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[WARNING] Entry: adam-distribution-spark2_2.11-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformSequencesArgs.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/CountReadKmers$.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.33.0-SNAPSHOT/scaladocs/org/bdgenomics/adam/cli/TransformFeatures.html longer than 100 characters.
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[WARNING] Entry: adam-distribution-spark2_2.11-0.33.0-SNAPSHOT/repo/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Entry: adam-distribution-spark2_2.11-0.33.0-SNAPSHOT/repo/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building zip: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-distribution/target/adam-distribution-spark2_2.11-0.33.0-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.11 0.33.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  9.092 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  6.229 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  8.468 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:41 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 19.992 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 29.573 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 15.926 s]
[INFO] ADAM_2.11: Python APIs ............................. SUCCESS [01:19 min]
[INFO] ADAM_2.11: Distribution ............................ SUCCESS [ 51.113 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  05:22 min
[INFO] Finished at: 2020-08-06T13:46:03-07:00
[INFO] ------------------------------------------------------------------------
+ grep bdgenomics.adam
+ tar tzvf adam-distribution/target/adam-distribution-spark2_2.11-0.33.0-SNAPSHOT-bin.tar.gz
+ grep egg
drwxrwxr-x jenkins/jenkins        0 2020-08-06 13:43 adam-distribution-spark2_2.11-0.33.0-SNAPSHOT/r/bdgenomics.adam.egg-info/
-rw-r--r-- jenkins/jenkins 38673944 2020-08-06 13:43 adam-distribution-spark2_2.11-0.33.0-SNAPSHOT/repo/bdgenomics.adam-0.32.0a0-py3.6.egg
+ ./bin/pyadam
Using PYSPARK=/tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7/bin/pyspark
2020-08-06 13:46:06 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
2020-08-06 13:46:06 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2020-08-06 13:46:06 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
2020-08-06 13:46:08 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2020-08-06 13:46:13 WARN  Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf.

[Stage 0:>                                                          (0 + 1) / 1]
                                                                                
+ source 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/jenkins/anaconda2/envs/adam-build-b224fadf-a196-4bab-b574-3c1be31b3abc/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/adam-build-b224fadf-a196-4bab-b574-3c1be31b3abc/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/adam-build-b224fadf-a196-4bab-b574-3c1be31b3abc/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
++ [[ 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/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/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 /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ]]

if (( $? == 0 )); then
    # Inverse of activation: run deactivate scripts prior to deactivating env
    _CONDA_D="${CONDA_PREFIX}/etc/conda/deactivate.d"
    if [[ -d $_CONDA_D ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi

#    # get the activation path that would have been provided for this prefix
#    _LAST_ACTIVATE_PATH=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$CONDA_PREFIX")
#
#    # in activate, we replace a placeholder so that conda keeps its place in the PATH order
#    # The activate script sets _CONDA_HOLD here to activate that behavior.
#    #   Otherwise, PATH is simply removed.
#    if [ -n "$_CONDA_HOLD" ]; then
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'CONDA_PATH_PLACEHOLDER\1', '$PATH', 1))")"
#    else
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'', '$PATH', 1))")"
#    fi
#
#    unset _LAST_ACTIVATE_PATH

    export PATH=$("$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX")

    unset CONDA_DEFAULT_ENV
    unset CONDA_PREFIX
    unset CONDA_PATH_BACKUP
    export PS1="$CONDA_PS1_BACKUP"
    unset CONDA_PS1_BACKUP
    unset _CONDA_PYTHON2
else
    unset _CONDA_PYTHON2
    return $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-b224fadf-a196-4bab-b574-3c1be31b3abc/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-b224fadf-a196-4bab-b574-3c1be31b3abc/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/adam-build-b224fadf-a196-4bab-b574-3c1be31b3abc/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/adam-build-b224fadf-a196-4bab-b574-3c1be31b3abc
++ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/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:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ unset CONDA_DEFAULT_ENV
++ unset CONDA_PREFIX
++ unset CONDA_PATH_BACKUP
++ export PS1=
++ PS1=
++ unset CONDA_PS1_BACKUP
++ unset _CONDA_PYTHON2

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ conda remove -y -n adam-build-b224fadf-a196-4bab-b574-3c1be31b3abc --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/adam-build-b224fadf-a196-4bab-b574-3c1be31b3abc:

The following packages will be REMOVED:

    _libgcc_mutex:    0.1-main               
    ca-certificates:  2020.6.24-0            
    certifi:          2020.6.20-py36_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:          1.1.1g-h7b6447c_0      
    pip:              20.1.1-py36_1          
    python:           3.6.10-h7579374_2      
    readline:         8.0-h7b6447c_0         
    setuptools:       49.2.0-py36_0          
    sqlite:           3.32.3-h62c20be_0      
    tk:               8.6.10-hbc83047_0      
    wheel:            0.34.2-py36_0          
    xz:               5.2.5-h7b6447c_0       
    zlib:             1.2.11-h7b6447c_3      

+ cp -r adam-python/target /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/../adam-python/
+ pushd adam-python
/tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu
+ make clean
pip uninstall -y adam
Skipping adam as it is not installed.
rm -rf bdgenomics/*.egg*
rm -rf build/
rm -rf dist/
+ make clean_sdist
rm -rf dist
+ popd
/tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu

if [ ${SPARK_VERSION} == 3.0.0 ]
then
    echo "Unable to build R support for Spark 3.0.0, SparkR is not available"
else
    # make a directory to install SparkR into, and set the R user libs path
    export R_LIBS_USER=${SPARK_HOME}/local_R_libs
    mkdir -p ${R_LIBS_USER}
    R CMD INSTALL \
      -l ${R_LIBS_USER} \
      ${SPARK_HOME}/R/lib/SparkR/

    export SPARKR_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} sparkr-shell"

