FailedConsole Output

Skipping 2,113 KB.. Full Log
R/conda" ..checkenv $_SHELL$EXT "$args"
++ /home/anaconda/bin/conda ..checkenv bash adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7
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-edbb3730-e630-48ea-99e4-38bd582fa7e7
+++ 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-ubuntu-testing/HADOOP_VERSION/2.7.3/SCALAVER/2.11/SPARK_VERSION/2.2.2/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-ubuntu-testing/HADOOP_VERSION/2.7.3/SCALAVER/2.11/SPARK_VERSION/2.2.2/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-edbb3730-e630-48ea-99e4-38bd582fa7e7
++ _NEW_PART=/home/jenkins/anaconda2/envs/adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7/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/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/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/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/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/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/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-edbb3730-e630-48ea-99e4-38bd582fa7e7/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/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-edbb3730-e630-48ea-99e4-38bd582fa7e7/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/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-edbb3730-e630-48ea-99e4-38bd582fa7e7
++ CONDA_DEFAULT_ENV=adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7
++ firstpath=/home/jenkins/anaconda2/envs/adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7/bin
echo ${firstpath} | sed "s|/bin$||"
+++ echo /home/jenkins/anaconda2/envs/adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7
"$_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-edbb3730-e630-48ea-99e4-38bd582fa7e7) '
++ PS1='(adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7) '
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7/etc/conda/activate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7/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
+ '[' 2.2.2 == 2.2.2 ']'
+ export R_LIBS_USER=/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.2-bin-hadoop2.7/local_R_libs
+ R_LIBS_USER=/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.2-bin-hadoop2.7/local_R_libs
+ mkdir -p /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.2-bin-hadoop2.7/local_R_libs
+ R CMD INSTALL -l /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.2-bin-hadoop2.7/local_R_libs /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.2-bin-hadoop2.7/R/lib/SparkR/
* installing *binary* package ‘SparkR’ ...
* DONE (SparkR)
+ export 'SPARKR_SUBMIT_ARGS=--jars /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.25.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.25.0-SNAPSHOT.jar sparkr-shell'
+ SPARKR_SUBMIT_ARGS='--jars /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.25.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.25.0-SNAPSHOT.jar sparkr-shell'
+ mvn -U -P python,r,distribution package '-Dsuites=select.no.suites*' -Dhadoop.version=2.7.3 -Dspark.version=2.2.2
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
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils
[INFO] ADAM_2.11: Core
[INFO] ADAM_2.11: APIs for Java, Python
[INFO] ADAM_2.11: CLI
[INFO] ADAM_2.11: Assembly
[INFO] ADAM_2.11: Python APIs
[INFO] ADAM_2.11: R APIs
[INFO] ADAM_2.11: Distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11 0.25.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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 127 of 428 .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] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-parent-spark2_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ adam-parent-spark2_2.11 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-parent-spark2_2.11 >>>
[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] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-parent-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark2_2.11 ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.25.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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:1.12:add-source (add-source) @ adam-codegen-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/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:3.0.1:resources (default-resources) @ adam-codegen-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.11 ---
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/2.11.12/classes at 1535579909194
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ adam-codegen-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:add-test-source (add-test-source) @ adam-codegen-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ adam-codegen-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestNTWURib/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:3.5.1:testCompile (default-testCompile) @ adam-codegen-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ adam-codegen-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ adam-codegen-spark2_2.11 ---
Discovery starting.
Discovery completed in 58 milliseconds.
