FailedConsole Output

Skipping 2,114 KB.. Full Log
ava/org/apache/spark/examples/streaming/JavaQueueStream.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaSqlNetworkWordCount.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaRecord.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaSparkSQLExample.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/hive/
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/hive/JavaSparkHiveExample.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaUserDefinedTypedAggregation.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaUserDefinedUntypedAggregation.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredKafkaWordCount.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredNetworkWordCount.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredNetworkWordCountWindowed.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredSessionization.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaSQLDataSourceExample.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaWordCount.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaLogQuery.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaPageRank.java
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/RSparkSQLExample.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/glm.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/als.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/kmeans.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/mlp.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/lda.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/ml.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/naiveBayes.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/kstest.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/gbt.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/survreg.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/svmLinear.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/bisectingKmeans.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/gaussianMixture.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/isoreg.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/randomForest.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/decisionTree.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/logit.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/ml/fpm.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/data-manipulation.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/streaming/
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/streaming/structured_network_wordcount.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/r/dataframe.R
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/people.csv
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/users.avro
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/employees.json
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/full_user.avsc
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/people.json
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/people.txt
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/kv1.txt
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/users.parquet
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/users.orc
spark-2.4.3-bin-hadoop2.7/examples/src/main/resources/user.avsc
spark-2.4.3-bin-hadoop2.7/NOTICE
spark-2.4.3-bin-hadoop2.7/data/
spark-2.4.3-bin-hadoop2.7/data/graphx/
spark-2.4.3-bin-hadoop2.7/data/graphx/users.txt
spark-2.4.3-bin-hadoop2.7/data/graphx/followers.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/
spark-2.4.3-bin-hadoop2.7/data/mllib/gmm_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/images/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/multi-channel/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/multi-channel/chr30.4.184.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/multi-channel/grayscale.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/multi-channel/BGRA_alpha_60.png
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/multi-channel/BGRA.png
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/kittens/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/kittens/DP153539.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/kittens/54893.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/kittens/not-image.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/kittens/DP802813.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/kittens/29.5.a_b_EGDP022204.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/origin/license.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/images/license.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=multichannel/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=multichannel/date=2018-02/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=multichannel/date=2018-02/chr30.4.184.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=multichannel/date=2018-02/grayscale.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=multichannel/date=2018-01/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=multichannel/date=2018-01/BGRA_alpha_60.png
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=multichannel/date=2018-01/BGRA.png
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=kittens/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=kittens/date=2018-02/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=kittens/date=2018-02/DP153539.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=kittens/date=2018-02/54893.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=kittens/date=2018-02/DP802813.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=kittens/date=2018-01/
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=kittens/date=2018-01/not-image.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/images/partitioned/cls=kittens/date=2018-01/29.5.a_b_EGDP022204.jpg
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_linear_regression_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_lda_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/kmeans_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_svm_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/streaming_kmeans_data_test.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_kmeans_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_multiclass_classification_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_fpgrowth.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/pic_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/pagerank_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_isotonic_regression_libsvm_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/als/
spark-2.4.3-bin-hadoop2.7/data/mllib/als/test.data
spark-2.4.3-bin-hadoop2.7/data/mllib/als/sample_movielens_ratings.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_lda_libsvm_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_binary_classification_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/ridge-data/
spark-2.4.3-bin-hadoop2.7/data/mllib/ridge-data/lpsa.data
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_movielens_data.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/iris_libsvm.txt
spark-2.4.3-bin-hadoop2.7/data/mllib/sample_libsvm_data.txt
spark-2.4.3-bin-hadoop2.7/data/streaming/
spark-2.4.3-bin-hadoop2.7/data/streaming/AFINN-111.txt
spark-2.4.3-bin-hadoop2.7/README.md
spark-2.4.3-bin-hadoop2.7/LICENSE
export SPARK_HOME=${ADAM_TMP_DIR}/${SPARK}-bin-${HADOOP}
+ export SPARK_HOME=/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7
+ SPARK_HOME=/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7
    