    mvn -U \
    	-P r \
    	package \
    	-Dsuites=select.no.suites\* \
    	-Dhadoop.version=${HADOOP_VERSION}
fi
+ '[' 2.4.6 == 3.0.0 ']'
+ export R_LIBS_USER=/tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7/local_R_libs
+ R_LIBS_USER=/tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7/local_R_libs
+ mkdir -p /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7/local_R_libs
+ R CMD INSTALL -l /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7/local_R_libs /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7/R/lib/SparkR/
* installing *binary* package ‘SparkR’ ...
* DONE (SparkR)
+ export 'SPARKR_SUBMIT_ARGS=--jars /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar sparkr-shell'
+ SPARKR_SUBMIT_ARGS='--jars /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar sparkr-shell'
+ mvn -U -P r package '-Dsuites=select.no.suites*' -Dhadoop.version=2.7.5
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ADAM_2.11                                                          [pom]
[INFO] ADAM_2.11: Shader workaround                                       [jar]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils                           [jar]
[INFO] ADAM_2.11: Core                                                    [jar]
[INFO] ADAM_2.11: APIs for Java, Python                                   [jar]
[INFO] ADAM_2.11: CLI                                                     [jar]
[INFO] ADAM_2.11: Assembly                                                [jar]
[INFO] ADAM_2.11: R APIs                                                  [jar]
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-parent-spark2_2.11 >-------------
[INFO] Building ADAM_2.11 0.33.0-SNAPSHOT                                 [1/8]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.11 ---
[INFO] Modified 2 of 435 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-shade-spark2_2.11 >-------------
[INFO] Building ADAM_2.11: Shader workaround 0.33.0-SNAPSHOT              [2/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.11 ---
[INFO] Discovered 1 component descriptors(s)
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.11 ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-shade-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.11-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-codegen-spark2_2.11 >------------
[INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.33.0-SNAPSHOT  [3/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.11 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.11 ---
[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-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.11 ---
Discovery starting.
Discovery completed in 37 milliseconds.
Run starting. Expected test count is: 0
Run completed in 41 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-spark2_2.11 ---
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-core-spark2_2.11 >--------------
[INFO] Building ADAM_2.11: Core 0.33.0-SNAPSHOT                           [4/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.11 ---
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-spark2_2.11 ---
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-spark2_2.11 ---
[INFO] Modified 2 of 204 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.11 ---
[INFO] /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java:-1: info: compiling
[INFO] /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala:-1: info: compiling
[INFO] /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 140 source files to /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/classes at 1596746796982
[WARNING] /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3091: warning: no valid targets for annotation on value uTag - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @getter)
[WARNING]   @transient val uTag: TypeTag[U]
[WARNING]    ^
[WARNING] warning: there were 53 deprecation warnings; re-run with -deprecation for details
[WARNING] warning: there were 5 feature warnings; re-run with -feature for details
[WARNING] three warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 40 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.11 ---
[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-core-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.11 ---
[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-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.11 ---
Discovery starting.
Discovery completed in 1 second, 573 milliseconds.
Run starting. Expected test count is: 0
Run completed in 1 second, 580 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-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-apis-spark2_2.11 >--------------
[INFO] Building ADAM_2.11: APIs for Java, Python 0.33.0-SNAPSHOT          [5/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.11 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.11 ---
[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-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.11 ---
[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-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.11 ---
Discovery starting.
Discovery completed in 162 milliseconds.
Run starting. Expected test count is: 0
Run completed in 167 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-spark2_2.11 ---
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --------------< org.bdgenomics.adam:adam-cli-spark2_2.11 >--------------
[INFO] Building ADAM_2.11: CLI 0.33.0-SNAPSHOT                            [6/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 ---
[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/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.11 ---
[INFO] Modified 0 of 29 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.11 ---
[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-cli-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.11 ---
[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-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.11 ---
Discovery starting.
Discovery completed in 194 milliseconds.
Run starting. Expected test count is: 0
Run completed in 201 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-spark2_2.11 ---
[INFO] 
[INFO] -----------< org.bdgenomics.adam:adam-assembly-spark2_2.11 >------------
[INFO] Building ADAM_2.11: Assembly 0.33.0-SNAPSHOT                       [7/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 ---
[INFO] Request to add '/tmp/adamTestmbfHyt1/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-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.11 ---
[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-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark2_2.11 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11: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-spark2_2.11:jar:0.3.0 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11: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-spark2_2.11:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11: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-spark2_2.11:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11: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:2.11.12 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$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] parquet-common-1.10.1.jar, adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar define 83 overlapping classes: 