Run starting. Expected test count is: 0
Run completed in 64 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:3.0.1:jar (default-jar) @ adam-codegen-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.25.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark2_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ adam-codegen-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.25.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark2_2.11 >>>
[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:1.12:add-source (add-source) @ adam-codegen-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-codegen-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark2_2.11 ---
model contains 11 documentable templates
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.25.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Core 0.25.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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:1.12:add-source (add-source) @ adam-core-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestNTWURib/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 ---
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.11 ---
[INFO] Modified 2 of 199 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ adam-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.12
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.spire-math:spire_2.11:0.11.0 requires scala version: 2.11.12
[WARNING]  org.spire-math:spire-macros_2.11:0.11.0 requires scala version: 2.11.12
[WARNING]  org.typelevel:machinist_2.11:0.4.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.7 requires scala version: 2.11.12
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.adam:adam-core-spark2_2.11:0.25.0-SNAPSHOT requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java:-1: info: compiling
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala:-1: info: compiling
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 135 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/classes at 1535579928455
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala:3101: 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 77 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 32 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ adam-core-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 5 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:add-test-source (add-test-source) @ adam-core-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ adam-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 144 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.12
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.spire-math:spire_2.11:0.11.0 requires scala version: 2.11.12
[WARNING]  org.spire-math:spire-macros_2.11:0.11.0 requires scala version: 2.11.12
[WARNING]  org.typelevel:machinist_2.11:0.4.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.7 requires scala version: 2.11.12
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.adam:adam-core-spark2_2.11:0.25.0-SNAPSHOT requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala:-1: info: compiling
[INFO] Compiling 69 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/test-classes at 1535579963732
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/FastqRecordConverterSuite.scala:48: warning: Adaptation of argument list by inserting () has been deprecated: this is unlikely to be what you want.
[WARNING]         signature: Equalizer.===(rightSide: Any)(implicit equality: org.scalactic.Equality[L]): Boolean
[WARNING]   given arguments: <none>
[WARNING]  after adaptation: Equalizer.===((): Unit)
[WARNING]     assert(converter.readNameSuffixAndIndexOfPairMustMatch(readName, isFirstOfPair) === ())
[WARNING]                                                                                     ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]       .build()
[WARNING]             ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val new_cigar = NormalizationUtils.leftAlignIndel(read)
[WARNING]                                                       ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(RichAlignmentRecord(read).samtoolsCigar.getReadLength === new_cigar.getReadLength)
[WARNING]                                ^
[WARNING] /tmp/adamTestNTWURib/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(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                       ^
[WARNING] /tmp/adamTestNTWURib/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(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                       ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:37: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.start == featureToConvert.start)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:38: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.end == featureToConvert.end)
[WARNING]                                                            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:39: warning: variable contigName in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.contigName == featureToConvert.contigName)
[WARNING]                                                                   ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:40: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.count == featureToConvert.score)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:194: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(read.mdTag.get.end === read.getEnd)
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:475: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:482: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:495: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:496: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read, withGaps = true) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:510: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar)
[WARNING]                                      ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:526: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:544: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "GGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:562: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:580: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala:726: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala:754: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala:785: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala:816: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala:847: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDSuite.scala:878: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala:267: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala:298: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala:329: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala:360: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala:391: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageRDDSuite.scala:422: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala:973: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala:1004: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala:1032: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala:1063: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala:1094: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureRDDSuite.scala:1125: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDSuite.scala:399: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDSuite.scala:430: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDSuite.scala:458: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDSuite.scala:489: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDSuite.scala:520: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDSuite.scala:551: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala:1383: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala:1405: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala:1436: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala:1464: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala:1495: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala:1526: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDSuite.scala:1557: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:82: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(TargetOrdering.contains(targets.head, read))
[WARNING]                                                  ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:190: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]         if (read.getStart < 105) {
[WARNING]             ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:193: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.start === read.getStart)
[WARNING]                                                   ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:194: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.end === read.getEnd)
[WARNING]                                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:195: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]           assert(check_indel(targets.head, read))
[WARNING]                                            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala:344: warning: variable contigName in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(vc.variant.variant.contigName === "1")
[WARNING]                               ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala:400: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala:431: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala:459: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala:490: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala:521: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeRDDSuite.scala:552: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantContextRDDSuite.scala:178: warning: variable start in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     val filtered = vcs.toGenotypes().rdd.filter(_.start == 66631043)
[WARNING]                                                   ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala:370: warning: variable contigName in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(vc.variant.variant.contigName === "1")
[WARNING]                               ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala:423: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala:454: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala:482: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala:513: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala:544: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantRDDSuite.scala:575: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:31: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithoutClipping.unclippedStart == 42L)
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:32: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithClipping.unclippedStart == 40L)
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:33: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithHardClipping.unclippedStart == 37L)
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:41: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithoutClipping.unclippedEnd == 20L)
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:42: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithClipping.unclippedEnd == 20L)
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:43: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithHardClipping.unclippedEnd == 20L)
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:49: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(rec.tags.size === 2)
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:50: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(rec.tags(0) === Attribute("XX", TagType.Integer, 3))
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:51: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(rec.tags(1) === Attribute("YY", TagType.String, "foo"))
[WARNING]            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentRecordSuite.scala:57: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val overlaps = unmappedRead.overlapsReferencePosition(ReferencePosition("chr1", 10))
[WARNING]                    ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:34: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:37: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar2.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                             ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:49: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:52: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar2.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                             ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:64: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:66: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                            ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:78: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:80: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                            ^
[WARNING] warning: there was one inliner warning; re-run with -Yinline-warnings for details
[WARNING] 90 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 45 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ adam-core-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ adam-core-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ adam-core-spark2_2.11 ---
Discovery starting.
