Console Output

Skipping 1,038 KB.. Full Log
++ [[ '' == */* ]]
++ export CONDA_DEFAULT_ENV=adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee
++ CONDA_DEFAULT_ENV=adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee
++ firstpath=/home/jenkins/anaconda2/envs/adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee/bin
echo ${firstpath} | sed "s|/bin$||"
+++ echo /home/jenkins/anaconda2/envs/adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee
"$_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-0b9e1823-e18c-406d-85a3-98e7b74543ee) '
++ PS1='(adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee) '
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee/etc/conda/activate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee/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/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu
+ make prepare
pip install pytest==3.9.1
Collecting pytest==3.9.1
  Using cached pytest-3.9.1-py2.py3-none-any.whl (213 kB)
Collecting six>=1.10.0
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting py>=1.5.0
  Using cached py-1.9.0-py2.py3-none-any.whl (99 kB)
Collecting atomicwrites>=1.0
  Using cached atomicwrites-1.4.0-py2.py3-none-any.whl (6.8 kB)
Collecting more-itertools>=4.0.0
  Using cached more_itertools-8.4.0-py3-none-any.whl (43 kB)
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee/lib/python3.6/site-packages (from pytest==3.9.1) (47.3.1.post20200622)
Collecting attrs>=17.4.0
  Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Collecting pluggy>=0.7
  Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting importlib-metadata>=0.12; python_version < "3.8"
  Using cached importlib_metadata-1.6.1-py2.py3-none-any.whl (31 kB)
Collecting zipp>=0.5
  Using cached zipp-3.1.0-py3-none-any.whl (4.9 kB)
Installing collected packages: six, py, atomicwrites, more-itertools, attrs, zipp, importlib-metadata, pluggy, pytest
Successfully installed atomicwrites-1.4.0 attrs-19.3.0 importlib-metadata-1.6.1 more-itertools-8.4.0 pluggy-0.13.1 py-1.9.0 pytest-3.9.1 six-1.15.0 zipp-3.1.0
+ popd
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.0/label/ubuntu
+ export R_LIBS_USER=/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/local_R_libs
+ R_LIBS_USER=/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/local_R_libs
+ mkdir -p /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/local_R_libs
+ R CMD INSTALL -l /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/local_R_libs /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/R/lib/SparkR/
* installing *binary* package ‘SparkR’ ...
* DONE (SparkR)
+ export 'SPARKR_SUBMIT_ARGS=--jars /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar sparkr-shell'
+ SPARKR_SUBMIT_ARGS='--jars /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-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_2.12                                                          [pom]
[INFO] ADAM_2.12: Shader workaround                                       [jar]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils                           [jar]
[INFO] ADAM_2.12: Core                                                    [jar]
[INFO] ADAM_2.12: APIs for Java, Python                                   [jar]
[INFO] ADAM_2.12: CLI                                                     [jar]
[INFO] ADAM_2.12: Assembly                                                [jar]
[INFO] ADAM_2.12: Python APIs                                             [jar]
[INFO] ADAM_2.12: R APIs                                                  [jar]
[INFO] ADAM_2.12: Distribution                                            [pom]
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-parent-spark2_2.12 >-------------
[INFO] Building ADAM_2.12 0.32.0-SNAPSHOT                                [1/10]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.12 ---
[INFO] Modified 129 of 439 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-parent-spark2_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-parent-spark2_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-parent-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-parent-spark2_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark2_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-shade-spark2_2.12 >-------------
[INFO] Building ADAM_2.12: Shader workaround 0.32.0-SNAPSHOT             [2/10]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.12 ---
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/java:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.12.8/classes at 1593147998230
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.12.8/classes
[INFO] 
[INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.12 ---
[INFO] Discovered 1 component descriptors(s)
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.12 ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-shade-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.12-0.32.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.12-0.32.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-shade-spark2_2.12 ---
[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/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-frame.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-summary.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-tree.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/constant-values.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/class-use/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/overview-tree.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index-all.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-shade-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-shade-spark2_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark2_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-codegen-spark2_2.12 >------------
[INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.32.0-SNAPSHOT [3/10]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.12 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.12 ---
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/2.12.8/classes at 1593148010961
[WARNING] warning: there were 5 deprecation warnings (since 2.12.0); re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.12 ---
[INFO] Test Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.12 ---
Discovery starting.