[WARNING]   - org.apache.parquet.SemanticVersion$SemanticVersionParseException
[WARNING]   - org.apache.parquet.bytes.SingleBufferInputStream
[WARNING]   - org.apache.parquet.Ints
[WARNING]   - org.apache.parquet.Version
[WARNING]   - org.apache.parquet.SemanticVersion$NumberOrString
[WARNING]   - org.apache.parquet.glob.GlobNode$Atom
[WARNING]   - org.apache.parquet.util.DynMethods$Builder
[WARNING]   - org.apache.parquet.bytes.BytesInput$EmptyBytesInput
[WARNING]   - org.apache.parquet.Exceptions
[WARNING]   - org.apache.parquet.bytes.MultiBufferInputStream$ConcatIterator
[WARNING]   - 73 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, checker-qual-2.5.2.jar define 302 overlapping classes: 
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil
[WARNING]   - org.checkerframework.checker.units.qual.MixedUnits
[WARNING]   - org.checkerframework.checker.regex.qual.PolyRegex
[WARNING]   - org.checkerframework.checker.units.qual.PolyUnit
[WARNING]   - org.checkerframework.checker.formatter.FormatUtil$IllegalFormatConversionCategoryException
[WARNING]   - org.checkerframework.framework.qual.Unqualified
[WARNING]   - org.checkerframework.checker.units.qual.C
[WARNING]   - org.checkerframework.common.reflection.qual.UnknownMethod
[WARNING]   - org.checkerframework.framework.qual.EnsuresQualifierIf
[WARNING]   - org.checkerframework.checker.signedness.SignednessUtil
[WARNING]   - 292 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, commons-codec-1.11.jar define 96 overlapping classes: 
[WARNING]   - org.apache.commons.codec.language.Nysiis
[WARNING]   - org.apache.commons.codec.language.bm.Rule$1
[WARNING]   - org.apache.commons.codec.language.bm.Rule$RPattern
[WARNING]   - org.apache.commons.codec.language.ColognePhonetic$CologneInputBuffer
[WARNING]   - org.apache.commons.codec.digest.HmacUtils
[WARNING]   - org.apache.commons.codec.language.bm.BeiderMorseEncoder
[WARNING]   - org.apache.commons.codec.digest.UnixCrypt
[WARNING]   - org.apache.commons.codec.language.Soundex
[WARNING]   - org.apache.commons.codec.cli.Digest
[WARNING]   - org.apache.commons.codec.binary.BinaryCodec
[WARNING]   - 86 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, guava-27.0-jre.jar define 1955 overlapping classes: 
[WARNING]   - com.google.common.collect.CompactHashMap$Itr
[WARNING]   - com.google.common.collect.ImmutableMapValues$1
[WARNING]   - com.google.common.util.concurrent.AbstractService$5
[WARNING]   - com.google.common.io.LineProcessor
[WARNING]   - com.google.common.io.BaseEncoding$StandardBaseEncoding$2
[WARNING]   - com.google.common.io.ByteProcessor
[WARNING]   - com.google.common.math.package-info
[WARNING]   - com.google.common.util.concurrent.SimpleTimeLimiter
[WARNING]   - com.google.common.cache.AbstractCache$StatsCounter
[WARNING]   - com.google.common.util.concurrent.CycleDetectingLockFactory$Policies
[WARNING]   - 1945 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, parquet-jackson-1.10.1.jar define 623 overlapping classes: 
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.InjectableValues$Std
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.introspect.POJOPropertyBuilder$Node
[WARNING]   - shaded.parquet.org.codehaus.jackson.util.TokenBuffer$1
[WARNING]   - shaded.parquet.org.codehaus.jackson.type.TypeReference
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.std.FromStringDeserializer$LocaleDeserializer
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.ser.BasicSerializerFactory
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.StdKeyDeserializer
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.deser.std.StdKeyDeserializer$EnumKD
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.ser.std.InetAddressSerializer
[WARNING]   - shaded.parquet.org.codehaus.jackson.map.jsontype.impl.StdTypeResolverBuilder
[WARNING]   - 613 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, parquet-format-2.4.0.jar define 461 overlapping classes: 
[WARNING]   - shaded.parquet.org.apache.thrift.transport.TSimpleFileTransport
[WARNING]   - shaded.parquet.org.apache.thrift.transport.TServerSocket
[WARNING]   - shaded.parquet.org.apache.thrift.transport.TFileTransport$TruncableBufferedInputStream
[WARNING]   - shaded.parquet.org.apache.thrift.TFieldIdEnum
[WARNING]   - org.apache.parquet.format.SchemaElement$SchemaElementStandardScheme
[WARNING]   - shaded.parquet.org.apache.thrift.server.AbstractNonblockingServer$AbstractSelectThread
[WARNING]   - shaded.parquet.org.apache.thrift.TEnumHelper
[WARNING]   - org.apache.parquet.format.JsonType$JsonTypeStandardScheme
[WARNING]   - org.apache.parquet.format.DictionaryPageHeader$DictionaryPageHeaderTupleScheme
[WARNING]   - org.apache.parquet.format.UUIDType$1
[WARNING]   - 451 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, ngs-java-2.9.0.jar define 73 overlapping classes: 
[WARNING]   - ngs.itf.ReadItf
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.cause.JvmErrorCause
[WARNING]   - ngs.ReferenceIterator
[WARNING]   - gov.nih.nlm.ncbi.ngs.Manager$1
[WARNING]   - gov.nih.nlm.ncbi.ngs.LMProperties
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.LibraryLoadError
[WARNING]   - gov.nih.nlm.ncbi.ngs.LibDependencies
[WARNING]   - gov.nih.nlm.ncbi.ngs.error.cause.ConnectionProblemCause
[WARNING]   - ngs.itf.PileupEventItf
[WARNING]   - gov.nih.nlm.ncbi.ngs.LibManager$Location
[WARNING]   - 63 more...
[WARNING] httpcore-4.4.11.jar, adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar define 252 overlapping classes: 
[WARNING]   - org.apache.http.protocol.HttpRequestHandler
[WARNING]   - org.apache.http.impl.io.ChunkedOutputStream
[WARNING]   - org.apache.http.protocol.ChainBuilder
[WARNING]   - org.apache.http.impl.entity.DisallowIdentityContentLengthStrategy
[WARNING]   - org.apache.http.impl.ConnSupport
[WARNING]   - org.apache.http.impl.io.DefaultHttpResponseParserFactory
[WARNING]   - org.apache.http.HttpClientConnection
[WARNING]   - org.apache.http.NameValuePair
[WARNING]   - org.apache.http.protocol.HttpExpectationVerifier
[WARNING]   - org.apache.http.impl.io.AbstractMessageWriter
[WARNING]   - 242 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, minlog-1.2.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, animal-sniffer-annotations-1.17.jar define 1 overlapping classes: 
[WARNING]   - org.codehaus.mojo.animal_sniffer.IgnoreJRERequirement
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, jsr203hadoop-1.0.3.jar define 27 overlapping classes: 
[WARNING]   - hdfs.jsr203.HadoopDirectoryStream
[WARNING]   - hdfs.jsr203.HadoopPath
[WARNING]   - hdfs.jsr203.HadoopFileSystem$1
[WARNING]   - hdfs.jsr203.HadoopFileOwnerAttributeView
[WARNING]   - hdfs.jsr203.HadoopUserPrincipal
[WARNING]   - hdfs.jsr203.IAttributeReader
[WARNING]   - hdfs.jsr203.HadoopPath$1
[WARNING]   - hdfs.jsr203.HadoopBasicFileAttributes
[WARNING]   - hdfs.jsr203.HadoopDirectoryStream$1
[WARNING]   - hdfs.jsr203.package-info
[WARNING]   - 17 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, objenesis-2.1.jar define 37 overlapping classes: 
