FailedConsole Output

Skipping 3,385 KB.. Full Log
 Using cached https://files.pythonhosted.org/packages/67/c6/4dbf5dfdbe1140cadf765c3896acc098578626c35721bc7d3eb35f6a8fc1/pathlib2-2.3.4-py2.py3-none-any.whl
Collecting py>=1.5.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/76/bc/394ad449851729244a97857ee14d7cba61ddb268dce3db538ba2f2ba1f0f/py-1.8.0-py2.py3-none-any.whl
Collecting six>=1.10.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl
Collecting funcsigs; python_version < "3.0" (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting importlib-metadata>=0.12 (from pluggy>=0.7->pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/bd/23/dce4879ec58acf3959580bfe769926ed8198727250c5e395e6785c764a02/importlib_metadata-0.18-py2.py3-none-any.whl
Collecting scandir; python_version < "3.5" (from pathlib2>=2.2.0; python_version < "3.6"->pytest==3.9.1)
Collecting configparser>=3.5; python_version < "3" (from importlib-metadata>=0.12->pluggy>=0.7->pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/ba/05/6c96328e92e625fc31445d24d75a2c92ef9ba34fc5b037fe69693c362a0d/configparser-3.7.4-py2.py3-none-any.whl
Collecting zipp>=0.5 (from importlib-metadata>=0.12->pluggy>=0.7->pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/a0/0f/9bf71d438d2e9d5fd0e4569ea4d1a2b6f5a524c234c6d221b494298bb4d1/zipp-0.5.1-py2.py3-none-any.whl
Collecting contextlib2; python_version < "3" (from importlib-metadata>=0.12->pluggy>=0.7->pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/a2/71/8273a7eeed0aff6a854237ab5453bc9aa67deb49df4832801c21f0ff3782/contextlib2-0.5.5-py2.py3-none-any.whl
Installing collected packages: atomicwrites, six, more-itertools, configparser, zipp, contextlib2, scandir, pathlib2, importlib-metadata, pluggy, attrs, py, funcsigs, pytest
Successfully installed atomicwrites-1.3.0 attrs-19.1.0 configparser-3.7.4 contextlib2-0.5.5 funcsigs-1.0.2 importlib-metadata-0.18 more-itertools-5.0.0 pathlib2-2.3.4 pluggy-0.12.0 py-1.8.0 pytest-3.9.1 scandir-1.10.0 six-1.12.0 zipp-0.5.1
+ popd
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.3/label/ubuntu
+ export R_LIBS_USER=/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/local_R_libs
+ R_LIBS_USER=/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/local_R_libs
+ mkdir -p /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/local_R_libs
+ R CMD INSTALL -l /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/local_R_libs /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/R/lib/SparkR/
* installing *binary* package ‘SparkR’ ...
* DONE (SparkR)
+ export 'SPARKR_SUBMIT_ARGS=--jars /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar sparkr-shell'
+ SPARKR_SUBMIT_ARGS='--jars /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-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
[INFO] ADAM_2.12: Shader workaround
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils
[INFO] ADAM_2.12: Core
[INFO] ADAM_2.12: APIs for Java, Python
[INFO] ADAM_2.12: CLI
[INFO] ADAM_2.12: Assembly
[INFO] ADAM_2.12: Python APIs
[INFO] ADAM_2.12: R APIs
[INFO] ADAM_2.12: Distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12 0.28.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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 128 of 433 .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] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark2_2.12 ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: Shader workaround 0.28.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/java:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.12.8/classes at 1561757221547
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestCejsCpr/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/adamTestCejsCpr/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:3.1.2:jar (default-jar) @ adam-shade-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.12-0.28.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.12-0.28.0-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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-frame.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-summary.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-tree.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/constant-values.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/class-use/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/overview-tree.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index-all.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.12-0.28.0-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] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark2_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.28.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/2.12.8/classes at 1561757228608
[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 4 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/adamTestCejsCpr/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/adamTestCejsCpr/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 68 milliseconds.
Run starting. Expected test count is: 0
Run completed in 74 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-codegen-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.28.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark2_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.28.0-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/adamTestCejsCpr/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] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark2_2.12 ---
model contains 11 documentable templates
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: Core 0.28.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestCejsCpr/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 202 .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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java:-1: info: compiling
[INFO] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala:-1: info: compiling
[INFO] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 138 source files to /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/classes at 1561757246101
[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 were 36 deprecation warnings (since 2.0.0)
[WARNING] warning: there was one deprecation warning (since 2.11.0)
[WARNING] warning: there were 173 deprecation warnings (since 2.12.0)
[WARNING] warning: there was one deprecation warning (since 2.12.7)
[WARNING] warning: there were 264 deprecation warnings in total; re-run with -deprecation for details
[WARNING] warning: there were 5 feature warnings; re-run with -feature for details
[WARNING] 9 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 25 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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala:-1: info: compiling
[INFO] Compiling 70 source files to /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.12.8/test-classes at 1561757273807
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]       .build()
[WARNING]             ^
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val new_cigar = NormalizationUtils.leftAlignIndel(read)
[WARNING]                                                       ^
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(RichAlignmentRecord(read).samtoolsCigar.getReadLength === new_cigar.getReadLength)
[WARNING]                                ^
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:274: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.scala:311: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters
[WARNING]       .setAlignments(seqAsJavaList(alignments))
[WARNING]                      ^
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentRecordConverterSuite.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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:54: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                       ^
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:89: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignmentRecord.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                       ^
[WARNING] /tmp/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:194: warning: method recordToRichRecord in object RichAlignmentRecord 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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:475: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:482: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:495: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:496: warning: method recordToRichRecord in object RichAlignmentRecord 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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:510: warning: method recordToRichRecord in object RichAlignmentRecord is deprecated (since 0.21.0): Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar)
[WARNING]                                      ^
