbjni-all-1.8.jar
spark-3.0.2-bin-hadoop3.2/jars/kubernetes-model-common-4.9.2.jar
spark-3.0.2-bin-hadoop3.2/jars/kubernetes-model-4.9.2.jar
spark-3.0.2-bin-hadoop3.2/jars/kubernetes-client-4.9.2.jar
spark-3.0.2-bin-hadoop3.2/jars/kryo-shaded-4.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/kerby-xdr-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerby-util-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerby-pkix-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerby-config-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerby-asn1-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerb-util-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerb-simplekdc-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerb-server-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerb-identity-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerb-crypto-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerb-core-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerb-common-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerb-client-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/kerb-admin-1.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/jul-to-slf4j-1.7.30.jar
spark-3.0.2-bin-hadoop3.2/jars/jta-1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/jsr305-3.0.0.jar
spark-3.0.2-bin-hadoop3.2/jars/jsp-api-2.1.jar
spark-3.0.2-bin-hadoop3.2/jars/json4s-scalap_2.12-3.6.6.jar
spark-3.0.2-bin-hadoop3.2/jars/json4s-jackson_2.12-3.6.6.jar
spark-3.0.2-bin-hadoop3.2/jars/json4s-core_2.12-3.6.6.jar
spark-3.0.2-bin-hadoop3.2/jars/json4s-ast_2.12-3.6.6.jar
spark-3.0.2-bin-hadoop3.2/jars/json-smart-2.3.jar
spark-3.0.2-bin-hadoop3.2/jars/json-1.8.jar
spark-3.0.2-bin-hadoop3.2/jars/jpam-1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/jodd-core-3.5.2.jar
spark-3.0.2-bin-hadoop3.2/jars/joda-time-2.10.5.jar
spark-3.0.2-bin-hadoop3.2/jars/jline-2.14.6.jar
spark-3.0.2-bin-hadoop3.2/jars/jersey-server-2.30.jar
spark-3.0.2-bin-hadoop3.2/jars/jersey-media-jaxb-2.30.jar
spark-3.0.2-bin-hadoop3.2/jars/jersey-hk2-2.30.jar
spark-3.0.2-bin-hadoop3.2/jars/jersey-container-servlet-core-2.30.jar
spark-3.0.2-bin-hadoop3.2/jars/jersey-container-servlet-2.30.jar
spark-3.0.2-bin-hadoop3.2/jars/jersey-common-2.30.jar
spark-3.0.2-bin-hadoop3.2/jars/jersey-client-2.30.jar
spark-3.0.2-bin-hadoop3.2/jars/jdo-api-3.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/jcl-over-slf4j-1.7.30.jar
spark-3.0.2-bin-hadoop3.2/jars/jcip-annotations-1.0-1.jar
spark-3.0.2-bin-hadoop3.2/jars/jaxb-runtime-2.3.2.jar
spark-3.0.2-bin-hadoop3.2/jars/jaxb-api-2.2.11.jar
spark-3.0.2-bin-hadoop3.2/jars/javolution-5.5.1.jar
spark-3.0.2-bin-hadoop3.2/jars/javax.servlet-api-3.1.0.jar
spark-3.0.2-bin-hadoop3.2/jars/javax.jdo-3.2.0-m3.jar
spark-3.0.2-bin-hadoop3.2/jars/javax.inject-1.jar
spark-3.0.2-bin-hadoop3.2/jars/javassist-3.25.0-GA.jar
spark-3.0.2-bin-hadoop3.2/jars/janino-3.0.16.jar
spark-3.0.2-bin-hadoop3.2/jars/jakarta.xml.bind-api-2.3.2.jar
spark-3.0.2-bin-hadoop3.2/jars/jakarta.ws.rs-api-2.1.6.jar
spark-3.0.2-bin-hadoop3.2/jars/jakarta.validation-api-2.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/jakarta.inject-2.6.1.jar
spark-3.0.2-bin-hadoop3.2/jars/jakarta.annotation-api-1.3.5.jar
spark-3.0.2-bin-hadoop3.2/jars/jakarta.activation-api-1.2.1.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-module-scala_2.12-2.10.0.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-module-paranamer-2.10.0.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-module-jaxb-annotations-2.10.0.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-mapper-asl-1.9.13.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-jaxrs-json-provider-2.9.5.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-jaxrs-base-2.9.5.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-datatype-jsr310-2.10.3.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-dataformat-yaml-2.10.0.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-databind-2.10.0.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-core-asl-1.9.13.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-core-2.10.0.jar
spark-3.0.2-bin-hadoop3.2/jars/jackson-annotations-2.10.0.jar
spark-3.0.2-bin-hadoop3.2/jars/ivy-2.4.0.jar
spark-3.0.2-bin-hadoop3.2/jars/istack-commons-runtime-3.0.8.jar
spark-3.0.2-bin-hadoop3.2/jars/httpcore-4.4.12.jar
spark-3.0.2-bin-hadoop3.2/jars/httpclient-4.5.6.jar
spark-3.0.2-bin-hadoop3.2/jars/htrace-core4-4.1.0-incubating.jar
spark-3.0.2-bin-hadoop3.2/jars/hk2-utils-2.6.1.jar
spark-3.0.2-bin-hadoop3.2/jars/hk2-locator-2.6.1.jar
spark-3.0.2-bin-hadoop3.2/jars/hk2-api-2.6.1.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-vector-code-gen-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-storage-api-2.7.1.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-shims-scheduler-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-shims-common-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-shims-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-shims-0.23-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-serde-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-metastore-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-llap-common-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-jdbc-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-exec-2.3.7-core.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-common-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-cli-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hive-beeline-2.3.7.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-yarn-server-web-proxy-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-yarn-server-common-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-yarn-registry-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-yarn-common-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-yarn-client-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-yarn-api-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-mapreduce-client-jobclient-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-mapreduce-client-core-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-mapreduce-client-common-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-hdfs-client-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-common-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-client-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-auth-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/hadoop-annotations-3.2.0.jar
spark-3.0.2-bin-hadoop3.2/jars/guice-servlet-4.0.jar
spark-3.0.2-bin-hadoop3.2/jars/guice-4.0.jar
spark-3.0.2-bin-hadoop3.2/jars/guava-14.0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/gson-2.2.4.jar
spark-3.0.2-bin-hadoop3.2/jars/geronimo-jcache_1.0_spec-1.0-alpha-1.jar
spark-3.0.2-bin-hadoop3.2/jars/generex-1.0.2.jar
spark-3.0.2-bin-hadoop3.2/jars/flatbuffers-java-1.9.0.jar
spark-3.0.2-bin-hadoop3.2/jars/ehcache-3.3.1.jar
spark-3.0.2-bin-hadoop3.2/jars/dropwizard-metrics-hadoop-metrics2-reporter-0.1.2.jar
spark-3.0.2-bin-hadoop3.2/jars/dnsjava-2.1.7.jar
spark-3.0.2-bin-hadoop3.2/jars/derby-10.12.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/datanucleus-rdbms-4.1.19.jar
spark-3.0.2-bin-hadoop3.2/jars/datanucleus-core-4.1.17.jar
spark-3.0.2-bin-hadoop3.2/jars/datanucleus-api-jdo-4.2.4.jar
spark-3.0.2-bin-hadoop3.2/jars/curator-recipes-2.13.0.jar
spark-3.0.2-bin-hadoop3.2/jars/curator-framework-2.13.0.jar
spark-3.0.2-bin-hadoop3.2/jars/curator-client-2.13.0.jar
spark-3.0.2-bin-hadoop3.2/jars/core-1.1.2.jar
spark-3.0.2-bin-hadoop3.2/jars/compress-lzf-1.0.3.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-text-1.6.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-pool-1.5.4.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-net-3.1.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-math3-3.4.1.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-logging-1.1.3.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-lang3-3.9.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-lang-2.6.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-io-2.4.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-httpclient-3.1.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-dbcp-1.4.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-daemon-1.0.13.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-crypto-1.1.0.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-configuration2-2.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-compress-1.20.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-compiler-3.0.16.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-collections-3.2.2.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-codec-1.10.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-cli-1.2.jar
spark-3.0.2-bin-hadoop3.2/jars/commons-beanutils-1.9.4.jar
spark-3.0.2-bin-hadoop3.2/jars/chill_2.12-0.9.5.jar
spark-3.0.2-bin-hadoop3.2/jars/chill-java-0.9.5.jar
spark-3.0.2-bin-hadoop3.2/jars/cats-kernel_2.12-2.0.0-M4.jar
spark-3.0.2-bin-hadoop3.2/jars/breeze_2.12-1.0.jar
spark-3.0.2-bin-hadoop3.2/jars/breeze-macros_2.12-1.0.jar
spark-3.0.2-bin-hadoop3.2/jars/bonecp-0.8.0.RELEASE.jar
spark-3.0.2-bin-hadoop3.2/jars/avro-mapred-1.8.2-hadoop2.jar
spark-3.0.2-bin-hadoop3.2/jars/avro-ipc-1.8.2.jar
spark-3.0.2-bin-hadoop3.2/jars/avro-1.8.2.jar
spark-3.0.2-bin-hadoop3.2/jars/automaton-1.11-8.jar
spark-3.0.2-bin-hadoop3.2/jars/audience-annotations-0.5.0.jar
spark-3.0.2-bin-hadoop3.2/jars/arrow-vector-0.15.1.jar
spark-3.0.2-bin-hadoop3.2/jars/arrow-memory-0.15.1.jar
spark-3.0.2-bin-hadoop3.2/jars/arrow-format-0.15.1.jar
spark-3.0.2-bin-hadoop3.2/jars/arpack_combined_all-0.1.jar
spark-3.0.2-bin-hadoop3.2/jars/aopalliance-repackaged-2.6.1.jar
spark-3.0.2-bin-hadoop3.2/jars/aopalliance-1.0.jar
spark-3.0.2-bin-hadoop3.2/jars/antlr4-runtime-4.7.1.jar
spark-3.0.2-bin-hadoop3.2/jars/antlr-runtime-3.5.2.jar
spark-3.0.2-bin-hadoop3.2/jars/algebra_2.12-2.0.0-M2.jar
spark-3.0.2-bin-hadoop3.2/jars/aircompressor-0.10.jar
spark-3.0.2-bin-hadoop3.2/jars/activation-1.1.1.jar
spark-3.0.2-bin-hadoop3.2/jars/accessors-smart-1.2.jar
spark-3.0.2-bin-hadoop3.2/jars/ST4-4.0.4.jar
spark-3.0.2-bin-hadoop3.2/jars/RoaringBitmap-0.7.45.jar
spark-3.0.2-bin-hadoop3.2/jars/JTransforms-3.1.jar
spark-3.0.2-bin-hadoop3.2/jars/JLargeArrays-1.5.jar
spark-3.0.2-bin-hadoop3.2/jars/HikariCP-2.5.1.jar
spark-3.0.2-bin-hadoop3.2/RELEASE
export SPARK_HOME=${ADAM_TMP_DIR}/${SPARK}-bin-${HADOOP}
+ export SPARK_HOME=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2
+ SPARK_HOME=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2