Discovery completed in 1 second, 251 milliseconds.
Run starting. Expected test count is: 0
Run completed in 1 second, 261 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:3.0.1:jar (default-jar) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.25.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.25.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ adam-core-spark2_2.11 ---
[ERROR] Error fetching link: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/apidocs/package-list. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.adam.io...
Constructing Javadoc information...
Standard Doclet version 1.8.0_181
Building tree for all the packages and classes...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/constant-values.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-tree.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index-all.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.25.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark2_2.11 >>>
[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:1.12:add-source (add-source) @ adam-core-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestNTWURib/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 ---
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-core-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.12
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.spire-math:spire_2.11:0.11.0 requires scala version: 2.11.12
[WARNING]  org.spire-math:spire-macros_2.11:0.11.0 requires scala version: 2.11.12
[WARNING]  org.typelevel:machinist_2.11:0.4.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.7 requires scala version: 2.11.12
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.adam:adam-core-spark2_2.11:0.25.0-SNAPSHOT requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.12
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.12
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.spire-math:spire_2.11:0.11.0 requires scala version: 2.11.12
[WARNING]  org.spire-math:spire-macros_2.11:0.11.0 requires scala version: 2.11.12
[WARNING]  org.typelevel:machinist_2.11:0.4.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.7 requires scala version: 2.11.12
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.adam:adam-core-spark2_2.11:0.25.0-SNAPSHOT requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala:222: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala:782: warning: Octal escape literals are deprecated, use \u0001 instead.
      binaryCodec.writeBytes("BAM\001".getBytes())
                                 ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala:3101: warning: no valid targets for annotation on value uTag - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @getter)
  @transient val uTag: TypeTag[U]
   ^
warning: there were 5 feature warnings; re-run with -feature for details
model contains 271 documentable templates
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDD.scala:349: warning: Could not find any member to link for "UnsupportedOperationException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1337: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1366: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1386: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:73: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:176: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:450: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3070: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:405: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala:746: 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/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala:747: 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/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicRDD.scala:748: 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/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/RecordGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentError".
/**
^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:252: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:236: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:420: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:330: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
25 warnings found
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.25.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.0.1:test-jar (default) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.25.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: APIs for Java, Python 0.25.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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:1.12:add-source (add-source) @ adam-apis-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/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:3.0.1:resources (default-resources) @ adam-apis-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.adam:adam-apis-spark2_2.11:0.25.0-SNAPSHOT requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/classes at 1535580050799
[WARNING] warning: there were two feature warnings; re-run with -feature for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ adam-apis-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:add-test-source (add-test-source) @ adam-apis-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1: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 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.adam:adam-apis-spark2_2.11:0.25.0-SNAPSHOT requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/java:-1: info: compiling
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 8 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/test-classes at 1535580056574
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ adam-apis-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 7 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ adam-apis-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ adam-apis-spark2_2.11 ---
Discovery starting.
Discovery completed in 120 milliseconds.