[WARNING]   - org.objenesis.ObjenesisBase
[WARNING]   - org.objenesis.instantiator.gcj.GCJInstantiator
[WARNING]   - org.objenesis.strategy.SingleInstantiatorStrategy
[WARNING]   - org.objenesis.ObjenesisHelper
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactoryHelper
[WARNING]   - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator
[WARNING]   - org.objenesis.instantiator.sun.SunReflectionFactoryInstantiator
[WARNING]   - org.objenesis.instantiator.basic.NullInstantiator
[WARNING]   - org.objenesis.instantiator.android.Android17Instantiator
[WARNING]   - org.objenesis.instantiator.ObjectInstantiator
[WARNING]   - 27 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, httpclient-4.5.7.jar define 467 overlapping classes: 
[WARNING]   - org.apache.http.impl.cookie.RFC2109Spec
[WARNING]   - org.apache.http.impl.execchain.MainClientExec
[WARNING]   - org.apache.http.conn.routing.RouteInfo$TunnelType
[WARNING]   - org.apache.http.client.methods.HttpGet
[WARNING]   - org.apache.http.impl.cookie.BrowserCompatSpecFactory
[WARNING]   - org.apache.http.impl.client.HttpAuthenticator
[WARNING]   - org.apache.http.conn.ManagedClientConnection
[WARNING]   - org.apache.http.client.protocol.RequestAuthCache
[WARNING]   - org.apache.http.conn.params.ConnConnectionParamBean
[WARNING]   - org.apache.http.impl.client.IdleConnectionEvictor
[WARNING]   - 457 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, slf4j-api-1.7.30.jar define 34 overlapping classes: 
[WARNING]   - org.slf4j.helpers.SubstituteLogger
[WARNING]   - org.slf4j.helpers.NamedLoggerBase
[WARNING]   - org.slf4j.helpers.NOPMDCAdapter
[WARNING]   - org.slf4j.MarkerFactory
[WARNING]   - org.slf4j.spi.LoggerFactoryBinder
[WARNING]   - org.slf4j.helpers.BasicMarker
[WARNING]   - org.slf4j.MDC$MDCCloseable
[WARNING]   - org.slf4j.spi.LocationAwareLogger
[WARNING]   - org.slf4j.helpers.MessageFormatter
[WARNING]   - org.slf4j.helpers.Util$ClassContextSecurityManager
[WARNING]   - 24 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, scala-guice_2.11-4.2.1.jar define 95 overlapping classes: 
[WARNING]   - net.codingwell.scalaguice.ScalaModule$
[WARNING]   - net.codingwell.scalaguice.ScalaModule$ScalaScopedBindingBuilder
[WARNING]   - net.codingwell.scalaguice.InjectorExtensions$ScalaInjector$$typecreator2$1
[WARNING]   - net.codingwell.scalaguice.ScalaModule$ScalaLinkedBindingBuilder$$anon$2$$typecreator1$1
[WARNING]   - net.codingwell.scalaguice.binder.ScopedBindingBuilderProxy
[WARNING]   - net.codingwell.scalaguice.InternalModule$BindingBuilder$$typecreator1$2
[WARNING]   - net.codingwell.scalaguice.ScalaModule$$anonfun$filterTrace$2
[WARNING]   - net.codingwell.scalaguice.ScalaPrivateModule$ElementBuilder
[WARNING]   - net.codingwell.scalaguice.binder.LinkedBindingBuilderProxy$class
[WARNING]   - net.codingwell.scalaguice.ScalaModule$ScalaAnnotatedBindingBuilder
[WARNING]   - 85 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, commons-io-2.6.jar define 127 overlapping classes: 
[WARNING]   - org.apache.commons.io.FileCleaningTracker
[WARNING]   - org.apache.commons.io.comparator.SizeFileComparator
[WARNING]   - org.apache.commons.io.input.CloseShieldInputStream
[WARNING]   - org.apache.commons.io.ByteOrderParser
[WARNING]   - org.apache.commons.io.filefilter.EmptyFileFilter
[WARNING]   - org.apache.commons.io.monitor.FileEntry
[WARNING]   - org.apache.commons.io.output.ThresholdingOutputStream
[WARNING]   - org.apache.commons.io.input.TailerListener
[WARNING]   - org.apache.commons.io.IOExceptionWithCause
[WARNING]   - org.apache.commons.io.filefilter.NotFileFilter
[WARNING]   - 117 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, fastutil-6.6.5.jar define 10700 overlapping classes: 
[WARNING]   - it.unimi.dsi.fastutil.doubles.Double2IntRBTreeMap$Submap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2CharAVLTreeMap$2$1
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2ObjectLinkedOpenHashMap$EntryIterator
[WARNING]   - it.unimi.dsi.fastutil.ints.Int2ReferenceRBTreeMap$Submap
[WARNING]   - it.unimi.dsi.fastutil.shorts.Short2FloatOpenCustomHashMap$KeySet
[WARNING]   - it.unimi.dsi.fastutil.bytes.Byte2BooleanRBTreeMap$Submap$1
[WARNING]   - it.unimi.dsi.fastutil.floats.AbstractFloat2ShortSortedMap$ValuesCollection
[WARNING]   - it.unimi.dsi.fastutil.longs.Long2ReferenceRBTreeMap$Submap$2
[WARNING]   - it.unimi.dsi.fastutil.chars.AbstractChar2LongSortedMap$ValuesIterator
[WARNING]   - it.unimi.dsi.fastutil.doubles.DoubleHeaps
[WARNING]   - 10690 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, utils-cli-spark2_2.11-0.3.0.jar define 19 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.cli.Args4j
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$class
[WARNING]   - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$run$1
[WARNING]   - org.bdgenomics.utils.cli.ParquetArgs$class
[WARNING]   - org.bdgenomics.utils.cli.SaveArgs
[WARNING]   - org.bdgenomics.utils.cli.Args4jBase
[WARNING]   - org.bdgenomics.utils.cli.ParquetSaveArgs
[WARNING]   - org.bdgenomics.utils.cli.ParquetLoadSaveArgs
[WARNING]   - org.bdgenomics.utils.cli.BDGCommandCompanion
[WARNING]   - 9 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, avro-1.8.2.jar define 1172 overlapping classes: 
[WARNING]   - org.apache.avro.message.SchemaStore
[WARNING]   - avro.shaded.com.google.common.collect.SingletonImmutableList
[WARNING]   - org.apache.avro.io.EncoderFactory$DefaultEncoderFactory
[WARNING]   - avro.shaded.com.google.common.collect.Iterables$15
[WARNING]   - org.apache.avro.GuavaClasses
[WARNING]   - avro.shaded.com.google.common.collect.Sets$PowerSet$1$1
[WARNING]   - avro.shaded.com.google.common.collect.RegularImmutableMap
[WARNING]   - org.apache.avro.generic.GenericDatumReader$2
[WARNING]   - avro.shaded.com.google.common.collect.Synchronized$SynchronizedSortedSet
[WARNING]   - org.apache.avro.file.BZip2Codec
[WARNING]   - 1162 more...
[WARNING] commons-logging-1.2.jar, adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar define 28 overlapping classes: 
[WARNING]   - org.apache.commons.logging.LogSource
[WARNING]   - org.apache.commons.logging.impl.ServletContextCleaner
[WARNING]   - org.apache.commons.logging.Log
[WARNING]   - org.apache.commons.logging.LogFactory$3
[WARNING]   - org.apache.commons.logging.impl.LogFactoryImpl$2
[WARNING]   - org.apache.commons.logging.impl.LogKitLogger
[WARNING]   - org.apache.commons.logging.impl.Jdk14Logger
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable$Referenced
[WARNING]   - org.apache.commons.logging.impl.WeakHashtable$WeakKey
[WARNING]   - 18 more...
[WARNING] error_prone_annotations-2.2.0.jar, adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar define 22 overlapping classes: 
[WARNING]   - com.google.errorprone.annotations.NoAllocation
[WARNING]   - com.google.errorprone.annotations.Var
[WARNING]   - com.google.errorprone.annotations.IncompatibleModifiers
[WARNING]   - com.google.errorprone.annotations.CompatibleWith
[WARNING]   - com.google.errorprone.annotations.concurrent.LockMethod
[WARNING]   - com.google.errorprone.annotations.FormatString
[WARNING]   - com.google.errorprone.annotations.DoNotCall
[WARNING]   - com.google.errorprone.annotations.Immutable