# set the path to the adam submit script
ADAM=./bin/adam-submit
+ ADAM=./bin/adam-submit

# test running adam-shell
./bin/adam-shell -i scripts/jenkins-test-adam-shell.scala
+ ./bin/adam-shell -i scripts/jenkins-test-adam-shell.scala
Using SPARK_SHELL=/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/bin/spark-shell
19/05/14 12:50:04 WARN Utils: Your hostname, amp-jenkins-staging-worker-02 resolves to a loopback address: 127.0.1.1; using 192.168.10.32 instead (on interface eno1)
19/05/14 12:50:04 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/05/14 12:50:04 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Spark context Web UI available at http://192.168.10.32:4040
Spark context available as 'sc' (master = local[*], app id = local-1557863411979).
Spark session available as 'spark'.
java.lang.NoSuchMethodError: scala.Predef$.refArrayOps([Ljava/lang/Object;)[Ljava/lang/Object;
  at org.bdgenomics.adam.rdd.ADAMContext.getFiles(ADAMContext.scala:1355)
  at org.bdgenomics.adam.rdd.ADAMContext.getFsAndFiles(ADAMContext.scala:1385)
  at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:1526)
  at scala.Option.fold(Option.scala:158)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1523)
  at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3282)
  at scala.Option.fold(Option.scala:158)
  at org.apache.spark.rdd.Timer.time(Timer.scala:48)
  at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3273)
  ... 65 elided
Welcome to
      ____              __
     / __/__  ___ _____/ /__
    _\ \/ _ \/ _ `/ __/  '_/
   /___/ .__/\_,_/_/ /_/\_\   version 2.4.3
      /_/
         
Using Scala version 2.11.12 (Java HotSpot(TM) 64-Bit Server VM, Java 1.8.0_191)
Type in expressions to have them evaluated.
Type :help for more information.

scala> :quit
    
# add pyspark to the python path
PY4J_ZIP="$(ls -1 "${SPARK_HOME}/python/lib" | grep py4j)"
ls -1 "${SPARK_HOME}/python/lib" | grep py4j
++ ls -1 /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/python/lib
++ grep py4j
+ PY4J_ZIP=py4j-0.10.7-src.zip
export PYTHONPATH=${SPARK_HOME}/python:${SPARK_HOME}/python/lib/${PY4J_ZIP}:${PYTHONPATH}
+ export PYTHONPATH=/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/python:/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip:
+ PYTHONPATH=/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/python:/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip:

# put adam jar on the pyspark path
ASSEMBLY_DIR="${ADAM_TMP_DIR}/adam-assembly/target"
+ ASSEMBLY_DIR=/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target
ASSEMBLY_JAR="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true
++ ls -1 /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target
++ grep '^adam[0-9A-Za-z\_\.-]*\.jar$'
++ grep -v javadoc
++ grep -v sources
+ ASSEMBLY_JAR=adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar
export PYSPARK_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} pyspark-shell"
+ export 'PYSPARK_SUBMIT_ARGS=--jars /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar --driver-class-path /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar pyspark-shell'
+ PYSPARK_SUBMIT_ARGS='--jars /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar --driver-class-path /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar pyspark-shell'

# create a conda environment for python build, if necessary
pythons=( 2.7 3.6 )
+ pythons=(2.7 3.6)

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

    # prepare adam python
    pushd adam-python
    make prepare
    popd
    	
    # make a directory to install SparkR into, and set the R user libs path
    export R_LIBS_USER=${SPARK_HOME}/local_R_libs
    mkdir -p ${R_LIBS_USER}
    R CMD INSTALL \
      -l ${R_LIBS_USER} \
      ${SPARK_HOME}/R/lib/SparkR/
    	    
    export SPARKR_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} sparkr-shell"
    	    