[WARNING] 223 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 27 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 542 milliseconds.
Run starting. Expected test count is: 0
Run completed in 549 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-core-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.28.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.28.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark2_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-frame.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/constant-values.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-tree.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index-all.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-summary.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/help-doc.html...
6 warnings
[WARNING] Javadoc Warnings
[WARNING] /tmp/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.28.0-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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestCejsCpr/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] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark2_2.12 ---
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverters.scala:274: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordDataset.scala:837: warning: Octal escape literals are deprecated, use \u0001 instead.
      binaryCodec.writeBytes("BAM\001".getBytes())
                                 ^
/tmp/adamTestCejsCpr/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 289 documentable templates
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException".
/**
^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:755: warning: Variable x undefined in comment for method pipe in trait GenomicDataset
   * Files are substituted in to the command with a $x syntax. E.g., to invoke
                                                     ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:756: warning: Variable 0 undefined in comment for method pipe in trait GenomicDataset
   * a command that uses the first file from the files Seq, use $0. To access
                                                                 ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:757: warning: Variable root undefined in comment for method pipe in trait GenomicDataset
   * the path to the directory where the files are copied, use $root.
                                                                ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3472: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1864: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1844: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1815: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:474: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:444: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:429: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:354: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-core-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.12-0.28.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: APIs for Java, Python 0.28.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/classes at 1561757338086
[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 6 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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/java:-1: info: compiling
[INFO] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 9 source files to /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.12.8/test-classes at 1561757344305
[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/adamTestCejsCpr/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 154 milliseconds.
Run starting. Expected test count is: 0
Run completed in 162 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-apis-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.28.0-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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.28.0-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/adamTestCejsCpr/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] --- 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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:test-jar (default) @ adam-apis-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.12-0.28.0-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: CLI 0.28.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 18 source files to /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/classes at 1561757360120
[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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 12 source files to /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.12.8/test-classes at 1561757367934
[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 140 milliseconds.
Run starting. Expected test count is: 0
Run completed in 145 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ adam-cli-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.28.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.28.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark2_2.12 ---
[ERROR] Error fetching link: /tmp/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/constant-values.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/overview-tree.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index-all.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index.html...
Generating /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.28.0-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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestCejsCpr/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/adamTestCejsCpr/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] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark2_2.12 ---
model contains 55 documentable templates
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: Assembly 0.28.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/2.12.8/classes at 1561757386663
[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/adamTestCejsCpr/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/adamTestCejsCpr/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:3.1.2:jar (default-jar) @ adam-assembly-spark2_2.12 ---
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-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/adamTestCejsCpr/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/adamTestCejsCpr/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] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark2_2.12 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark2_2.12 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.12:jar:0.28.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.12:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.12:jar:0.2.15 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.12:jar:0.2.15 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
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[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.12:jar:0.2.15 in the shaded jar.
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[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.28.0-SNAPSHOT in the shaded jar.
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[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] 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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT.jar with /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.12-0.28.0-SNAPSHOT-shaded.jar
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[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: Python APIs 0.28.0-SNAPSHOT
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[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-python) @ adam-python-spark2_2.12 ---
pip install -e .
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Obtaining file:///tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-python
Collecting pyspark>=1.6.0 (from bdgenomics.adam==0.28.0a0)
Collecting py4j==0.10.7 (from pyspark>=1.6.0->bdgenomics.adam==0.28.0a0)
  Using cached https://files.pythonhosted.org/packages/e3/53/c737818eb9a7dc32a7cd4f1396e787bd94200c3997c72c1dbe028587bd76/py4j-0.10.7-py2.py3-none-any.whl
Installing collected packages: py4j, pyspark, bdgenomics.adam
  Running setup.py develop for bdgenomics.adam
Successfully installed bdgenomics.adam py4j-0.10.7 pyspark-2.4.3
python setup.py bdist_egg
Could not import pypandoc - required to package bdgenomics.adam
running bdist_egg
running egg_info
writing requirements to bdgenomics.adam.egg-info/requires.txt
writing bdgenomics.adam.egg-info/PKG-INFO
writing top-level names to bdgenomics.adam.egg-info/top_level.txt
writing dependency_links to bdgenomics.adam.egg-info/dependency_links.txt
package init file 'deps/jars/__init__.py' not found (or not a regular file)