[WARNING]   - com.google.errorprone.annotations.RestrictedApi
[WARNING]   - com.google.errorprone.annotations.ForOverride
[WARNING]   - 12 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, guice-4.2.0.jar define 573 overlapping classes: 
[WARNING]   - com.google.inject.Scope
[WARNING]   - com.google.inject.Binding
[WARNING]   - com.google.inject.internal.cglib.core.$EmitUtils$3
[WARNING]   - com.google.inject.spi.TypeConverter
[WARNING]   - com.google.inject.internal.ConstructionProxy
[WARNING]   - com.google.inject.spi.InjectionPoint
[WARNING]   - com.google.inject.spi.StaticInjectionRequest
[WARNING]   - com.google.inject.internal.cglib.proxy.$FixedValueGenerator
[WARNING]   - com.google.inject.internal.cglib.proxy.$DispatcherGenerator
[WARNING]   - com.google.inject.spi.Elements$ElementsAsModule
[WARNING]   - 563 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, parquet-hadoop-1.10.1.jar define 162 overlapping classes: 
[WARNING]   - org.apache.parquet.hadoop.mapred.DeprecatedParquetOutputFormat
[WARNING]   - org.apache.parquet.hadoop.api.WriteSupport$WriteContext
[WARNING]   - org.apache.parquet.format.converter.ParquetMetadataConverter$RangeMetadataFilter
[WARNING]   - org.apache.parquet.hadoop.ColumnChunkPageReadStore$ColumnChunkPageReader$1
[WARNING]   - org.apache.parquet.format.converter.ParquetMetadataConverter$2
[WARNING]   - org.apache.parquet.hadoop.metadata.ColumnChunkMetaData
[WARNING]   - org.apache.parquet.hadoop.api.WriteSupport$FinalizedWriteContext
[WARNING]   - org.apache.parquet.hadoop.util.HadoopPositionOutputStream
[WARNING]   - org.apache.parquet.HadoopReadOptions$1
[WARNING]   - org.apache.parquet.format.converter.ParquetMetadataConverter$NoFilter
[WARNING]   - 152 more...
[WARNING] commons-compress-1.8.1.jar, adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar define 191 overlapping classes: 
[WARNING]   - org.apache.commons.compress.archivers.sevenz.SevenZArchiveEntry
[WARNING]   - org.apache.commons.compress.archivers.dump.ShortFileException
[WARNING]   - org.apache.commons.compress.utils.CountingInputStream
[WARNING]   - org.apache.commons.compress.compressors.bzip2.CRC
[WARNING]   - org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream
[WARNING]   - org.apache.commons.compress.archivers.dump.DumpArchiveEntry
[WARNING]   - org.apache.commons.compress.changes.ChangeSetPerformer$ArchiveEntryIterator
[WARNING]   - org.apache.commons.compress.compressors.bzip2.BlockSort
[WARNING]   - org.apache.commons.compress.archivers.tar.TarArchiveEntry
[WARNING]   - org.apache.commons.compress.archivers.dump.UnsupportedCompressionAlgorithmException
[WARNING]   - 181 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, j2objc-annotations-1.1.jar define 12 overlapping classes: 
[WARNING]   - com.google.j2objc.annotations.Property
[WARNING]   - com.google.j2objc.annotations.RetainedWith
[WARNING]   - com.google.j2objc.annotations.RetainedLocalRef
[WARNING]   - com.google.j2objc.annotations.J2ObjCIncompatible
[WARNING]   - com.google.j2objc.annotations.AutoreleasePool
[WARNING]   - com.google.j2objc.annotations.LoopTranslation$LoopStyle
[WARNING]   - com.google.j2objc.annotations.ReflectionSupport$Level
[WARNING]   - com.google.j2objc.annotations.ReflectionSupport
[WARNING]   - com.google.j2objc.annotations.WeakOuter
[WARNING]   - com.google.j2objc.annotations.Weak
[WARNING]   - 2 more...
[WARNING] bdg-formats-0.15.0.jar, adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar define 58 overlapping classes: 
[WARNING]   - org.bdgenomics.formats.avro.VariantCallingAnnotations$Builder
[WARNING]   - org.bdgenomics.formats.avro.VariantAnnotation$Builder
[WARNING]   - org.bdgenomics.formats.avro.Reference$1
[WARNING]   - org.bdgenomics.formats.avro.VariantAnnotationMessage
[WARNING]   - org.bdgenomics.formats.avro.Alignment$Builder
[WARNING]   - org.bdgenomics.formats.avro.OntologyTerm$1
[WARNING]   - org.bdgenomics.formats.avro.Alignment$1
[WARNING]   - org.bdgenomics.formats.avro.Feature$1
[WARNING]   - org.bdgenomics.formats.avro.Sequence$1
[WARNING]   - org.bdgenomics.formats.avro.ReadGroup$Builder
[WARNING]   - 48 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, utils-misc-spark2_2.11-0.3.0.jar define 5 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.misc.MathUtils
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$scalarArrayMultiply$1
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$aggregateArray$1
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$$anonfun$softmax$1
[WARNING]   - org.bdgenomics.utils.misc.MathUtils$
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, parquet-encoding-1.10.1.jar define 305 overlapping classes: 
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingForLongBE$Packer25
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer14
[WARNING]   - org.apache.parquet.column.values.bitpacking.BytePackerForLong
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer10
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingForLongLE$Packer54
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingForLongLE$Packer41
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer30
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer23
[WARNING]   - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$Packer19
[WARNING]   - org.apache.parquet.column.values.bitpacking.ByteBitPackingForLongLE$Packer21
[WARNING]   - 295 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, parquet-column-1.10.1.jar define 792 overlapping classes: 
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.longs.LongComparator
[WARNING]   - org.apache.parquet.column.values.dictionary.DictionaryValuesWriter$PlainIntegerDictionaryValuesWriter
[WARNING]   - org.apache.parquet.io.PrimitiveColumnIO
[WARNING]   - org.apache.parquet.io.api.Binary$ByteBufferBackedBinary
[WARNING]   - org.apache.parquet.it.unimi.dsi.fastutil.doubles.DoubleSortedSet
[WARNING]   - org.apache.parquet.io.BaseRecordReader
[WARNING]   - org.apache.parquet.column.ParquetProperties$1
[WARNING]   - org.apache.parquet.column.UnknownColumnException
[WARNING]   - org.apache.parquet.filter.ColumnPredicates$12
[WARNING]   - org.apache.parquet.schema.Types$BaseMapBuilder$ListValueBuilder
[WARNING]   - 782 more...
[WARNING] jackson-core-asl-1.9.13.jar, adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar define 121 overlapping classes: 
[WARNING]   - org.codehaus.jackson.annotate.JsonManagedReference
[WARNING]   - org.codehaus.jackson.util.DefaultPrettyPrinter$FixedSpaceIndenter
[WARNING]   - org.codehaus.jackson.JsonGenerationException
[WARNING]   - org.codehaus.jackson.util.BufferRecycler$CharBufferType
[WARNING]   - org.codehaus.jackson.io.UTF32Reader
[WARNING]   - org.codehaus.jackson.sym.Name1
[WARNING]   - org.codehaus.jackson.util.MinimalPrettyPrinter
[WARNING]   - org.codehaus.jackson.impl.JsonParserBase
[WARNING]   - org.codehaus.jackson.sym.CharsToNameCanonicalizer$Bucket
[WARNING]   - org.codehaus.jackson.annotate.JsonValue
[WARNING]   - 111 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, kryo-2.24.0.jar define 193 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.BeanSerializer$1
[WARNING]   - com.esotericsoftware.kryo.Registration
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.kryo.util.IntMap$Values