Run starting. Expected test count is: 0
Run completed in 127 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:3.0.1:jar (default-jar) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.25.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.25.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark2_2.11 >>>
[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:1.12:add-source (add-source) @ adam-apis-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.adam:adam-apis-spark2_2.11:0.25.0-SNAPSHOT requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.adam:adam-apis-spark2_2.11:0.25.0-SNAPSHOT requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
warning: there were two feature warnings; re-run with -feature for details
model contains 124 documentable templates
one warning found
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.25.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.0.1:test-jar (default) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.25.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: CLI 0.25.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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] --- git-commit-id-plugin:2.2.1: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/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:add-source (add-source) @ adam-cli-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/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 30 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ adam-cli-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/classes at 1535580069932
[WARNING] warning: there was one deprecation warning; re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ adam-cli-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:add-test-source (add-test-source) @ adam-cli-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1: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 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 14 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/test-classes at 1535580078267
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ adam-cli-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ adam-cli-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ adam-cli-spark2_2.11 ---
Discovery starting.
Discovery completed in 136 milliseconds.
Run starting. Expected test count is: 0
Run completed in 142 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:3.0.1:jar (default-jar) @ adam-cli-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.25.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.25.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ adam-cli-spark2_2.11 ---
[ERROR] Error fetching link: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/apidocs/package-list. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.adam.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_181
Building tree for all the packages and classes...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/constant-values.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/overview-tree.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index-all.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index.html...
Generating /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.25.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark2_2.11 >>>
[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] --- git-commit-id-plugin:2.2.1: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/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:add-source (add-source) @ adam-cli-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark2_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.2.2 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-ast_2.11:3.2.11 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-core_2.11:3.2.11 requires scala version: 2.11.0
[WARNING] Multiple versions of scala libraries detected!
model contains 55 documentable templates
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.25.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Assembly 0.25.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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:2.2.1: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/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:add-source (add-source) @ adam-assembly-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/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:3.0.1:resources (default-resources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.11 ---
[INFO] /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/2.11.12/classes at 1535580097996
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ adam-assembly-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:add-test-source (add-test-source) @ adam-assembly-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestNTWURib/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:3.5.1:testCompile (default-testCompile) @ adam-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ adam-assembly-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.0.1:jar (default-jar) @ adam-assembly-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.25.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark2_2.11 >>>
[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:2.2.1: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/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.12:add-source (add-source) @ adam-assembly-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark2_2.11 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.25.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.4.3:shade (default) @ adam-assembly-spark2_2.11 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.25.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.9 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.25 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.11.3 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.1 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:2.7 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:0.25.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.hammerlab:genomic-loci_2.11:jar:1.4.4 in the shaded jar.
[INFO] Including org.hammerlab:args4s_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including org.hammerlab:iterator_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including org.spire-math:spire_2.11:jar:0.11.0 in the shaded jar.
[INFO] Including org.spire-math:spire-macros_2.11:jar:0.11.0 in the shaded jar.
[INFO] Including org.typelevel:machinist_2.11:jar:0.4.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.6.1 in the shaded jar.
[INFO] Including org.hammerlab:string-utils_2.11:jar:1.0.0 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:2.5 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.2 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.8.2 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.2 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.2 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:2.13.2 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:1.2.4 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:16.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.25.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.25.0-SNAPSHOT in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.1.0 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.1.0 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 com.google.inject.extensions:guice-multibindings:jar:4.1.0 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:3.0.1 in the shaded jar.
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.25.0-SNAPSHOT.jar with /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.25.0-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Python APIs 0.25.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-python-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-python-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-python-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ adam-python-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-python-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-python) @ adam-python-spark2_2.11 ---
pip install -e .
Obtaining file:///tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-python
Requirement already satisfied: pyspark>=1.6.0 in /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/spark-2.2.2-bin-hadoop2.7/python (from bdgenomics.adam==0.24.0a0) (2.2.2)
Collecting py4j==0.10.7 (from pyspark>=1.6.0->bdgenomics.adam==0.24.0a0)
  Using cached https://files.pythonhosted.org/packages/e3/53/c737818eb9a7dc32a7cd4f1396e787bd94200c3997c72c1dbe028587bd76/py4j-0.10.7-py2.py3-none-any.whl
distributed 1.21.8 requires msgpack, which is not installed.
grin 1.2.1 requires argparse>=1.1, which is not installed.