package init file 'deps/bin/__init__.py' not found (or not a regular file)
reading manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
writing manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/adam
copying bdgenomics/adam/rdd.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/find_adam_home.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/models.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/stringency.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/__init__.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/adamContext.py -> build/lib/bdgenomics/adam
creating build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/variantDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/coverageDataset_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/genotypeDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/__init__.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/alignmentRecordDataset_test.py -> build/lib/bdgenomics/adam/test
creating build/lib/bdgenomics/adam/jars
copying deps/jars/adam.jar -> build/lib/bdgenomics/adam/jars
creating build/lib/bdgenomics/adam/bin
copying deps/bin/adam-shell -> build/lib/bdgenomics/adam/bin
copying deps/bin/adam-submit -> build/lib/bdgenomics/adam/bin
copying deps/bin/adamR -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-assembly.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-egg.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-home -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-spark.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/pyadam -> build/lib/bdgenomics/adam/bin
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/rdd.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/find_adam_home.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-shell -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-submit -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/pyadam -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adamR -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-home -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-spark.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/jars/adam.jar -> build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/models.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/stringency.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/adamContext.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/variantDataset_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/adamContext_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/featureDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/genotypeDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/alignmentRecordDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.pyc
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byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/models.py to models.pyc
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byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/adamContext.py to adamContext.pyc
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byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/featureDataset_test.py to featureDataset_test.pyc
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byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/alignmentRecordDataset_test.py to alignmentRecordDataset_test.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-2.7
copying deps/bin/adam-shell -> build/scripts-2.7
copying deps/bin/adam-submit -> build/scripts-2.7
copying deps/bin/pyadam -> build/scripts-2.7
copying deps/bin/adamR -> build/scripts-2.7
copying deps/bin/find-adam-home -> build/scripts-2.7
copying deps/bin/find-adam-assembly.sh -> build/scripts-2.7
copying deps/bin/find-spark.sh -> build/scripts-2.7
copying deps/bin/find-adam-egg.sh -> build/scripts-2.7
copying and adjusting bdgenomics/adam/find_adam_home.py -> build/scripts-2.7
changing mode of build/scripts-2.7/find_adam_home.py from 664 to 775
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/adam-shell -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/adam-submit -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/pyadam -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find_adam_home.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/adamR -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-adam-home -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-spark.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-shell to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-submit to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pyadam to 775
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changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adamR to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-home to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-assembly.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-spark.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-egg.sh to 775
copying bdgenomics.adam.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
bdgenomics.__init__: module references __path__
bdgenomics.adam.find_adam_home: module references __file__
creating dist
creating 'dist/bdgenomics.adam-0.28.0a0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
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[INFO] 
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[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 linux2 -- Python 2.7.16, pytest-3.9.1, py-1.8.0, pluggy-0.12.0 -- /home/jenkins/anaconda2/envs/adam-build-fbc3dd9e-5b0d-4934-a7dc-7cc182148c66/bin/python
cachedir: .pytest_cache
rootdir: /tmp/adamTestCejsCpr/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/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_broadcast_inner_join PASSED [ 19%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_broadcast_right_outer_join PASSED [ 20%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_caching PASSED [ 22%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_count_kmers PASSED [ 23%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_filterByOverlappingRegion PASSED [ 25%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_filterByOverlappingRegions PASSED [ 26%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_load_indexed_bam PASSED [ 28%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_persisting PASSED [ 30%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_pipe_as_sam PASSED [ 31%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_realignIndels_known_indels PASSED [ 33%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_realignIndels_reads PASSED [ 34%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_save_as_bam PASSED [ 36%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_save_sorted_sam PASSED [ 38%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_save_unordered_sam PASSED [ 39%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_full_outer_join PASSED [ 41%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_inner_join PASSED [ 42%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_inner_join_groupBy_left PASSED [ 44%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_left_outer_join PASSED [ 46%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_right_outer_join PASSED [ 47%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_shuffle_right_outer_join_groupBy_left PASSED [ 49%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_to_coverage PASSED [ 50%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_to_fragments PASSED [ 52%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_transform PASSED [ 53%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::test_transmute_to_coverage PASSED [ 55%]
bdgenomics/adam/test/alignmentRecordDataset_test.py::AlignmentRecordDatasetTest::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/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml -
========================== 63 passed in 84.25 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:3.1.2:jar (default-jar) @ adam-python-spark2_2.12 ---
[WARNING] JAR will be empty - no content was marked for inclusion!
[INFO] Building jar: /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/adam-python-spark2_2.12-0.28.0-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] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-python-spark2_2.12 ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building ADAM_2.12: R APIs 0.28.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[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/adamTestCejsCpr/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
Creating a new generic function for ‘pipe’ in package ‘bdgenomics.adam’
Creating a new generic function for ‘transform’ in package ‘bdgenomics.adam’
Creating a new generic function for ‘save’ in package ‘bdgenomics.adam’
Creating a new generic function for ‘sort’ in package ‘bdgenomics.adam’