Discovery completed in 62 milliseconds.
Run starting. Expected test count is: 0
Run completed in 68 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-codegen-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.32.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.32.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-codegen-spark2_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark2_2.12 ---
model contains 11 documentable templates
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-core-spark2_2.12 >--------------
[INFO] Building ADAM_2.12: Core 0.32.0-SNAPSHOT                          [4/10]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestQTMDdWT/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_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.12 ---
[INFO] Modified 2 of 204 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.12 ---
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java:-1: info: compiling
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala:-1: info: compiling
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 140 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/classes at 1593148031524
[WARNING] warning: there were 21 deprecation warnings
[WARNING] warning: there were 31 deprecation warnings (since 0.21.0)
[WARNING] warning: there was one deprecation warning (since 1.0.6)
[WARNING] warning: there was one deprecation warning (since 2.11.0)
[WARNING] warning: there were 175 deprecation warnings (since 2.12.0)
[WARNING] warning: there was one deprecation warning (since 2.12.7)
[WARNING] warning: there were 230 deprecation warnings in total; re-run with -deprecation for details
[WARNING] warning: there were 5 feature warnings; re-run with -feature for details
[WARNING] 8 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 35 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 6 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.12 ---
[INFO] Test Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 152 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.12 ---
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala:-1: info: compiling
[INFO] Compiling 70 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/test-classes at 1593148069537
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]       .build()
[WARNING]             ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val new_cigar = NormalizationUtils.leftAlignIndel(read)
[WARNING]                                                       ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(RichAlignment(read).samtoolsCigar.getReadLength === new_cigar.getReadLength)
[WARNING]                          ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:171: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val newSAMRecord = newSAMReader.iterator().dropWhile(r => r.getReadName != readName)
[WARNING]                                             ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:274: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:311: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala:335: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val fragment = Fragment.newBuilder().setAlignments(List(record)).build()
[WARNING]                                                            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:54: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:89: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       val samIter = asScalaIterator(newSAMReader.iterator())
[WARNING]                     ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in class SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path)))
[WARNING]                                                       ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:63: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                  ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:69: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("T"), Allele.create("G")))
[WARNING]                  ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:75: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<NON_REF>", false)))
[WARNING]                  ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     .alleles(List(Allele.create("A", true), Allele.create("<CN0>", false)))
[WARNING]                  ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .alleles(List(Allele.create("A", true), Allele.create("T")))
[WARNING]                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:143: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       GenotypeBuilder.create("NA12878", vcb.getAlleles(), genotypeAttributes))
[WARNING]                                                           ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:154: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.ALT)))
[WARNING]                   ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:184: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamVariant.variant.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                  ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:219: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       assert(adamGT.getVariantCallingAnnotations.getFiltersFailed.sameElements(List("LowMQ")))
[WARNING]                                                  ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:234: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(htsjdkVC.getAlternateAlleles.sameElements(List(Allele.create("T"))))
[WARNING]                     ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:245: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2, 4, 6).map(i => i: java.lang.Integer))
[WARNING]                                                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:246: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:279: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:280: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:298: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setStrandBiasComponents(List(0, 2).map(i => i: java.lang.Integer))
[WARNING]                                              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:299: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
[WARNING]                       ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:320: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     for ((allele, idx) <- vc.getAlternateAlleles.zipWithIndex) {
[WARNING]                              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:328: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("T"), Allele.create("G")))
[WARNING]                                                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:347: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT)))
[WARNING]                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:349: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT1.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:354: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT)))
[WARNING]                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:356: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT2.getGenotypeLikelihoods
[WARNING]                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:380: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val gb = new GenotypeBuilder("NA12878", List(Allele.create("A", true), Allele.create("A", true)))
[WARNING]                                                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:393: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.REF)))
[WARNING]                   ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:396: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(adamGT.getNonReferenceLikelihoods
[WARNING]                   ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:421: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 1)
[WARNING]                            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:433: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(variant.variant.getNames.length === 2)
[WARNING]                            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:543: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       genotypeAttributes)))((bldr, fn) => {