Installing collected packages: bdgenomics.adam, py4j
  Running setup.py develop for bdgenomics.adam
Successfully installed bdgenomics.adam py4j-0.10.7
You are using pip version 10.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
python2.7 setup.py bdist_egg
Could not import pypandoc - required to package bdgenomics.adam
running bdist_egg
running egg_info
writing requirements to bdgenomics.adam.egg-info/requires.txt
writing bdgenomics.adam.egg-info/PKG-INFO
writing top-level names to bdgenomics.adam.egg-info/top_level.txt
writing dependency_links to bdgenomics.adam.egg-info/dependency_links.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/rdd.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/find_adam_home.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/models.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/stringency.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/__init__.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/adamContext.py -> build/lib/bdgenomics/adam
creating build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/variantRdd_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/genotypeRdd_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/adamContext_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/__init__.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/featureRdd_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/alignmentRecordRdd_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/coverageRdd_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
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/rdd.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/bin
copying build/lib/bdgenomics/adam/bin/adam-shell -> 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/pyadam -> 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/find-adam-home -> 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/find-spark.sh -> 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
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/stringency.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/adamContext.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/variantRdd_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/genotypeRdd_test.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/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/featureRdd_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/alignmentRecordRdd_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/coverageRdd_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/rdd.py to rdd.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/find_adam_home.py to find_adam_home.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/models.py to models.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/stringency.py to stringency.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/adamContext.py to adamContext.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/variantRdd_test.py to variantRdd_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/genotypeRdd_test.py to genotypeRdd_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/adamContext_test.py to adamContext_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/featureRdd_test.py to featureRdd_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/alignmentRecordRdd_test.py to alignmentRecordRdd_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/coverageRdd_test.py to coverageRdd_test.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-2.7
copying deps/bin/adam-shell -> build/scripts-2.7
copying deps/bin/adam-submit -> build/scripts-2.7
copying deps/bin/pyadam -> build/scripts-2.7
copying deps/bin/adamR -> build/scripts-2.7
copying deps/bin/find-adam-home -> build/scripts-2.7
copying deps/bin/find-adam-assembly.sh -> build/scripts-2.7
copying deps/bin/find-spark.sh -> build/scripts-2.7
copying deps/bin/find-adam-egg.sh -> build/scripts-2.7
copying and adjusting bdgenomics/adam/find_adam_home.py -> build/scripts-2.7
changing mode of build/scripts-2.7/find_adam_home.py from 664 to 775
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/adam-shell -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/adam-submit -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/pyadam -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find_adam_home.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/adamR -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-adam-home -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-spark.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
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/adam-submit 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.py 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 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/find-spark.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-egg.sh 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.__init__: module references __path__
bdgenomics.adam.find_adam_home: module references __file__
creating dist
creating 'dist/bdgenomics.adam-0.24.0a0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
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mkdir -p target
python2.7 -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux2 -- Python 2.7.15, pytest-3.5.1, py-1.5.3, pluggy-0.6.0 -- /home/jenkins/anaconda2/envs/adam-build-edbb3730-e630-48ea-99e4-38bd582fa7e7/bin/python2.7
cachedir: .pytest_cache
rootdir: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-python, inifile:
collecting ... collected 60 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_contig_fragments PASSED [  5%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_coverage PASSED [  6%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_genotypes PASSED [  8%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_gtf PASSED [ 10%]