# set the path to the adam submit script
ADAM=./bin/adam-submit
+ ADAM=./bin/adam-submit

# test running adam-shell
./bin/adam-shell -i scripts/jenkins-test-adam-shell.scala
+ ./bin/adam-shell -i scripts/jenkins-test-adam-shell.scala
Using SPARK_SHELL=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/bin/spark-shell
21/02/20 18:29:26 WARN Utils: Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
21/02/20 18:29:26 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
21/02/20 18:29:26 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Spark context Web UI available at http://192.168.10.31:4040
Spark context available as 'sc' (master = local[*], app id = local-1613874572474).
Spark session available as 'spark'.
scripts/jenkins-test-adam-shell.scala:41: error: object rdd is not a member of package org.bdgenomics.adam
import org.bdgenomics.adam.rdd.ADAMContext._
                           ^
scripts/jenkins-test-adam-shell.scala:43: error: value loadAlignments is not a member of org.apache.spark.SparkContext
val reads = sc.loadAlignments("adam-core/src/test/resources/small.sam").rdd.count()
               ^
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /___/ .__/\_,_/_/ /_/\_\   version 3.0.2
      /_/
         
Using Scala version 2.12.10 (OpenJDK 64-Bit Server VM, Java 1.8.0_222)
Type in expressions to have them evaluated.
Type :help for more information.

scala> :quit
    
# add pyspark to the python path
PY4J_ZIP="$(ls -1 "${SPARK_HOME}/python/lib" | grep py4j)"
ls -1 "${SPARK_HOME}/python/lib" | grep py4j
++ ls -1 /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/lib
++ grep py4j
+ PY4J_ZIP=py4j-0.10.9-src.zip
export PYTHONPATH=${SPARK_HOME}/python:${SPARK_HOME}/python/lib/${PY4J_ZIP}:${PYTHONPATH}
+ export PYTHONPATH=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/lib/py4j-0.10.9-src.zip:
+ PYTHONPATH=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python:/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/lib/py4j-0.10.9-src.zip:

# put adam jar on the pyspark path
ASSEMBLY_DIR="${ADAM_TMP_DIR}/adam-assembly/target"
+ ASSEMBLY_DIR=/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target
ASSEMBLY_JAR="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true
++ ls -1 /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target
++ grep '^adam[0-9A-Za-z\_\.-]*\.jar$'
++ grep -v javadoc
++ grep -v sources
+ ASSEMBLY_JAR=adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar
export PYSPARK_SUBMIT_ARGS="--conf spark.driver.memory=4g --conf spark.executor.memory=4g --jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} pyspark-shell"
+ export 'PYSPARK_SUBMIT_ARGS=--conf spark.driver.memory=4g --conf spark.executor.memory=4g --jars /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar pyspark-shell'
+ PYSPARK_SUBMIT_ARGS='--conf spark.driver.memory=4g --conf spark.executor.memory=4g --jars /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar pyspark-shell'

# create a conda environment for python build, if necessary
pythons=( 3.6 )
+ pythons=(3.6)

for python in ${pythons[*]}
do
    uuid=$(uuidgen)
    conda create -y -q -n adam-build-${uuid} python=${python}
    source activate adam-build-${uuid}

    # prepare adam python
    pushd adam-python
    make prepare
    popd
    	    
    # we can run the python build, now that we have a spark executable
    # -DskipTests appears to skip the python/r tests?
    mvn -U \
    	-P python,distribution \
    	package \
    	-Dsuites=select.no.suites\* \
    	-Dhadoop.version=${HADOOP_VERSION}

    # make sure that the distribution package contains an egg
    # if no assembly jar is found, this will exit with code 1 and fail the build
    tar tzvf adam-distribution/target/adam-distribution*-bin.tar.gz | \
    	grep bdgenomics.adam | \
    	grep egg
    	
    # run pyadam test
    ./bin/pyadam < scripts/jenkins-test-pyadam.py
    	
    # deactivate and remove the conda env
    source deactivate
    conda remove -y -n adam-build-${uuid} --all

    # copy python targets back
    cp -r adam-python/target ${PROJECT_ROOT}/adam-python/

    # clean after each python version
    pushd adam-python
    make clean
    make clean_sdist
    popd

done
+ for python in '${pythons[*]}'
uuidgen
++ uuidgen
+ uuid=fcd2223c-a4e5-4f5c-a966-121bc529034f
+ conda create -y -q -n adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f python=3.6


Package plan for installation in environment /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f:

The following NEW packages will be INSTALLED:

    _libgcc_mutex:    0.1-main                
    ca-certificates:  2021.1.19-h06a4308_0    
    certifi:          2020.12.5-py36h06a4308_0
    ld_impl_linux-64: 2.33.1-h53a641e_7       
    libedit:          3.1.20191231-h14c3975_1 
    libffi:           3.3-he6710b0_2          
    libgcc-ng:        9.1.0-hdf63c60_0        
    libstdcxx-ng:     9.1.0-hdf63c60_0        
    ncurses:          6.2-he6710b0_1          
    openssl:          1.1.1j-h27cfd23_0       
    pip:              21.0.1-py36h06a4308_0   
    python:           3.6.12-hcff3b4d_2       
    readline:         8.1-h27cfd23_0          
    setuptools:       52.0.0-py36h06a4308_0   
    sqlite:           3.33.0-h62c20be_0       
    tk:               8.6.10-hbc83047_0       
    wheel:            0.36.2-pyhd3eb1b0_0     
    xz:               5.2.5-h7b6447c_0        
    zlib:             1.2.11-h7b6447c_3       


+ source activate adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/anaconda/bin/activate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/anaconda/bin/activate
++ _CONDA_DIR=/home/anaconda/bin

if [ $# -gt 1 ]; then
    (>&2 echo "Error: did not expect more than one argument.")
    (>&2 echo "    (Got $@)")
    return 1
fi
++ '[' 1 -gt 1 ']'