[WARNING]       ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:693: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(0) < -0.99e-1 && gls(0) > -1.1e-1)
[WARNING]                                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:694: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(1) < -0.99e-3 && gls(1) > -1.1e-3)
[WARNING]                                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:695: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(gls(2) < -0.99e-6 && gls(2) > -1.1e-6)
[WARNING]                                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:714: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(0) === 10)
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:715: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(1) === 12)
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:716: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(2) === 14)
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:717: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(sb(3) === 16)
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:762: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER")
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:776: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(0) === "FAILED_FILTER1")
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:777: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(1) === "FAILED_FILTER2")
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:778: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(failedFilters(2) === "FAILED_FILTER3")
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:930: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(d => d: java.lang.Double))
[WARNING]             ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:954: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]           .map(i => i: java.lang.Integer))
[WARNING]               ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:962: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         .map(i => i: java.lang.Integer))
[WARNING]             ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1089: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq"))
[WARNING]                            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("lowmq", "lowdp"))
[WARNING]                            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1195: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 1)
[WARNING]              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1205: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     assert(v.getNames.length === 2)
[WARNING]              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1262: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]         vcb.filters(Set("FAILED1", "FAILED2", "FAILED3"))
[WARNING]                        ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1267: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val failedSet = v.getFiltersFailed.toSet
[WARNING]                       ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1285: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name"))
[WARNING]                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1295: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setNames(Seq("name1", "name2"))
[WARNING]                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1364: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED"))
[WARNING]                            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1378: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setFiltersFailed(Seq("FAILED1", "FAILED2"))
[WARNING]                            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1493: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10).map(i => i: java.lang.Integer)
[WARNING]              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1501: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                      ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1516: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f).map(i => i: java.lang.Float)
[WARNING]                ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1523: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("+Inf")
[WARNING]                                              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1530: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("-Inf")
[WARNING]                                              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1538: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       0.1f, 0.01f, 0.001f).map(i => i: java.lang.Float)
[WARNING]                               ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1552: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M")
[WARNING]                                              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1559: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]     val acList: java.util.List[String] = List("10D90M", "100M", "90M10D")
[WARNING]                                              ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1575: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1584: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1601: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1610: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1627: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10).map(i => i: java.lang.Integer)
[WARNING]                 ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:1636: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       5, 10, 13, 16).map(i => i: java.lang.Integer)
[WARNING]                         ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2436: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("ONE_INT", "42")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2459: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_INTS", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2482: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("FOUR_FLOATS", "5.0,10.1,15.2,20.3")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2505: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("A_INT", "10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2528: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_INT", "5,10,15,20")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2551: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("R_STRING", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:2574: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       Map[String, java.lang.Object](("STRING_G", "foo,bar,baz")))
[WARNING]                                    ^
[WARNING] /tmp/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:194: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(read.mdTag.get.end === read.getEnd)
[WARNING]            ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:475: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:482: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:495: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:496: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read, withGaps = true) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:510: warning: method recordToRichRecord in object RichAlignment is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar)
[WARNING]                                      ^
[WARNING] 168 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 48 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.12 ---
Discovery starting.
Discovery completed in 1 second, 510 milliseconds.
Run starting. Expected test count is: 0
Run completed in 1 second, 523 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-core-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.32.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.32.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark2_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestQTMDdWT/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/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-frame.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/constant-values.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-tree.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index-all.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-summary.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/help-doc.html...