    # we can run the python build, now that we have a spark executable
    # -DskipTests appears to skip the python/r tests?
    mvn -U \
    	-P python,r,distribution \
    	package \
    	-Dsuites=select.no.suites\* \
    	-Dhadoop.version=${HADOOP_VERSION}

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

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

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

done
+ for python in '${pythons[*]}'
uuidgen
++ uuidgen
+ uuid=030b89b7-3a36-4150-8106-1e7708107c4a
+ conda create -y -q -n adam-build-030b89b7-3a36-4150-8106-1e7708107c4a python=2.7


Package plan for installation in environment /home/jenkins/anaconda2/envs/adam-build-030b89b7-3a36-4150-8106-1e7708107c4a:

The following NEW packages will be INSTALLED:

    ca-certificates: 2019.1.23-0            
    certifi:         2019.3.9-py27_0        
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       8.2.0-hdf63c60_1       
    libstdcxx-ng:    8.2.0-hdf63c60_1       
    ncurses:         6.1-he6710b0_1         
    openssl:         1.1.1b-h7b6447c_1      
    pip:             19.1.1-py27_0          
    python:          2.7.16-h9bab390_0      
    readline:        7.0-h7b6447c_5         
    setuptools:      41.0.1-py27_0          
    sqlite:          3.28.0-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.2-py27_0          
    zlib:            1.2.11-h7b6447c_3      


+ source activate adam-build-030b89b7-3a36-4150-8106-1e7708107c4a
#!/bin/bash

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

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

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

# Ensure that this script is sourced, not executed
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "activate" ]]; then
    (>&2 echo "Error: activate must be sourced. Run 'source activate envname'
instead of 'activate envname'.
")
    "$_CONDA_DIR/conda" ..activate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \a\c\t\i\v\a\t\e ]]

if [ "$#" -eq "0" ]; then
    args=('root')
else
    args=$@
fi
++ '[' 1 -eq 0 ']'
++ args=adam-build-030b89b7-3a36-4150-8106-1e7708107c4a

"$_CONDA_DIR/conda" ..checkenv $_SHELL$EXT "$args"
++ /home/anaconda/bin/conda ..checkenv bash adam-build-030b89b7-3a36-4150-8106-1e7708107c4a
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-030b89b7-3a36-4150-8106-1e7708107c4a
+++ case $key in
+++ shift
+++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
+++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
++++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu/scripts/jenkins-test
+++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
+++ [[ -z '' ]]
+++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
++++ basename /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/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-030b89b7-3a36-4150-8106-1e7708107c4a
++ _NEW_PART=/home/jenkins/anaconda2/envs/adam-build-030b89b7-3a36-4150-8106-1e7708107c4a/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-030b89b7-3a36-4150-8106-1e7708107c4a/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-030b89b7-3a36-4150-8106-1e7708107c4a/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-030b89b7-3a36-4150-8106-1e7708107c4a
++ CONDA_DEFAULT_ENV=adam-build-030b89b7-3a36-4150-8106-1e7708107c4a
++ firstpath=/home/jenkins/anaconda2/envs/adam-build-030b89b7-3a36-4150-8106-1e7708107c4a/bin
echo ${firstpath} | sed "s|/bin$||"
+++ echo /home/jenkins/anaconda2/envs/adam-build-030b89b7-3a36-4150-8106-1e7708107c4a/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/adam-build-030b89b7-3a36-4150-8106-1e7708107c4a
"$_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-030b89b7-3a36-4150-8106-1e7708107c4a) '
++ PS1='(adam-build-030b89b7-3a36-4150-8106-1e7708107c4a) '
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-030b89b7-3a36-4150-8106-1e7708107c4a/etc/conda/activate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-030b89b7-3a36-4150-8106-1e7708107c4a/etc/conda/activate.d ]]
++ unset _CONDA_PYTHON