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        # ignore any windows backup paths from bat-based activation
        if [ "${CONDA_PATH_BACKUP:0:1}" != "/"  ]; then
           unset CONDA_PATH_BACKUP
        fi
        export _CONDA_PYTHON="$_CONDA_DIR/../python"
        ;;
    *)
        EXT=""
        export _CONDA_PYTHON="$_CONDA_DIR/python"
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=
++ export _CONDA_PYTHON=/home/anaconda/bin/python
++ _CONDA_PYTHON=/home/anaconda/bin/python

# Ensure that this script is sourced, not executed
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "activate" ]]; then
    (>&2 echo "Error: activate must be sourced. Run 'source activate envname'
instead of 'activate envname'.
")
    "$_CONDA_DIR/conda" ..activate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \a\c\t\i\v\a\t\e ]]

if [ "$#" -eq "0" ]; then
    args=('root')
else
    args=$@
fi
++ '[' 1 -eq 0 ']'
++ args=adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f

"$_CONDA_DIR/conda" ..checkenv $_SHELL$EXT "$args"
++ /home/anaconda/bin/conda ..checkenv bash adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f
if (( $? != 0 )); then
    return 1
fi
++ ((  0 != 0  ))

# Ensure we deactivate any scripts from the old env
_CONDA_HOLD=true
++ _CONDA_HOLD=true
source "$_CONDA_DIR/deactivate"
++ source /home/anaconda/bin/deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
+++ [[ -n 4.3.48(1)-release ]]
+++ _SCRIPT_LOCATION=/home/anaconda/bin/deactivate
+++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
++++ dirname /home/anaconda/bin/deactivate
+++ _CONDA_DIR=/home/anaconda/bin

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
+++ case "$(uname -s)" in
uname -s
++++ uname -s
+++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
+++ [[ 1 > 0 ]]
+++ key=adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f
+++ case $key in
+++ shift
+++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
+++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
++++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/jenkins-test
+++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
+++ [[ -z '' ]]
+++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
++++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/jenkins-test
+++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]
+++ return 0
unset _CONDA_HOLD
++ unset _CONDA_HOLD

_NEW_PART=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$args")
"$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$args"
+++ /home/anaconda/bin/conda ..activate bash adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f
++ _NEW_PART=/home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin
if (( $? == 0 )); then
    export CONDA_PATH_BACKUP="$PATH"
    # export this to restore it upon deactivation
    export CONDA_PS1_BACKUP="$PS1"

    # look if the deactivate script left a placeholder for us
    if [[ $PATH == *"CONDA_PATH_PLACEHOLDER"* ]]; then
        # If it did, replace it with our _NEW_PART
        export PATH="$($_CONDA_PYTHON -c "import re; print(re.sub(r'CONDA_PATH_PLACEHOLDER', r'$_NEW_PART', '$PATH', 1))")"
    else
        export PATH="$_NEW_PART:$PATH"
    fi

    # CONDA_DEFAULT_ENV is the shortest representation of how conda recognizes your env.
    #    It can be an env name, or a full path.
    #    Last date of change: 2016-06-21
    # If the string contains / it's a path
    if [[ "$@" == */* ]]; then
        export CONDA_DEFAULT_ENV=$(get_abs_filename "$args")
    else
        export CONDA_DEFAULT_ENV="$args"
    fi
    # CONDA_PREFIX is always the full path to the activated environment.  It is not set
    #    when no environment is active.
    # Legacy support: CONDA_DEFAULT_ENV is either env name or full path if given as path.
    #    CONDA_PREFIX is always the full path, for consistency.
    #    Last date of change: 2016-06-21
    firstpath=${_NEW_PART%%:*}
    export CONDA_PREFIX="$(echo ${firstpath} | sed "s|/bin$||")" &>/dev/null

    # if CONDA_DEFAULT_ENV not in PS1, prepend it with parentheses
    if [ $("$_CONDA_DIR/conda" ..changeps1) = "1" ]; then
        if ! $(grep -q CONDA_DEFAULT_ENV <<<$PS1); then
            if ! $(grep -q "POWERLINE" <<<$PS1); then
                export PS1="(${CONDA_DEFAULT_ENV}) $PS1"
            fi
        fi
    fi

    # Load any of the scripts found $PREFIX/etc/conda/activate.d AFTER activation
    _CONDA_D="${CONDA_PREFIX}/etc/conda/activate.d"
    if [[ -d "$_CONDA_D" ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi
    unset _CONDA_PYTHON
else
    unset _CONDA_PYTHON
    return $?
fi
++ ((  0 == 0  ))
++ export CONDA_PATH_BACKUP=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/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
++ CONDA_PATH_BACKUP=/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/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 CONDA_PS1_BACKUP=
++ CONDA_PS1_BACKUP=
++ [[ /usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/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 == *\C\O\N\D\A\_\P\A\T\H\_\P\L\A\C\E\H\O\L\D\E\R* ]]
++ export PATH=/home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin:/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/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=/home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin:/usr/java/latest/bin/:/usr/java/latest/bin/:/home/anaconda/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 CONDA_DEFAULT_ENV=adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f
++ CONDA_DEFAULT_ENV=adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f
++ firstpath=/home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin
echo ${firstpath} | sed "s|/bin$||"
+++ echo /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f
"$_CONDA_DIR/conda" ..changeps1
+++ /home/anaconda/bin/conda ..changeps1
++ '[' 1 = 1 ']'
grep -q CONDA_DEFAULT_ENV <<<$PS1
+++ grep -q CONDA_DEFAULT_ENV
grep -q "POWERLINE" <<<$PS1
+++ grep -q POWERLINE
++ export 'PS1=(adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f) '
++ PS1='(adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f) '
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/etc/conda/activate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/etc/conda/activate.d ]]
++ unset _CONDA_PYTHON