6 warnings
[WARNING] Javadoc Warnings
[WARNING] /tmp/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/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/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestQTMDdWT/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_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.12 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-core-spark2_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark2_2.12 ---
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverters.scala:274: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentDataset.scala:840: warning: Octal escape literals are deprecated, use \u0001 instead.
      binaryCodec.writeBytes("BAM\001".getBytes())
                                 ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment
    /**
    ^
warning: there were 5 feature warnings; re-run with -feature for details
model contains 283 documentable templates
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException".
/**
^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:747: warning: Variable x undefined in comment for method pipe in trait GenomicDataset
   * Files are substituted in to the command with a $x syntax. E.g., to invoke
                                                     ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:748: warning: Variable 0 undefined in comment for method pipe in trait GenomicDataset
   * a command that uses the first file from the files Seq, use $0. To access
                                                                 ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:749: warning: Variable root undefined in comment for method pipe in trait GenomicDataset
   * the path to the directory where the files are copied, use $root.
                                                                ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3464: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1859: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1839: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1810: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:474: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:444: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:429: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:354: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java/org/bdgenomics/adam/io/FastqRecordReader.java:377: warning: Could not find any member to link for "RuntimeException".
    /**
    ^
24 warnings found
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-core-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.32.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-apis-spark2_2.12 >--------------
[INFO] Building ADAM_2.12: APIs for Java, Python 0.32.0-SNAPSHOT         [5/10]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.12 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.12 ---
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/classes at 1593148187662
[WARNING] warning: there was one deprecation warning (since 2.12.0); re-run with -deprecation for details
[WARNING] warning: there were two feature warnings; re-run with -feature for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.12 ---
[INFO] Test Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.12 ---
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/java:-1: info: compiling
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 9 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/test-classes at 1593148196206
[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_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 8 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.12 ---
Discovery starting.
Discovery completed in 159 milliseconds.
Run starting. Expected test count is: 0
Run completed in 165 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-apis-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.32.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark2_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark2_2.12 ---
warning: there were two feature warnings; re-run with -feature for details
model contains 192 documentable templates
one warning found
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-apis-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.32.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] --------------< org.bdgenomics.adam:adam-cli-spark2_2.12 >--------------
[INFO] Building ADAM_2.12: CLI 0.32.0-SNAPSHOT                           [6/10]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestQTMDdWT/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_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.12 ---
[INFO] Modified 0 of 29 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.12 ---
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 18 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/classes at 1593148214953
[WARNING] warning: there was one deprecation warning
[WARNING] warning: there was one deprecation warning (since 2.12.0)
[WARNING] warning: there were two deprecation warnings in total; re-run with -deprecation for details
[WARNING] three warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.12 ---
[INFO] Test Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 15 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.12 ---
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 12 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/test-classes at 1593148223651
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.12 ---
Discovery starting.
Discovery completed in 134 milliseconds.
Run starting. Expected test count is: 0
Run completed in 142 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-cli-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.32.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.32.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark2_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestQTMDdWT/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/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/constant-values.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/overview-tree.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index-all.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index.html...
Generating /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.12 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestQTMDdWT/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_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark2_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark2_2.12 ---
model contains 55 documentable templates
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.32.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -----------< org.bdgenomics.adam:adam-assembly-spark2_2.12 >------------
[INFO] Building ADAM_2.12: Assembly 0.32.0-SNAPSHOT                      [7/10]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 ---
[INFO] Request to add '/tmp/adamTestQTMDdWT/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_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.12 ---
[INFO] /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/2.12.8/classes at 1593148241307
[INFO] prepare-compile in 0 s
[INFO] compile in 2 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.12 ---
[INFO] Test Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-assembly-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.12 ---
[INFO] Request to add '/tmp/adamTestQTMDdWT/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_2.12 ---
[INFO] Source directory: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark2_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark2_2.12 ---
model contains 6 documentable templates
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[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.12:jar:0.32.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.12:jar:0.3.0 in the shaded jar.