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 [ 13%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_narrowPeak PASSED [ 15%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_variants PASSED [ 16%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_broadcast_inner_join PASSED [ 18%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_broadcast_right_outer_join PASSED [ 20%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_caching PASSED [ 21%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_count_kmers PASSED [ 23%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_filterByOverlappingRegion PASSED [ 25%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_filterByOverlappingRegions PASSED [ 26%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_load_indexed_bam PASSED [ 28%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_persisting PASSED [ 30%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_pipe_as_sam PASSED [ 31%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_save_as_bam PASSED [ 33%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_save_sorted_sam PASSED [ 35%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_save_unordered_sam PASSED [ 36%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_shuffle_full_outer_join PASSED [ 38%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_shuffle_inner_join PASSED [ 40%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_shuffle_inner_join_groupBy_left PASSED [ 41%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_shuffle_left_outer_join PASSED [ 43%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_shuffle_right_outer_join PASSED [ 45%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_shuffle_right_outer_join_groupBy_left PASSED [ 46%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_to_coverage PASSED [ 48%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_to_fragments PASSED [ 50%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_transform PASSED [ 51%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_transmute_to_coverage PASSED [ 53%]
bdgenomics/adam/test/alignmentRecordRdd_test.py::AlignmentRecordRDDTest::test_union PASSED [ 55%]
bdgenomics/adam/test/coverageRdd_test.py::CoverageRDDTest::test_aggregatedCoverage PASSED [ 56%]
bdgenomics/adam/test/coverageRdd_test.py::CoverageRDDTest::test_collapse PASSED [ 58%]
bdgenomics/adam/test/coverageRdd_test.py::CoverageRDDTest::test_flatten PASSED [ 60%]
bdgenomics/adam/test/coverageRdd_test.py::CoverageRDDTest::test_save PASSED [ 61%]
bdgenomics/adam/test/coverageRdd_test.py::CoverageRDDTest::test_toFeatures PASSED [ 63%]
bdgenomics/adam/test/featureRdd_test.py::FeatureRDDTest::test_round_trip_bed PASSED [ 65%]
bdgenomics/adam/test/featureRdd_test.py::FeatureRDDTest::test_round_trip_gtf PASSED [ 66%]
bdgenomics/adam/test/featureRdd_test.py::FeatureRDDTest::test_round_trip_interval_list PASSED [ 68%]
bdgenomics/adam/test/featureRdd_test.py::FeatureRDDTest::test_round_trip_narrowPeak PASSED [ 70%]
bdgenomics/adam/test/featureRdd_test.py::FeatureRDDTest::test_transform PASSED [ 71%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_to_variants PASSED [ 73%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_transform PASSED [ 75%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_filter PASSED [ 76%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_format_all_array PASSED [ 78%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_format_alts_array PASSED [ 80%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_format_array PASSED [ 81%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_format_genotype_array PASSED [ 83%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_format_scalar PASSED [ 85%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_info_all_array PASSED [ 86%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_info_alts_array PASSED [ 88%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_info_array PASSED [ 90%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_add_info_scalar PASSED [ 91%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_round_trip PASSED [ 93%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_sort PASSED [ 95%]
bdgenomics/adam/test/genotypeRdd_test.py::GenotypeRDDTest::test_vcf_sort_lex PASSED [ 96%]
bdgenomics/adam/test/variantRdd_test.py::VariantRDDTest::test_transform PASSED [ 98%]
bdgenomics/adam/test/variantRdd_test.py::VariantRDDTest::test_vcf_round_trip PASSED [100%]

 generated xml file: /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml 
========================== 60 passed in 79.84 seconds ==========================
[INFO] 
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[INFO]                                                                         
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[INFO] Building ADAM_2.11: R APIs 0.25.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
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R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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()
Updating bdgenomics.adam documentation
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

Updating roxygen version in  /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdgenomics.adam/DESCRIPTION 
Writing ADAMContext.Rd
Writing GenomicDataset.Rd
Writing AlignmentRecordRDD.Rd
Writing CoverageRDD.Rd
Writing FragmentRDD.Rd
Writing toVariantContexts.Rd
Writing toVariants.Rd
Writing NucleotideContigFragmentRDD.Rd
Writing VariantContextRDD.Rd
Writing createADAMContext.Rd
Writing loadAlignments-ADAMContext-character-method.Rd
Writing loadContigFragments-ADAMContext-character-method.Rd
Writing loadFragments-ADAMContext-character-method.Rd