Attaching package: ‘SparkR’

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

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

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

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

Updating roxygen version in  /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdgenomics.adam/DESCRIPTION 
Writing NAMESPACE
Writing ADAMContext.Rd
Writing GenomicDataset.Rd
Writing AlignmentRecordDataset.Rd
Writing CoverageDataset.Rd
Writing FragmentDataset.Rd
Writing toVariantContexts.Rd
Writing toVariants.Rd
Writing SliceDataset.Rd
Writing VariantContextDataset.Rd
Writing createADAMContext.Rd
Writing loadAlignments-ADAMContext-character-method.Rd
Writing loadDnaSequences-ADAMContext-character-method.Rd
Writing loadProteinSequences-ADAMContext-character-method.Rd
Writing loadRnaSequences-ADAMContext-character-method.Rd
Writing loadSlices-ADAMContext-character-method.Rd
Writing loadFragments-ADAMContext-character-method.Rd
Writing loadFeatures-ADAMContext-character-method.Rd
Writing loadCoverage-ADAMContext-character-method.Rd
Writing loadGenotypes-ADAMContext-character-method.Rd
Writing loadVariants-ADAMContext-character-method.Rd
Writing FeatureDataset.Rd
Writing GenotypeDataset.Rd
Writing SequenceDataset.Rd
Writing VariantDataset.Rd
Writing pipe-GenomicDataset-ANY-character-character-character-method.Rd
Writing cache-GenomicDataset-method.Rd
Writing persist-GenomicDataset-character-method.Rd
Writing unpersist-GenomicDataset-method.Rd
Writing sort-GenomicDataset-method.Rd
Writing sortLexicographically-GenomicDataset-method.Rd
Writing toDF-GenomicDataset-method.Rd
Writing transform-GenomicDataset-function-method.Rd
Writing transmute-GenomicDataset-function-character-method.Rd
Writing broadcastRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterBroadcastRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing broadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
Writing shuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing leftOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing leftOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing fullOuterShuffleRegionJoin-GenomicDataset-GenomicDataset-method.Rd
Writing rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing shuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd
Writing toFragments-AlignmentRecordDataset-method.Rd
Writing saveAsSam-AlignmentRecordDataset-character-method.Rd
Writing toCoverage-AlignmentRecordDataset-method.Rd
Writing save-AlignmentRecordDataset-character-method.Rd
Writing countKmers-AlignmentRecordDataset-numeric-method.Rd
Writing sortByReadName-AlignmentRecordDataset-method.Rd
Writing sortByReferencePosition-AlignmentRecordDataset-method.Rd
Writing sortByReferencePositionAndIndex-AlignmentRecordDataset-method.Rd
Writing markDuplicates-AlignmentRecordDataset-method.Rd
Writing recalibrateBaseQualities-AlignmentRecordDataset-VariantDataset-character-method.Rd
Writing realignIndels-AlignmentRecordDataset-method.Rd
Writing save-CoverageDataset-character-method.Rd
Writing collapse-CoverageDataset-method.Rd
Writing toFeatures-CoverageDataset-method.Rd
Writing coverage-CoverageDataset-method.Rd
Writing flatten-CoverageDataset-method.Rd
Writing save-FeatureDataset-character-method.Rd
Writing toCoverage-FeatureDataset-method.Rd
Writing toAlignments-FragmentDataset-method.Rd
Writing markDuplicates-FragmentDataset-method.Rd
Writing save-FragmentDataset-character-method.Rd
Writing saveAsParquet-GenotypeDataset-character-method.Rd
Writing toVariants-GenotypeDataset-method.Rd
Writing toVariantContexts-GenotypeDataset-method.Rd
Writing save-SequenceDataset-character-method.Rd
Writing save-SliceDataset-character-method.Rd
Writing flankAdjacentFragments-SliceDataset-numeric-method.Rd
Writing saveAsParquet-VariantDataset-character-method.Rd
Writing toVariantContexts-VariantDataset-method.Rd
Writing saveAsVcf-VariantContextDataset-character-method.Rd
Warning message:
In setup_ns_exports(pkg, export_all) :
  Objects listed as exports, but not present in namespace: sortReadsByReferencePosition, sortReadsByReferencePositionAndIndex, toReads
> 
> 
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-r) @ adam-r-spark2_2.12 ---
* checking for file ‘bdgenomics.adam/DESCRIPTION’ ... OK
* preparing ‘bdgenomics.adam’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘bdgenomics.adam_0.27.0.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘bdgenomics.adam/man/recalibrateBaseQualities-AlignmentRecordDataset-VariantDataset-character-method.Rd’
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘bdgenomics.adam/man/rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd’
Warning in utils::tar(filepath, pkgname, compression = "gzip", compression_level = 9L,  :
  storing paths of more than 100 bytes is not portable:
  ‘bdgenomics.adam/man/rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd’