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[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.32.0-SNAPSHOT in the shaded jar.
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[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
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[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
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[WARNING] single version of the class is copied to the uber jar.
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[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/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT.jar with /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.32.0-SNAPSHOT-shaded.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-python-spark2_2.12 >-------------
[INFO] Building ADAM_2.12: Python APIs 0.32.0-SNAPSHOT                   [8/10]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
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[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-python-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-python) @ adam-python-spark2_2.12 ---
pip install -e .
Obtaining file:///tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-python
Requirement already satisfied: pyspark>=1.6.0 in /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python (from bdgenomics.adam==0.32.0a0) (3.0.0)
Collecting py4j==0.10.9
  Using cached py4j-0.10.9-py2.py3-none-any.whl (198 kB)
Installing collected packages: bdgenomics.adam, py4j
  Running setup.py develop for bdgenomics.adam
Successfully installed bdgenomics.adam py4j-0.10.9
python setup.py bdist_egg
running bdist_egg
running egg_info
writing bdgenomics.adam.egg-info/PKG-INFO
writing dependency_links to bdgenomics.adam.egg-info/dependency_links.txt
writing requirements to bdgenomics.adam.egg-info/requires.txt
writing top-level names to bdgenomics.adam.egg-info/top_level.txt
package init file 'deps/jars/__init__.py' not found (or not a regular file)
package init file 'deps/bin/__init__.py' not found (or not a regular file)
reading manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
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writing manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/adam
copying bdgenomics/adam/models.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/stringency.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/adamContext.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/find_adam_home.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/rdd.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/__init__.py -> build/lib/bdgenomics/adam
creating build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/genotypeDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/coverageDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/variantDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/alignmentDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/adamContext_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/featureDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/__init__.py -> build/lib/bdgenomics/adam/test
creating build/lib/bdgenomics/adam/jars
copying deps/jars/adam.jar -> build/lib/bdgenomics/adam/jars
creating build/lib/bdgenomics/adam/bin
copying deps/bin/adam-shell -> build/lib/bdgenomics/adam/bin
copying deps/bin/adam-submit -> build/lib/bdgenomics/adam/bin
copying deps/bin/adamR -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-assembly.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-egg.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-home -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-spark.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/pyadam -> build/lib/bdgenomics/adam/bin
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/models.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-shell -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-home -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/pyadam -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adamR -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-submit -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-spark.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/genotypeDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/coverageDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/variantDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/alignmentDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/adamContext_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/featureDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/stringency.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/jars/adam.jar -> build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/adamContext.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/find_adam_home.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/rdd.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/models.py to models.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/genotypeDataset_test.py to genotypeDataset_test.cpython-36.pyc
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byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/variantDataset_test.py to variantDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/alignmentDataset_test.py to alignmentDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/adamContext_test.py to adamContext_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/featureDataset_test.py to featureDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/stringency.py to stringency.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/adamContext.py to adamContext.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/find_adam_home.py to find_adam_home.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/rdd.py to rdd.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.cpython-36.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.6
copying deps/bin/adam-shell -> build/scripts-3.6
copying deps/bin/find-adam-home -> build/scripts-3.6
copying deps/bin/pyadam -> build/scripts-3.6
copying deps/bin/adamR -> build/scripts-3.6
copying deps/bin/find-adam-assembly.sh -> build/scripts-3.6
copying deps/bin/adam-submit -> build/scripts-3.6
copying deps/bin/find-spark.sh -> build/scripts-3.6
copying deps/bin/find-adam-egg.sh -> build/scripts-3.6
copying and adjusting bdgenomics/adam/find_adam_home.py -> build/scripts-3.6
changing mode of build/scripts-3.6/find_adam_home.py from 664 to 775
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adam-shell -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-home -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/pyadam -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adamR -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adam-submit -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-spark.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find_adam_home.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-shell to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-home to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pyadam to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adamR to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-assembly.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-submit to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-spark.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find_adam_home.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-egg.sh to 775
copying bdgenomics.adam.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
bdgenomics.__pycache__.__init__.cpython-36: module references __path__
bdgenomics.adam.__pycache__.find_adam_home.cpython-36: module references __file__
creating dist
creating 'dist/bdgenomics.adam-0.32.0a0-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-python-spark2_2.12 ---
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[INFO] 
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[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/test/resources
[INFO] 
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[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-python) @ adam-python-spark2_2.12 ---
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux -- Python 3.6.10, pytest-3.9.1, py-1.9.0, pluggy-0.13.1 -- /home/jenkins/anaconda2/envs/adam-build-0b9e1823-e18c-406d-85a3-98e7b74543ee/bin/python
cachedir: .pytest_cache
rootdir: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-python, inifile:
collecting ... collected 63 items

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

- generated xml file: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml -
=============================== warnings summary ===============================
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-python/bdgenomics/adam/test/alignmentDataset_test.py:143: DeprecationWarning: Please use assertEqual instead.