[WARNING]   - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl
[WARNING]   - com.esotericsoftware.kryo.serializers.JavaSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField
[WARNING]   - 183 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, utils-intervalrdd-spark2_2.11-0.3.0.jar define 51 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$collect$2
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$4
[WARNING]   - org.bdgenomics.utils.interval.array.Interval$class
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$get$1
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$4
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$1
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$
[WARNING]   - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$filter$1
[WARNING]   - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$mapValues$1
[WARNING]   - 41 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, jackson-mapper-asl-1.9.13.jar define 502 overlapping classes: 
[WARNING]   - org.codehaus.jackson.map.ext.DOMSerializer
[WARNING]   - org.codehaus.jackson.node.POJONode
[WARNING]   - org.codehaus.jackson.map.ser.StdSerializers$UtilDateSerializer
[WARNING]   - org.codehaus.jackson.map.deser.std.JsonNodeDeserializer$ArrayDeserializer
[WARNING]   - org.codehaus.jackson.map.ext.JodaDeserializers$LocalDateDeserializer
[WARNING]   - org.codehaus.jackson.map.deser.std.PrimitiveArrayDeserializers$StringDeser
[WARNING]   - org.codehaus.jackson.map.util.Comparators$1
[WARNING]   - org.codehaus.jackson.map.util.StdDateFormat
[WARNING]   - org.codehaus.jackson.map.KeyDeserializer
[WARNING]   - org.codehaus.jackson.map.MapperConfig$Impl
[WARNING]   - 492 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, commons-jexl-2.1.1.jar define 178 overlapping classes: 
[WARNING]   - org.apache.commons.jexl2.internal.AbstractExecutor$Get
[WARNING]   - org.apache.commons.jexl2.introspection.JexlPropertyGet
[WARNING]   - org.apache.commons.jexl2.parser.StringParser
[WARNING]   - org.apache.commons.jexl2.parser.ASTBitwiseOrNode
[WARNING]   - org.apache.commons.jexl2.internal.introspection.MethodKey$1
[WARNING]   - org.apache.commons.jexl2.Main
[WARNING]   - org.apache.commons.jexl2.parser.ASTForeachStatement
[WARNING]   - org.apache.commons.jexl2.introspection.Sandbox
[WARNING]   - org.apache.commons.jexl2.internal.introspection.ClassMap
[WARNING]   - org.apache.commons.jexl2.parser.ASTFunctionNode
[WARNING]   - 168 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, snappy-java-1.1.1.3.jar define 19 overlapping classes: 
[WARNING]   - org.xerial.snappy.SnappyLoader
[WARNING]   - org.xerial.snappy.SnappyFramedInputStream$FrameMetaData
[WARNING]   - org.xerial.snappy.SnappyFramedInputStream
[WARNING]   - org.xerial.snappy.SnappyOutputStream
[WARNING]   - org.xerial.snappy.SnappyErrorCode
[WARNING]   - org.xerial.snappy.SnappyBundleActivator
[WARNING]   - org.xerial.snappy.SnappyFramedOutputStream
[WARNING]   - org.xerial.snappy.BufferRecycler
[WARNING]   - org.xerial.snappy.SnappyError
[WARNING]   - org.xerial.snappy.SnappyFramedInputStream$FrameAction
[WARNING]   - 9 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, adam-apis-spark2_2.11-0.33.0-SNAPSHOT.jar define 205 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.api.java.FeaturesToFragmentsConverter
[WARNING]   - org.bdgenomics.adam.api.java.ToVariantDatasetConversion$class
[WARNING]   - org.bdgenomics.adam.api.java.ToCoverageDatasetConversion$class
[WARNING]   - org.bdgenomics.adam.api.java.FeaturesToVariantsDatasetConverter
[WARNING]   - org.bdgenomics.adam.api.java.ToFragmentDatasetConversion$$typecreator3$1
[WARNING]   - org.bdgenomics.adam.api.java.ToSliceDatasetConversion$class
[WARNING]   - org.bdgenomics.adam.api.java.AlignmentsToFeaturesConverter
[WARNING]   - org.bdgenomics.adam.api.java.FeaturesToReadsDatasetConverter
[WARNING]   - org.bdgenomics.adam.api.java.VariantsToVariantsConverter
[WARNING]   - org.bdgenomics.adam.api.java.CoverageToReadsDatasetConverter
[WARNING]   - 195 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, adam-codegen-spark2_2.11-0.33.0-SNAPSHOT.jar define 18 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$getters$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$setters$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$apply$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$fields$1
[WARNING]   - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$$anonfun$fields$1
[WARNING]   - 8 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, javax.inject-1.jar define 6 overlapping classes: 
[WARNING]   - javax.inject.Inject
[WARNING]   - javax.inject.Singleton
[WARNING]   - javax.inject.Scope
[WARNING]   - javax.inject.Named
[WARNING]   - javax.inject.Provider
[WARNING]   - javax.inject.Qualifier
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, utils-io-spark2_2.11-0.3.0.jar define 22 overlapping classes: 
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$3
[WARNING]   - org.bdgenomics.utils.io.FileLocator
[WARNING]   - org.bdgenomics.utils.io.ByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$readByteStream$1
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$1
[WARNING]   - org.bdgenomics.utils.io.ByteAccess$$anonfun$readFully$2
[WARNING]   - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$2
[WARNING]   - org.bdgenomics.utils.io.LocalFileByteAccess
[WARNING]   - org.bdgenomics.utils.io.HTTPFileLocator$
[WARNING]   - 12 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, xz-1.5.jar define 105 overlapping classes: 
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder$LengthDecoder
[WARNING]   - org.tukaani.xz.index.IndexDecoder
[WARNING]   - org.tukaani.xz.lzma.LZMADecoder
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoderFast
[WARNING]   - org.tukaani.xz.lzma.LZMAEncoder$LengthEncoder
[WARNING]   - org.tukaani.xz.BlockOutputStream
[WARNING]   - org.tukaani.xz.simple.SimpleFilter
[WARNING]   - org.tukaani.xz.rangecoder.RangeCoder
[WARNING]   - org.tukaani.xz.XZOutputStream
[WARNING]   - org.tukaani.xz.UncompressedLZMA2OutputStream
[WARNING]   - 95 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, adam-core-spark2_2.11-0.33.0-SNAPSHOT.jar define 2916 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.rdd.feature.FeatureDataset$$anonfun$filterToTranscript$2$$anonfun$apply$9$$anonfun$apply$10
[WARNING]   - org.bdgenomics.adam.models.SnpTable$$anonfun$2
[WARNING]   - org.bdgenomics.adam.sql.VariantCallingAnnotations$$anonfun$toAvro$58
[WARNING]   - org.bdgenomics.adam.rdd.GenomicDataset$$anonfun$shuffleRegionJoin$2
[WARNING]   - org.bdgenomics.adam.rdd.feature.DatasetBoundFeatureDataset$$anonfun$filterByAttribute$1
[WARNING]   - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$63
[WARNING]   - org.bdgenomics.adam.io.InterleavedFastqInputFormat
[WARNING]   - org.bdgenomics.adam.util.FileMerger$$anonfun$mergeFilesAcrossFilesystems$4
[WARNING]   - org.bdgenomics.adam.rdd.fragment.DatasetBoundFragmentDataset
[WARNING]   - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$extractStrandBiasComponents$1
[WARNING]   - 2906 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, adam-cli-spark2_2.11-0.33.0-SNAPSHOT.jar define 152 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.PrintADAMArgs