unset CONDA_PATH
++ unset CONDA_PATH

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ pushd adam-python
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
+ make prepare
pip install pytest==3.9.1
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting pytest==3.9.1
  Using cached https://files.pythonhosted.org/packages/bf/14/a16e1ac03aeb9776d98374bb76495a6623d56dff0f7b815ed5a1e04d893e/pytest-3.9.1-py2.py3-none-any.whl
Collecting atomicwrites>=1.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/52/90/6155aa926f43f2b2a22b01be7241be3bfd1ceaf7d0b3267213e8127d41f4/atomicwrites-1.3.0-py2.py3-none-any.whl
Collecting more-itertools>=4.0.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/2f/9d/dcfe59e213093695f108508af1214cf9cd95cc5489e46877ec5cb56369e5/more_itertools-5.0.0-py2-none-any.whl
Collecting pluggy>=0.7 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/cc/e4/2003a5e4e445424602c8f06a436eeed9e78bcae4947128f64741c66c7216/pluggy-0.11.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/adam-build-030b89b7-3a36-4150-8106-1e7708107c4a/lib/python2.7/site-packages (from pytest==3.9.1) (41.0.1)
Collecting attrs>=17.4.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/23/96/d828354fa2dbdf216eaa7b7de0db692f12c234f7ef888cc14980ef40d1d2/attrs-19.1.0-py2.py3-none-any.whl
Collecting pathlib2>=2.2.0; python_version < "3.6" (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/2a/46/c696dcf1c7aad917b39b875acdc5451975e3a9b4890dca8329983201c97a/pathlib2-2.3.3-py2.py3-none-any.whl
Collecting py>=1.5.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/76/bc/394ad449851729244a97857ee14d7cba61ddb268dce3db538ba2f2ba1f0f/py-1.8.0-py2.py3-none-any.whl
Collecting six>=1.10.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting funcsigs; python_version < "3.0" (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting scandir; python_version < "3.5" (from pathlib2>=2.2.0; python_version < "3.6"->pytest==3.9.1)
Installing collected packages: atomicwrites, six, more-itertools, pluggy, attrs, scandir, pathlib2, py, funcsigs, pytest
Successfully installed atomicwrites-1.3.0 attrs-19.1.0 funcsigs-1.0.2 more-itertools-5.0.0 pathlib2-2.3.3 pluggy-0.11.0 py-1.8.0 pytest-3.9.1 scandir-1.10.0 six-1.12.0
+ popd
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
+ export R_LIBS_USER=/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/local_R_libs
+ R_LIBS_USER=/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/local_R_libs
+ mkdir -p /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/local_R_libs
+ R CMD INSTALL -l /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/local_R_libs /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-hadoop2.7/R/lib/SparkR/
* installing *binary* package ‘SparkR’ ...
* DONE (SparkR)
+ export 'SPARKR_SUBMIT_ARGS=--jars /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar --driver-class-path /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar sparkr-shell'
+ SPARKR_SUBMIT_ARGS='--jars /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar --driver-class-path /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar sparkr-shell'
+ mvn -U -P python,r,distribution package '-Dsuites=select.no.suites*' -Dhadoop.version=2.7.5
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ADAM_2.11
[INFO] ADAM_2.11: Shader workaround
[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 0.27.0-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 128 of 432 .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:3.1.0:jar (attach-javadoc) @ 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] --- 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: Shader workaround 0.27.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.11 ---
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/java:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.11.12/classes at 1557863439278
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.11.12/classes
[INFO] 
[INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.11 ---
[INFO] Discovered 1 component descriptors(s)
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.11 ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-shade-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.11-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-shade-spark2_2.11 ---
[INFO] 
Loading source files for package org.bdgenomics.adam.shade...
Constructing Javadoc information...
Standard Doclet version 1.8.0_191
Building tree for all the packages and classes...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-frame.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-summary.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-tree.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/constant-values.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/class-use/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/overview-tree.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index-all.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-shade-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-shade-spark2_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark2_2.11 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.27.0-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:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.11 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/2.11.12/classes at 1557863446024
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.11 ---
Discovery starting.
Discovery completed in 54 milliseconds.
Run starting. Expected test count is: 0
Run completed in 59 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:3.1.2:jar (default-jar) @ adam-codegen-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.27.0-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:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Core 0.27.0-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:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.11 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.11 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.11 ---
[INFO] Modified 2 of 199 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.11 ---
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java:-1: info: compiling
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala:-1: info: compiling
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 136 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/classes at 1557863462483
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3099: 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 84 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 30 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 6 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 150 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.11 ---
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala:-1: info: compiling
[INFO] Compiling 69 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/test-classes at 1557863495079
[WARNING] /tmp/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path)))
[WARNING]                                                       ^
[WARNING] /tmp/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:57: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.start == featureToConvert.start)
[WARNING]                                                              ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:58: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.end == featureToConvert.end)
[WARNING]                                                            ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:60: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.count == featureToConvert.score)
[WARNING]                                                              ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:61: warning: variable sampleId in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.optSampleId == Some(featureToConvert.sampleId))
[WARNING]                                                                         ^
[WARNING] /tmp/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:48: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
[WARNING]                                              ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:62: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
[WARNING]                                              ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:75: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