  self.assertEquals(readsAsCoverage.toDF().count(), 5)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-python/bdgenomics/adam/test/coverageDataset_test.py:59: DeprecationWarning: Please use assertEqual instead.
  self.assertEquals(features.toDF().count(), coverage.toDF().count())

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)
/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

/tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-bin-hadoop2.7/python/pyspark/sql/context.py:77: DeprecationWarning: Deprecated in 3.0.0. Use SparkSession.builder.getOrCreate() instead.
  DeprecationWarning)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
=================== 63 passed, 114 warnings in 83.21 seconds ===================
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-python-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-python-spark2_2.12 ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-python-spark2_2.12 ---
[WARNING] JAR will be empty - no content was marked for inclusion!
[INFO] Building jar: /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/adam-python-spark2_2.12-0.32.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-python-spark2_2.12 ---
[INFO] No sources in project. Archive not created.
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-python-spark2_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-python-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-python-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-python-spark2_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-python-spark2_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-python-spark2_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] ---------------< org.bdgenomics.adam:adam-r-spark2_2.12 >---------------
[INFO] Building ADAM_2.12: R APIs 0.32.0-SNAPSHOT                        [9/10]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-r-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-r-spark2_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-r-spark2_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-r-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestQTMDdWT/deleteMePleaseThisIsNoLongerNeeded/adam-r/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-r-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (doc-r) @ adam-r-spark2_2.12 ---

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

  Natural language support but running in an English locale

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

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

> library(devtools);devtools::document()
Updating bdgenomics.adam documentation
Loading bdgenomics.adam
Error in (function (dep_name, dep_ver = NA, dep_compare = NA)  : 
  Dependency package SparkR not available.
Calls: <Anonymous> -> load_all -> load_imports -> mapply -> <Anonymous>
Execution halted
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
    at org.apache.commons.exec.DefaultExecutor.executeInternal (DefaultExecutor.java:404)
    at org.apache.commons.exec.DefaultExecutor.execute (DefaultExecutor.java:166)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:764)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:711)
    at org.codehaus.mojo.exec.ExecMojo.execute (ExecMojo.java:289)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:957)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:289)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:193)
    at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:498)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.12 0.32.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [ 12.912 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [ 13.013 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 12.690 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [02:43 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 26.580 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 27.572 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 15.156 s]
[INFO] ADAM_2.12: Python APIs ............................. SUCCESS [01:27 min]
[INFO] ADAM_2.12: R APIs .................................. FAILURE [  1.021 s]
[INFO] ADAM_2.12: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  06:00 min
[INFO] Finished at: 2020-06-25T22:12:24-07:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (doc-r) on project adam-r-spark2_2.12: Command execution failed.: Process exited with an error: 1 (Exit value: 1) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :adam-r-spark2_2.12
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/fb3078ff8f7d92b795dd9a41e8e577497e27db9c
Finished: FAILURE