Writing loadFeatures-ADAMContext-character-method.Rd
Writing loadCoverage-ADAMContext-character-method.Rd
Writing loadGenotypes-ADAMContext-character-method.Rd
Writing loadVariants-ADAMContext-character-method.Rd
Writing FeatureRDD.Rd
Writing GenotypeRDD.Rd
Writing VariantRDD.Rd
Writing pipe-GenomicDataset-ANY-character-character-character-method.Rd
Writing cache-GenomicDataset-method.Rd
Writing persist-GenomicDataset-character-method.Rd
Writing unpersist-GenomicDataset-method.Rd
Writing sort-GenomicDataset-method.Rd
Writing sortLexicographically-GenomicDataset-method.Rd
Writing toDF-GenomicDataset-method.Rd
Writing transform-GenomicDataset-function-method.Rd
Writing transmute-GenomicDataset-function-character-method.Rd
Writing broadcastRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterBroadcastRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing broadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
Writing shuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing leftOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing leftOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing fullOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing shuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing toFragments-AlignmentRecordRDD-method.Rd
Writing saveAsSam-AlignmentRecordRDD-character-method.Rd
Writing toCoverage-AlignmentRecordRDD-method.Rd
Writing save-AlignmentRecordRDD-character-method.Rd
Writing countKmers-AlignmentRecordRDD-numeric-method.Rd
Writing sortReadsByReferencePosition-AlignmentRecordRDD-method.Rd
Writing sortReadsByReferencePositionAndIndex-AlignmentRecordRDD-method.Rd
Writing markDuplicates-AlignmentRecordRDD-method.Rd
Writing recalibrateBaseQualities-AlignmentRecordRDD-VariantRDD-character-method.Rd
Writing realignIndels-AlignmentRecordRDD-method.Rd
Writing save-CoverageRDD-character-method.Rd
Writing collapse-CoverageRDD-method.Rd
Writing toFeatures-CoverageRDD-method.Rd
Writing coverage-CoverageRDD-method.Rd
Writing flatten-CoverageRDD-method.Rd
Writing save-FeatureRDD-character-method.Rd
Writing toCoverage-FeatureRDD-method.Rd
Writing toReads-FragmentRDD-method.Rd
Writing markDuplicates-FragmentRDD-method.Rd
Writing save-FragmentRDD-character-method.Rd
Writing saveAsParquet-GenotypeRDD-character-method.Rd
Writing toVariants-GenotypeRDD-method.Rd
Writing toVariantContexts-GenotypeRDD-method.Rd
Writing save-NucleotideContigFragmentRDD-character-method.Rd
Writing flankAdjacentFragments-NucleotideContigFragmentRDD-numeric-method.Rd
Writing saveAsParquet-VariantRDD-character-method.Rd
Writing toVariantContexts-VariantRDD-method.Rd
Writing saveAsVcf-VariantContextRDD-character-method.Rd
> 
> 
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-r) @ adam-r-spark2_2.11 ---
* checking for file ‘bdgenomics.adam/DESCRIPTION’ ... OK
* preparing ‘bdgenomics.adam’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘bdgenomics.adam_0.24.0.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘bdgenomics.adam/man/rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd’
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘bdgenomics.adam/man/rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd’

[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ adam-r-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-r/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-r-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-r) @ adam-r-spark2_2.11 ---
* using log directory ‘/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdgenomics.adam.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘bdgenomics.adam/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bdgenomics.adam’ version ‘0.24.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  bdgenomics.adam/man/rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
  bdgenomics.adam/man/rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bdgenomics.adam’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by ‘R CMD build’.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Duplicated \argument entries in documentation object 'GenomicDataset':
  ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’
  ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’
  ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’ ‘genomicRdd’ ‘...’

Undocumented arguments in documentation object 'toVariants,GenotypeRDD-method'
  ‘ardd’

Undocumented arguments in documentation object 'toVariants'
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE

Status: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
  ‘/tmp/adamTestNTWURib/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdgenomics.adam.Rcheck/00check.log’
for details.

[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:134)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
	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:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [ 12.672 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [ 11.230 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [02:10 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 18.115 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 28.444 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 12.141 s]
[INFO] ADAM_2.11: Python APIs ............................. SUCCESS [01:26 min]
[INFO] ADAM_2.11: R APIs .................................. FAILURE [01:19 min]
[INFO] ADAM_2.11: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 06:20 min
[INFO] Finished at: 2018-08-29T15:04:35-07:00
[INFO] Final Memory: 99M/1433M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (test-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 <goals> -rf :adam-r-spark2_2.11
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
Finished: FAILURE