[WARNING]                                              ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:742: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:770: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:801: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:832: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:863: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDatasetSuite.scala:894: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:309: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:340: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:371: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:402: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:433: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala:464: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1022: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1053: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1081: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1112: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1143: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala:1174: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:400: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:431: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:459: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:490: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:521: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala:552: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1438: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1460: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1491: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1519: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1550: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1581: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDatasetSuite.scala:1613: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:83: 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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:191: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]         if (read.getStart < 105) {
[WARNING]             ^
[WARNING] /tmp/adamTest28NRbtO/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.start === read.getStart)
[WARNING]                                                   ^
[WARNING] /tmp/adamTest28NRbtO/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(targets.head.readRange.end === read.getEnd)
[WARNING]                                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:196: 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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:406: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:437: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:465: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:496: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:527: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:558: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:697: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:698: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                          ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:698: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:699: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation === null)
[WARNING]                          ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:699: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation === null)
[WARNING]                  ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:710: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:712: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                                     ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:712: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:714: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation === null)
[WARNING]                                     ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:714: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation === null)
[WARNING]                             ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:745: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:746: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                          ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:746: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable attributes in class VariantAnnotation is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                                     ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                          ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                  ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:758: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:759: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                                     ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:759: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable attributes in class VariantAnnotation is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                                                ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                                     ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                             ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantContextDatasetSuite.scala:181: 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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:422: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:453: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:481: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:512: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:543: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala:574: warning: method getOrCreate in object SQLContext is deprecated: Use SparkSession.builder instead
[WARNING]     val sqlContext = SQLContext.getOrCreate(sc)
[WARNING]                                 ^
[WARNING] /tmp/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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/adamTest28NRbtO/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] 115 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 35 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.11 ---
Discovery starting.
Discovery completed in 1 second, 323 milliseconds.
Run starting. Expected test count is: 0
Run completed in 1 second, 329 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:3.1.2:jar (default-jar) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark2_2.11 ---
[ERROR] Error fetching link: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.apache.parquet.avro...
Loading source files for package org.bdgenomics.adam.io...
Constructing Javadoc information...
Standard Doclet version 1.8.0_191
Building tree for all the packages and classes...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-frame.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/constant-values.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-tree.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index-all.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-summary.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/help-doc.html...
6 warnings
[WARNING] Javadoc Warnings
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @param for codec
[WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream,
[WARNING] ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @return
[WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream,
[WARNING] ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:235: warning: no @throws for java.io.IOException
[WARNING] protected final int positionAtFirstRecord(final FSDataInputStream stream,
[WARNING] ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:389: warning: no @throws for java.io.IOException
[WARNING] protected final boolean lowLevelFastqRead(final Text readName, final Text value)
[WARNING] ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:431: warning: no @throws for java.io.IOException
[WARNING] abstract protected boolean next(Text value) throws IOException;
[WARNING] ^
[WARNING] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:154: warning: no @throws for java.io.IOException
[WARNING] protected FastqRecordReader(final Configuration conf,
[WARNING] ^