[WARNING]   - org.bdgenomics.adam.cli.TransformVariants$$anonfun$maybeCoalesce$2
[WARNING]   - org.bdgenomics.adam.cli.FlagStat$
[WARNING]   - org.bdgenomics.adam.cli.TransformAlignments$$anonfun$7
[WARNING]   - org.bdgenomics.adam.cli.TransformAlignments$$anonfun$11
[WARNING]   - org.bdgenomics.adam.cli.TransformGenotypes$$anonfun$run$2
[WARNING]   - org.bdgenomics.adam.cli.TransformVariants$
[WARNING]   - org.bdgenomics.adam.cli.View$$anonfun$getFilter$1$1
[WARNING]   - org.bdgenomics.adam.cli.Coverage$$anonfun$run$1
[WARNING]   - org.bdgenomics.adam.cli.TransformAlignments$$anonfun$maybeCoalesce$2
[WARNING]   - 142 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, paranamer-2.8.jar define 21 overlapping classes: 
[WARNING]   - com.thoughtworks.paranamer.PositionalParanamer
[WARNING]   - com.thoughtworks.paranamer.JavadocParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$Type
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$1
[WARNING]   - com.thoughtworks.paranamer.JavadocParanamer$DirJavadocProvider
[WARNING]   - com.thoughtworks.paranamer.AnnotationParanamer$Jsr330Helper
[WARNING]   - com.thoughtworks.paranamer.BytecodeReadingParanamer$TypeCollector
[WARNING]   - com.thoughtworks.paranamer.AnnotationParanamer
[WARNING]   - com.thoughtworks.paranamer.NullParanamer
[WARNING]   - 11 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, aopalliance-1.0.jar define 9 overlapping classes: 
[WARNING]   - org.aopalliance.intercept.ConstructorInterceptor
[WARNING]   - org.aopalliance.intercept.MethodInvocation
[WARNING]   - org.aopalliance.intercept.MethodInterceptor
[WARNING]   - org.aopalliance.intercept.Invocation
[WARNING]   - org.aopalliance.aop.AspectException
[WARNING]   - org.aopalliance.intercept.Interceptor
[WARNING]   - org.aopalliance.intercept.Joinpoint
[WARNING]   - org.aopalliance.aop.Advice
[WARNING]   - org.aopalliance.intercept.ConstructorInvocation
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, htsjdk-2.19.0.jar define 993 overlapping classes: 
[WARNING]   - htsjdk.samtools.cram.ref.ReferenceSource
[WARNING]   - htsjdk.samtools.cram.compression.ExternalCompressor$3
[WARNING]   - htsjdk.samtools.HighAccuracyDownsamplingIterator
[WARNING]   - htsjdk.samtools.util.zip.DeflaterFactory
[WARNING]   - htsjdk.samtools.filter.DuplicateReadFilter
[WARNING]   - htsjdk.samtools.cram.encoding.core.huffmanUtils.HuffmanCode$1
[WARNING]   - htsjdk.samtools.cram.encoding.core.SubexponentialIntegerEncoding
[WARNING]   - htsjdk.variant.vcf.VCFEncoder
[WARNING]   - htsjdk.samtools.util.CloserUtil
[WARNING]   - htsjdk.tribble.TribbleException$FeatureFileDoesntExist
[WARNING]   - 983 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, grizzled-slf4j_2.11-1.3.4.jar define 4 overlapping classes: 
[WARNING]   - grizzled.slf4j.Logger$
[WARNING]   - grizzled.slf4j.Logging
[WARNING]   - grizzled.slf4j.Logging$class
[WARNING]   - grizzled.slf4j.Logger
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, jsr305-1.3.9.jar define 35 overlapping classes: 
[WARNING]   - javax.annotation.RegEx
[WARNING]   - javax.annotation.concurrent.Immutable
[WARNING]   - javax.annotation.meta.TypeQualifierDefault
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Nonnull
[WARNING]   - javax.annotation.CheckReturnValue
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - javax.annotation.MatchesPattern
[WARNING]   - 25 more...
[WARNING] args4j-2.33.jar, adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar define 74 overlapping classes: 
[WARNING]   - org.kohsuke.args4j.spi.DoubleOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.MethodSetter
[WARNING]   - org.kohsuke.args4j.spi.MacAddressOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.StringArrayOptionHandler
[WARNING]   - org.kohsuke.args4j.spi.SubCommand
[WARNING]   - org.kohsuke.args4j.spi.PatternOptionHandler
[WARNING]   - org.kohsuke.args4j.ParserProperties$1
[WARNING]   - org.kohsuke.args4j.OptionHandlerFilter$2
[WARNING]   - org.kohsuke.args4j.spi.MultiFileOptionHandler
[WARNING]   - org.kohsuke.args4j.OptionHandlerRegistry$DefaultConstructorHandlerFactory
[WARNING]   - 64 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, hadoop-bam-7.9.2.jar define 115 overlapping classes: 
[WARNING]   - org.seqdoop.hadoop_bam.BAMSplitGuesser
[WARNING]   - org.seqdoop.hadoop_bam.util.SAMHeaderReader
[WARNING]   - org.seqdoop.hadoop_bam.QseqInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter
[WARNING]   - org.seqdoop.hadoop_bam.FastaInputFormat$1
[WARNING]   - org.seqdoop.hadoop_bam.util.SAMOutputPreparer$1
[WARNING]   - org.seqdoop.hadoop_bam.QseqOutputFormat$QseqRecordWriter
[WARNING]   - org.seqdoop.hadoop_bam.FastaInputFormat
[WARNING]   - org.seqdoop.hadoop_bam.LineReader
[WARNING]   - org.seqdoop.hadoop_bam.util.BGZFCodec
[WARNING]   - 105 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, commons-pool-1.6.jar define 55 overlapping classes: 
[WARNING]   - org.apache.commons.pool.PoolUtils$PoolableObjectFactoryAdaptor
[WARNING]   - org.apache.commons.pool.impl.GenericObjectPool$1
[WARNING]   - org.apache.commons.pool.impl.GenericObjectPool$Latch
[WARNING]   - org.apache.commons.pool.PoolUtils$ErodingFactor
[WARNING]   - org.apache.commons.pool.BasePoolableObjectFactory
[WARNING]   - org.apache.commons.pool.PoolUtils$KeyedPoolableObjectFactoryAdaptor
[WARNING]   - org.apache.commons.pool.impl.EvictionTimer$PrivilegedGetTccl
[WARNING]   - org.apache.commons.pool.impl.StackKeyedObjectPool
[WARNING]   - org.apache.commons.pool.BaseKeyedPoolableObjectFactory
[WARNING]   - org.apache.commons.pool.impl.GenericKeyedObjectPool$ObjectQueue
[WARNING]   - 45 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, scala-reflect-2.11.12.jar define 2829 overlapping classes: 
[WARNING]   - scala.reflect.runtime.ReflectionUtils
[WARNING]   - scala.reflect.internal.Scopes$LookupInaccessible$
[WARNING]   - scala.reflect.internal.Types$LazyType
[WARNING]   - scala.reflect.internal.Definitions$DefinitionsClass$$anonfun$newT1NullaryMethod$1
[WARNING]   - scala.reflect.internal.SymbolPairs$Cursor
[WARNING]   - scala.reflect.internal.Types$StaticallyAnnotatedType$
[WARNING]   - scala.reflect.runtime.SynchronizedOps$SynchronizedScope$$anonfun$isEmpty$1
[WARNING]   - scala.reflect.internal.Kinds$TypeConKind$$anonfun$buildState$3
[WARNING]   - scala.reflect.api.StandardLiftables$StandardUnliftableInstances$$anonfun$unliftTuple18$1
[WARNING]   - scala.reflect.runtime.SynchronizedSymbols$SynchronizedClassSymbol
[WARNING]   - 2819 more...
[WARNING] adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar, 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/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT-shaded.jar
[INFO] 
[INFO] ---------------< org.bdgenomics.adam:adam-r-spark2_2.11 >---------------
[INFO] Building ADAM_2.11: R APIs 0.33.0-SNAPSHOT                         [8/8]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-r-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-r-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-r-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-r-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-r/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (doc-r) @ adam-r-spark2_2.11 ---