unset CONDA_PATH
++ unset CONDA_PATH

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ pushd adam-python
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu
+ make prepare
pip install pytest==3.9.1
Collecting pytest==3.9.1
  Using cached pytest-3.9.1-py2.py3-none-any.whl (213 kB)
Collecting pluggy>=0.7
  Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting six>=1.10.0
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting py>=1.5.0
  Using cached py-1.10.0-py2.py3-none-any.whl (97 kB)
Collecting attrs>=17.4.0
  Using cached attrs-20.3.0-py2.py3-none-any.whl (49 kB)
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/lib/python3.6/site-packages (from pytest==3.9.1) (52.0.0.post20210125)
Collecting atomicwrites>=1.0
  Using cached atomicwrites-1.4.0-py2.py3-none-any.whl (6.8 kB)
Collecting more-itertools>=4.0.0
  Using cached more_itertools-8.7.0-py3-none-any.whl (48 kB)
Collecting importlib-metadata>=0.12
  Using cached importlib_metadata-3.4.0-py3-none-any.whl (10 kB)
Collecting typing-extensions>=3.6.4
  Using cached typing_extensions-3.7.4.3-py3-none-any.whl (22 kB)
Collecting zipp>=0.5
  Using cached zipp-3.4.0-py3-none-any.whl (5.2 kB)
Installing collected packages: zipp, typing-extensions, importlib-metadata, six, py, pluggy, more-itertools, attrs, atomicwrites, pytest
Successfully installed atomicwrites-1.4.0 attrs-20.3.0 importlib-metadata-3.4.0 more-itertools-8.7.0 pluggy-0.13.1 py-1.10.0 pytest-3.9.1 six-1.15.0 typing-extensions-3.7.4.3 zipp-3.4.0
+ popd
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu
+ mvn -U -P python,distribution package '-Dsuites=select.no.suites*' -Dhadoop.version=3.2.1
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ADAM_2.12                                                          [pom]
[INFO] ADAM_2.12: Shader workaround                                       [jar]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils                           [jar]
[INFO] ADAM_2.12: Core                                                    [jar]
[INFO] ADAM_2.12: APIs for Java, Python                                   [jar]
[INFO] ADAM_2.12: CLI                                                     [jar]
[INFO] ADAM_2.12: Assembly                                                [jar]
[INFO] ADAM_2.12: Python APIs                                             [jar]
[INFO] ADAM_2.12: Distribution                                            [pom]
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-parent-spark3_2.12 >-------------
[INFO] Building ADAM_2.12 0.34.0-SNAPSHOT                                 [1/9]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark3_2.12 ---
[INFO] Modified 129 of 440 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-shade-spark3_2.12 >-------------
[INFO] Building ADAM_2.12: Shader workaround 0.34.0-SNAPSHOT              [2/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark3_2.12 ---
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/java:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.12.10/classes at 1613874615634
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.12.10/classes
[INFO] 
[INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark3_2.12 ---
[INFO] Discovered 1 component descriptors(s)
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark3_2.12 ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-shade-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-shade-spark3_2.12 ---
[INFO] 
Loading source files for package org.bdgenomics.adam.shade...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-frame.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-summary.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-tree.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/constant-values.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/class-use/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/overview-tree.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index-all.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-shade-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-shade-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark3_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-codegen-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.34.0-SNAPSHOT  [3/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark3_2.12 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark3_2.12 ---
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/2.12.10/classes at 1613874622525
[WARNING] warning: there were 5 deprecation warnings (since 2.12.0); re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-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) @ adam-codegen-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark3_2.12 ---
Discovery starting.
Discovery completed in 61 milliseconds.
Run starting. Expected test count is: 0
Run completed in 66 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-codegen-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-codegen-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark3_2.12 ---
model contains 11 documentable templates
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-core-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: Core 0.34.0-SNAPSHOT                           [4/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark3_2.12 ---
[INFO] Modified 2 of 204 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark3_2.12 ---
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java:-1: info: compiling
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala:-1: info: compiling
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 140 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.10/classes at 1613874637464
[WARNING] warning: there were 24 deprecation warnings
[WARNING] warning: there were 31 deprecation warnings (since 0.21.0)
[WARNING] warning: there was one deprecation warning (since 1.0.6)
[WARNING] warning: there was one deprecation warning (since 2.11.0)
[WARNING] warning: there were 174 deprecation warnings (since 2.12.0)
[WARNING] warning: there was one deprecation warning (since 2.12.7)
[WARNING] warning: there were 232 deprecation warnings in total; re-run with -deprecation for details
[WARNING] warning: there were 5 feature warnings; re-run with -feature for details
[WARNING] 8 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 20 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 6 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.10/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 152 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark3_2.12 ---
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala:-1: info: compiling
[INFO] Compiling 70 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.10/test-classes at 1613874659496
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]       .build()
[WARNING]             ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val new_cigar = NormalizationUtils.leftAlignIndel(read)
[WARNING]                                                       ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(RichAlignment(read).samtoolsCigar.getReadLength === new_cigar.getReadLength)
[WARNING]                          ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:171: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val newSAMRecord = newSAMReader.iterator().dropWhile(r => r.getReadName != readName)
[WARNING]                                             ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:274: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:311: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:335: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val fragment = Fragment.newBuilder().setAlignments(List(record)).build()
[WARNING]                                                            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:54: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:89: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       val samIter = asScalaIterator(newSAMReader.iterator())
[WARNING]                     ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in class SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path)))
[WARNING]                                                       ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:63: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                  ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:69: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T"), Allele.create("G")))
[WARNING]                  ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:75: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<NON_REF>", false)))
[WARNING]                  ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<CN0>", false)))
[WARNING]                  ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:143: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       GenotypeBuilder.create("NA12878", vcb.getAlleles(), genotypeAttributes))
[WARNING]                                                           ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:154: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.ALT)))
[WARNING]                   ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:184: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamVariant.variant.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                  ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:219: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamGT.getVariantCallingAnnotations.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                                  ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:234: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(htsjdkVC.getAlternateAlleles.sameElements(List(Allele.create("T"))))
[WARNING]                     ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:245: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2, 4, 6).map(i => i: java.lang.Integer))
[WARNING]                                                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:246: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:279: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:280: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:298: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:299: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:320: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     for ((allele, idx) <- vc.getAlternateAlleles.zipWithIndex) {
[WARNING]                              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:328: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("T"), Allele.create("G")))
[WARNING]                                                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:347: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT)))
[WARNING]                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:349: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:354: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT)))
[WARNING]                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:356: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:380: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("A", true), Allele.create("A", true)))
[WARNING]                                                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:393: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.REF)))
[WARNING]                   ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:396: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getNonReferenceLikelihoods
[WARNING]                   ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:421: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 1)
[WARNING]                            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:433: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 2)
[WARNING]                            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:543: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       genotypeAttributes)))((bldr, fn) => {