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-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:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.11 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.11 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] <<< 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 ---
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala:230: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.scala:803: warning: Octal escape literals are deprecated, use \u0001 instead.
      binaryCodec.writeBytes("BAM\001".getBytes())
                                 ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3099: 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 276 documentable templates
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDataset.scala:365: warning: Could not find any member to link for "UnsupportedOperationException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1339: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1368: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1388: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:456: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3085: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:411: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:755: 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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:756: 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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:757: 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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException".
/**
^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:426: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:336: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
25 warnings found
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.27.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: APIs for Java, Python 0.27.0-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:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.11 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.11 ---
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/classes at 1557863569479
[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:3.8.0:compile (default-compile) @ adam-apis-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.11 ---
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/java:-1: info: compiling
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 8 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/test-classes at 1557863574907
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 7 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.11 ---
Discovery starting.
Discovery completed in 101 milliseconds.
Run starting. Expected test count is: 0
Run completed in 109 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:3.1.2:jar (default-jar) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.27.0-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:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/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: there were two feature warnings; re-run with -feature for details
model contains 124 documentable templates
one warning found
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.27.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: CLI 0.27.0-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] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/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 31 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.11 ---
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 18 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/classes at 1557863587619
[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:3.8.0:compile (default-compile) @ adam-cli-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 15 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.11 ---
[INFO] /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 14 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/test-classes at 1557863595953
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.11 ---
Discovery starting.
Discovery completed in 145 milliseconds.
Run starting. Expected test count is: 0
Run completed in 149 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:3.1.2:jar (default-jar) @ adam-cli-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark2_2.11 ---
[ERROR] Error fetching link: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.adam.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_191
Building tree for all the packages and classes...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/constant-values.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/overview-tree.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index-all.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index.html...
Generating /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.27.0-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] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/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 ---
model contains 55 documentable templates
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Assembly 0.27.0-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:2.2.2:revision (default) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 ---
[INFO] Request to add '/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/2.11.12/classes at 1557863613189
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-assembly-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ 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:2.2.2:revision (default) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 ---
[INFO] Request to add '/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTest28NRbtO/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/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark2_2.11 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
[INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 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:0.12.0 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 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:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.18.2 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:2.9.0 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.27.0-SNAPSHOT in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar with /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.11: Python APIs 0.27.0-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:3.1.0:resources (default-resources) @ adam-python-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTest28NRbtO/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 .
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Obtaining file:///tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-python
    ERROR: Complete output from command python setup.py egg_info:
    ERROR: Assembly jars exist for multiple Scala versions (['/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.27.0-SNAPSHOT.jar', '/tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.27.0-SNAPSHOT.jar']), please cleanup assembly/target
    ----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 255 in /tmp/adamTest28NRbtO/deleteMePleaseThisIsNoLongerNeeded/adam-python/
Makefile:62: recipe for target 'develop' failed
make: *** [develop] Error 1
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 2 (Exit value: 2)
	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 [  8.930 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  7.209 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  9.083 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:54 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 17.061 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 25.913 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 15.458 s]
[INFO] ADAM_2.11: Python APIs ............................. FAILURE [  0.736 s]
[INFO] ADAM_2.11: R APIs .................................. SKIPPED
[INFO] ADAM_2.11: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:19 min
[INFO] Finished at: 2019-05-14T12:53:48-07:00
[INFO] Final Memory: 100M/1464M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (dev-python) on project adam-python-spark2_2.11: Command execution failed. Process exited with an error: 2 (Exit value: 2) -> [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-python-spark2_2.11
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/26bf66931a4c4bfb5f49f27d5dc0967ca3493575
Finished: FAILURE