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(devtools);devtools::document()
Loading required package: usethis
Updating bdgenomics.adam documentation
Updating roxygen version in /tmp/adamTestmbfHyt1/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdgenomics.adam/DESCRIPTION
Loading bdgenomics.adam
Creating a new generic function for ‘pipe’ in package ‘bdgenomics.adam’
Creating a new generic function for ‘transform’ in package ‘bdgenomics.adam’
Creating a new generic function for ‘save’ in package ‘bdgenomics.adam’
Creating a new generic function for ‘sort’ in package ‘bdgenomics.adam’

Attaching package: ‘SparkR’

The following objects are masked from ‘package:stats’:

    cov, filter, lag, na.omit, predict, sd, var, window

The following objects are masked from ‘package:base’:

    as.data.frame, colnames, colnames<-, drop, endsWith, intersect,
    rank, rbind, sample, startsWith, subset, summary, transform, union

Error in add_classes_to_exports(ns = nsenv, package = package, exports = exports,  : 
  in ‘bdgenomics.adam’ methods for export not found: toReads, sortReadsByReferencePositionAndIndex, sortReadsByReferencePosition
Calls: <Anonymous> ... <Anonymous> -> setup_ns_exports -> add_classes_to_exports
In addition: Warning messages:
1: roxygen2 requires Encoding: UTF-8 
2: In setup_ns_exports(path, export_all, export_imports) :
  Objects listed as exports, but not present in namespace: sortReadsByReferencePosition, sortReadsByReferencePositionAndIndex, toReads
3: no function found corresponding to methods exports from ‘bdgenomics.adam’ for: ‘sortReadsByReferencePosition’, ‘sortReadsByReferencePositionAndIndex’, ‘toReads’ 
Execution halted
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
    at org.apache.commons.exec.DefaultExecutor.executeInternal (DefaultExecutor.java:404)
    at org.apache.commons.exec.DefaultExecutor.execute (DefaultExecutor.java:166)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:764)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:711)
    at org.codehaus.mojo.exec.ExecMojo.execute (ExecMojo.java:289)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:957)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:289)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:193)
    at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:498)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.11 0.33.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  7.957 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  1.366 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.866 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [ 52.991 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  2.917 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  4.414 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 16.311 s]
[INFO] ADAM_2.11: R APIs .................................. FAILURE [  2.038 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  01:29 min
[INFO] Finished at: 2020-08-06T13:47:47-07:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (doc-r) on project adam-r-spark2_2.11: Command execution failed.: Process exited with an error: 1 (Exit value: 1) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :adam-r-spark2_2.11
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/956681ce6d9dd848d1e676096770f8a914b3e429
Finished: FAILURE