[WARNING]       ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]                                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]                                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]                                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:714: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(0) === 10)
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:715: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(1) === 12)
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:716: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(2) === 14)
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:717: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(3) === 16)
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:762: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER")
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:776: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER1")
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:777: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(1) === "FAILED_FILTER2")
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:778: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(2) === "FAILED_FILTER3")
[WARNING]            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:930: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(d => d: java.lang.Double))
[WARNING]             ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:954: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]           .map(i => i: java.lang.Integer))
[WARNING]               ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:962: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(i => i: java.lang.Integer))
[WARNING]             ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1089: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq"))
[WARNING]                            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq", "lowdp"))
[WARNING]                            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1195: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 1)
[WARNING]              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1205: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 2)
[WARNING]              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1262: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         vcb.filters(Set("FAILED1", "FAILED2", "FAILED3"))
[WARNING]                        ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1267: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val failedSet = v.getFiltersFailed.toSet
[WARNING]                       ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1285: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name"))
[WARNING]                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1295: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name1", "name2"))
[WARNING]                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1364: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED"))
[WARNING]                            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1378: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED1", "FAILED2"))
[WARNING]                            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1493: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10).map(i => i: java.lang.Integer)
[WARNING]              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1501: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                      ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1516: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f).map(i => i: java.lang.Float)
[WARNING]                ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1523: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("+Inf")
[WARNING]                                              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1530: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("-Inf")
[WARNING]                                              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1538: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f, 0.01f, 0.001f).map(i => i: java.lang.Float)
[WARNING]                               ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1552: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M")
[WARNING]                                              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1559: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M", "100M", "90M10D")
[WARNING]                                              ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1575: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1584: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1601: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1610: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1627: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1636: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2436: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("ONE_INT", "42")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2459: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_INTS", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2482: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_FLOATS", "5.0,10.1,15.2,20.3")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2505: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("A_INT", "10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2528: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_INT", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2551: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_STRING", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2574: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("STRING_G", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/fragment/FragmentDatasetSuite.scala:327: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       fragment.getAlignments.toSeq
[WARNING]                ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/AlignmentDatasetSuite.scala:988: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Seq("tee", "/dev/null"),
[WARNING]          ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/AlignmentDatasetSuite.scala:989: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       (List.empty[String]: java.util.List[String]),
[WARNING]                  ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/AlignmentDatasetSuite.scala:990: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       (Map.empty[String, String]: java.util.Map[String, String]),
[WARNING]                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/BinQualitiesSuite.scala:181: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(List(read))
[WARNING]                          ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/BinQualitiesSuite.scala:189: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     testQuals(newFragment.getAlignments.head.getQualityScores)
[WARNING]                           ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:83: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(TargetOrdering.contains(targets.head, read))
[WARNING]                                                  ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:191: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]         if (read.getStart < 105) {
[WARNING]             ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:194: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.start === read.getStart)
[WARNING]                                                   ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:195: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.end === read.getEnd)
[WARNING]                                                 ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala:196: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]           assert(check_indel(targets.head, read))
[WARNING]                                            ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/variant/GenotypeDatasetSuite.scala:697: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/ds/variant/GenotypeDatasetSuite.scala:698: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                          ^
[WARNING] 168 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 23 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-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) @ adam-core-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark3_2.12 ---
Discovery starting.
Discovery completed in 527 milliseconds.
Run starting. Expected test count is: 0
Run completed in 533 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-core-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark3_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.apache.parquet.avro...
Loading source files for package org.bdgenomics.adam.io...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-frame.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/constant-values.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-tree.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index-all.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-summary.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark3_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-core-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark3_2.12 ---
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverters.scala:274: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/read/AlignmentDataset.scala:844: warning: Octal escape literals are deprecated, use \u0001 instead.
      binaryCodec.writeBytes("BAM\001".getBytes())
                                 ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment
    /**
    ^
warning: there were 5 feature warnings; re-run with -feature for details
model contains 283 documentable templates
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException".
/**
^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:474: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:444: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:429: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:354: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDataset.scala:747: warning: Variable x undefined in comment for method pipe in trait GenomicDataset
   * Files are substituted in to the command with a $x syntax. E.g., to invoke
                                                     ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDataset.scala:748: warning: Variable 0 undefined in comment for method pipe in trait GenomicDataset
   * a command that uses the first file from the files Seq, use $0. To access
                                                                 ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDataset.scala:749: warning: Variable root undefined in comment for method pipe in trait GenomicDataset
   * the path to the directory where the files are copied, use $root.
                                                                ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala:3464: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala:1859: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala:1839: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala:1810: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:377: warning: Could not find any member to link for "RuntimeException".
    /**
    ^
24 warnings found
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-core-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark3_2.12-0.34.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-apis-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: APIs for Java, Python 0.34.0-SNAPSHOT          [5/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark3_2.12 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark3_2.12 ---
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.10/classes at 1613874714208
[WARNING] warning: there was one deprecation warning (since 2.12.0); re-run with -deprecation for details