[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-r-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-r-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-r/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-r-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-r) @ adam-r-spark2_2.12 ---
* using log directory ‘/tmp/adamTestCejsCpr/deleteMePleaseThisIsNoLongerNeeded/adam-r/bdgenomics.adam.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘bdgenomics.adam/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bdgenomics.adam’ version ‘0.27.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file paths:
  bdgenomics.adam/man/recalibrateBaseQualities-AlignmentRecordDataset-VariantDataset-character-method.Rd
  bdgenomics.adam/man/rightOuterBroadcastRegionJoinAndGroupByRight-GenomicDataset-GenomicDataset-method.Rd
  bdgenomics.adam/man/rightOuterShuffleRegionJoinAndGroupByLeft-GenomicDataset-GenomicDataset-method.Rd

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

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

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

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         signalCondition(e)
     }, "could not find function \"sortReadsByReferencePosition\"", quote(sortReadsByReferencePosition(reads))) at testthat/test_alignmentRecordDataset.R:51
  2: eval(code, test_env)
  
  
  [Stage 120:=========================================>          (159 + 33) / 200]
                                                                                  
  testthat results ================================================================
  OK: 33 SKIPPED: 0 FAILED: 3
  1. Error: save sorted sam (@test_alignmentRecordDataset.R#29) 
  2. Error: save unordered sam (@test_alignmentRecordDataset.R#40) 
  3. Error: save as bam (@test_alignmentRecordDataset.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: File `inconsolata.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.276 ^^M
         
!  ==> Fatal error occurred, no output PDF file produced!
* checking PDF version of manual without hyperrefs or index ... OK
* DONE

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

[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
	at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
	at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:764)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:711)
	at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:289)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  9.272 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  7.427 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  9.649 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:39 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 20.663 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 26.995 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 15.561 s]
[INFO] ADAM_2.12: Python APIs ............................. SUCCESS [01:31 min]
[INFO] ADAM_2.12: R APIs .................................. FAILURE [ 53.892 s]
[INFO] ADAM_2.12: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:34 min
[INFO] Finished at: 2019-06-28T14:32:26-07:00
[INFO] Final Memory: 86M/1463M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (test-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 <goals> -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/dfd674d33e931eca91ff5ebc8a55c88e1478fba5
Finished: FAILURE