[WARNING] warning: there were two feature warnings; re-run with -feature for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-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) @ adam-apis-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark3_2.12 ---
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/java:-1: info: compiling
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 9 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.10/test-classes at 1613874720217
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 8 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.10/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark3_2.12 ---
Discovery starting.
Discovery completed in 145 milliseconds.
Run starting. Expected test count is: 0
Run completed in 150 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark3_2.12 ---
warning: there were two feature warnings; re-run with -feature for details
model contains 192 documentable templates
one warning found
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-apis-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark3_2.12-0.34.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] --------------< org.bdgenomics.adam:adam-cli-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: CLI 0.34.0-SNAPSHOT                            [6/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark3_2.12 ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark3_2.12 ---
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 19 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.10/classes at 1613874736200
[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 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.10/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 15 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark3_2.12 ---
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 12 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.10/test-classes at 1613874743403
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-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) @ adam-cli-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark3_2.12 ---
Discovery starting.
Discovery completed in 127 milliseconds.
Run starting. Expected test count is: 0
Run completed in 132 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-cli-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark3_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.adam.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/constant-values.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/overview-tree.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index-all.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index.html...
Generating /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark3_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark3_2.12 ---
model contains 55 documentable templates
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -----------< org.bdgenomics.adam:adam-assembly-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Assembly 0.34.0-SNAPSHOT                       [7/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark3_2.12 ---
[INFO] /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/2.12.10/classes at 1613874759698
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-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) @ adam-assembly-spark3_2.12 ---
[INFO] Test Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark3_2.12 ---
[INFO] Source directory: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark3_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark3_2.12 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark3_2.12:jar:0.34.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.10 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.30 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark3_2.12:jar:0.34.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark3_2.12:jar:0.34.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.34.0-SNAPSHOT in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT.jar with /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.34.0-SNAPSHOT-shaded.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-python-spark3_2.12 >-------------
[INFO] Building ADAM_2.12: Python APIs 0.34.0-SNAPSHOT                    [8/9]
[INFO] --------------------------------[ jar ]---------------------------------
[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) @ adam-python-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-python) @ adam-python-spark3_2.12 ---
pip install -e .
Obtaining file:///tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-python
Collecting pyspark>=1.6.0
  Downloading pyspark-3.0.2.tar.gz (204.8 MB)
Collecting py4j==0.10.9
  Using cached py4j-0.10.9-py2.py3-none-any.whl (198 kB)
Building wheels for collected packages: pyspark
  Building wheel for pyspark (setup.py): started
  Building wheel for pyspark (setup.py): finished with status 'done'
  Created wheel for pyspark: filename=pyspark-3.0.2-py2.py3-none-any.whl size=205186687 sha256=3d5d117188f433cceb8cb075e226829b0fb6904c184492a93f11791042742ed6
  Stored in directory: /home/jenkins/.cache/pip/wheels/c4/d8/2a/76ccea83955f68136e56b8907439184619400dfa6e0491ece3
Successfully built pyspark
Installing collected packages: py4j, pyspark, bdgenomics.adam
  Running setup.py develop for bdgenomics.adam
Successfully installed bdgenomics.adam py4j-0.10.9 pyspark-3.0.2
python setup.py bdist_egg
running bdist_egg
running egg_info
writing bdgenomics.adam.egg-info/PKG-INFO
writing dependency_links to bdgenomics.adam.egg-info/dependency_links.txt
writing requirements to bdgenomics.adam.egg-info/requires.txt
writing top-level names to bdgenomics.adam.egg-info/top_level.txt
package init file 'deps/jars/__init__.py' not found (or not a regular file)
package init file 'deps/bin/__init__.py' not found (or not a regular file)
reading manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
writing manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/adam
copying bdgenomics/adam/stringency.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/adamContext.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/models.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/__init__.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/find_adam_home.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/ds.py -> build/lib/bdgenomics/adam
creating build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/variantDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/alignmentDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/coverageDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/__init__.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/adamContext_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/featureDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/genotypeDataset_test.py -> build/lib/bdgenomics/adam/test
creating build/lib/bdgenomics/adam/jars
copying deps/jars/adam.jar -> build/lib/bdgenomics/adam/jars
creating build/lib/bdgenomics/adam/bin
copying deps/bin/adam-shell -> build/lib/bdgenomics/adam/bin
copying deps/bin/adam-submit -> build/lib/bdgenomics/adam/bin
copying deps/bin/adamR -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-assembly.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-egg.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-home -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-spark.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/pyadam -> build/lib/bdgenomics/adam/bin
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-spark.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-submit -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-shell -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adamR -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/pyadam -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-home -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/stringency.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/adamContext.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/jars/adam.jar -> build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/models.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/find_adam_home.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/variantDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/alignmentDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/coverageDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/adamContext_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/featureDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/genotypeDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/ds.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/stringency.py to stringency.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/adamContext.py to adamContext.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/models.py to models.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/find_adam_home.py to find_adam_home.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/variantDataset_test.py to variantDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/alignmentDataset_test.py to alignmentDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/coverageDataset_test.py to coverageDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/adamContext_test.py to adamContext_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/featureDataset_test.py to featureDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/genotypeDataset_test.py to genotypeDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/ds.py to ds.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.cpython-36.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.6
copying deps/bin/find-spark.sh -> build/scripts-3.6
copying deps/bin/find-adam-assembly.sh -> build/scripts-3.6
copying deps/bin/adam-submit -> build/scripts-3.6
copying deps/bin/adam-shell -> build/scripts-3.6
copying deps/bin/find-adam-egg.sh -> build/scripts-3.6
copying deps/bin/adamR -> build/scripts-3.6
copying deps/bin/pyadam -> build/scripts-3.6
copying deps/bin/find-adam-home -> build/scripts-3.6
copying and adjusting bdgenomics/adam/find_adam_home.py -> build/scripts-3.6
changing mode of build/scripts-3.6/find_adam_home.py from 664 to 775
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-spark.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adam-submit -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adam-shell -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adamR -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find_adam_home.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/pyadam -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-home -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-spark.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-assembly.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-submit to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-shell to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-egg.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adamR to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find_adam_home.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pyadam to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-home to 775
copying bdgenomics.adam.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
bdgenomics.__pycache__.__init__.cpython-36: module references __path__
bdgenomics.adam.__pycache__.find_adam_home.cpython-36: module references __file__
creating dist
creating 'dist/bdgenomics.adam-0.34.0a0-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-python-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-python-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-python-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-python) @ adam-python-spark3_2.12 ---
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux -- Python 3.6.12, pytest-3.9.1, py-1.10.0, pluggy-0.13.1 -- /home/jenkins/anaconda2/envs/adam-build-fcd2223c-a4e5-4f5c-a966-121bc529034f/bin/python
cachedir: .pytest_cache
rootdir: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-python, inifile:
collecting ... collected 63 items

bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_alignments PASSED [  1%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_bed PASSED [  3%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_coverage PASSED [  4%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_dna_sequences PASSED [  6%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_genotypes PASSED [  7%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_gtf PASSED [  9%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_indexed_bam PASSED [ 11%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_interval_list PASSED [ 12%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_narrowPeak PASSED [ 14%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_slices PASSED [ 15%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_variants PASSED [ 17%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_broadcast_inner_join PASSED [ 19%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_broadcast_right_outer_join PASSED [ 20%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_caching PASSED [ 22%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_count_kmers PASSED [ 23%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_filterByOverlappingRegion PASSED [ 25%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_filterByOverlappingRegions PASSED [ 26%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_load_indexed_bam PASSED [ 28%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_persisting PASSED [ 30%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_pipe_as_sam PASSED [ 31%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_realignIndels_known_indels PASSED [ 33%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_realignIndels_reads PASSED [ 34%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_save_as_bam PASSED [ 36%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_save_sorted_sam PASSED [ 38%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_save_unordered_sam PASSED [ 39%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_full_outer_join PASSED [ 41%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_inner_join PASSED [ 42%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_inner_join_groupBy_left PASSED [ 44%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_left_outer_join PASSED [ 46%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_right_outer_join PASSED [ 47%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_right_outer_join_groupBy_left PASSED [ 49%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_to_coverage PASSED [ 50%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_to_fragments PASSED [ 52%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_transform PASSED [ 53%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_transmute_to_coverage PASSED [ 55%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_union PASSED [ 57%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_aggregatedCoverage PASSED [ 58%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_collapse PASSED [ 60%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_flatten PASSED [ 61%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_save PASSED [ 63%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_toFeatures PASSED [ 65%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_bed PASSED [ 66%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_gtf PASSED [ 68%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_interval_list PASSED [ 69%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_narrowPeak PASSED [ 71%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_transform PASSED [ 73%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_to_variants PASSED [ 74%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_transform PASSED [ 76%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_filter PASSED [ 77%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_all_array PASSED [ 79%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_alts_array PASSED [ 80%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_array PASSED [ 82%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_genotype_array PASSED [ 84%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_scalar PASSED [ 85%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_all_array PASSED [ 87%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_alts_array PASSED [ 88%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_array PASSED [ 90%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_scalar PASSED [ 92%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_round_trip PASSED [ 93%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_sort PASSED [ 95%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_sort_lex PASSED [ 96%]
bdgenomics/adam/test/variantDataset_test.py::VariantDatasetTest::test_transform PASSED [ 98%]
bdgenomics/adam/test/variantDataset_test.py::VariantDatasetTest::test_vcf_round_trip PASSED [100%]

- generated xml file: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml -
=============================== warnings summary ===============================
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-python/bdgenomics/adam/test/alignmentDataset_test.py:143: DeprecationWarning: Please use assertEqual instead.
  self.assertEquals(readsAsCoverage.toDF().count(), 5)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-python/bdgenomics/adam/test/coverageDataset_test.py:59: DeprecationWarning: Please use assertEqual instead.
  self.assertEquals(features.toDF().count(), coverage.toDF().count())

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.2-bin-hadoop3.2/python/pyspark/sql/context.py:78: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
=================== 63 passed, 51 warnings in 67.42 seconds ====================
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-python-spark3_2.12 ---
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[INFO] No tests to run.
[INFO] 
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[WARNING] JAR will be empty - no content was marked for inclusion!
[INFO] Building jar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/adam-python-spark3_2.12-0.34.0-SNAPSHOT.jar
[INFO] 
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[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-python-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-python-spark3_2.12 >>>
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[INFO] 
[INFO] ---------< org.bdgenomics.adam:adam-distribution-spark3_2.12 >----------
[INFO] Building ADAM_2.12: Distribution 0.34.0-SNAPSHOT                   [9/9]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
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[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-distribution-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-distribution-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-distribution-spark3_2.12 ---
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[INFO] 
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[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /tmp/adamTestvILfhHm/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark3_2.12-0.34.0-SNAPSHOT-bin.tar.gz
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