SuccessConsole Output

Skipping 133 KB.. Full Log
iIGKaihyfl5xfk5qXrOEBpkDgMEMDIxMFQUlDDI2RQXJOYpFJdU5qTaKoEttlJQNjBwdnF2sVayAwD4vuoDpQAAAA==Run starting. Expected test count is: 43
InstrumentedRDDSuite:
2019-03-21 09:26:55 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
2019-03-21 09:26:55 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:26:55 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- Operation is recorded correctly
- Function call is recorded correctly
- Instrumented Spark operation works correctly
InstrumentedOrderedRDDFunctionsSuite:
- Nested timings are not recorded for sortByKey operation
InstrumentedPairRDDFunctionsSuite:
- Persisting to Hadoop file is instrumented correctly
+-------------------------+--------------------+--------+
|          Col1           |        Col2        |  Col3  |
+-------------------------+--------------------+--------+
| Col1Value1              |    100 nanoseconds |    100 |
| Col1Value2 A Bit Longer | 200000 nanoseconds | 200000 |
+-------------------------+--------------------+--------+

MonitorTableSuite:
- Table is rendered correctly
TimerSuite:
- Time method does not error when no recorder is defined
- Function times are recorded correctly with explicit recorder
- Function times are recorded correctly with thread-local recorder
DurationFormattingSuite:
- Values with hours formatted correctly
- Values with minutes formatted correctly
- Values with seconds formatted correctly
- Values with milliseconds formatted correctly
- Values with microseconds formatted correctly
- Values with nanoseconds formatted correctly
- Negative duration does not throw an error
HistogramSuite:
- Histogram addition works
ServoTimerSuite:
- Total time computed correctly
- Count computed correctly
- Mean computed correctly
- Max computed correctly
- Min computed correctly
- Timer and sub-monitors tagged correctly
- Nanosecond timings recorded correctly
MetricsSuite:
- Timer metrics are computed correctly
- Timer metrics are computed correctly for RDD operations
MetricsListenerSuite:
- Listener accumulates metrics when registered with Spark
MetricsRecorderSuite:
- Timings are recorded correctly
- Nested timings are recorded correctly
- New top-level operations get new sequence IDs
- Repeated top-level operations get new sequence IDs
- Non-matching timer name causes assertion error
- Nested RDD operations are not recorded
ASCIITableSuite:
- Table is rendered correctly
- Inequal sizes between header and rows are rejected
AggregatorSuite:
- UniqueAggregator only collects unique values
- HistogramAggregator counts values correctly
ServoTimersAccumulableParamSuite:
- Values accumulated correctly
- Paths with different properties are treated as distinct timers
- Accumulable params can be merged together
SparkMetricsSuite:
- Task metrics are captured correctly
- Stage metrics are captured correctly
- Metrics are rendered correctly
Run completed in 7 seconds, 341 milliseconds.
Total number of tests run: 43
Suites: completed 16, aborted 0
Tests: succeeded 43, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-metrics-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-metrics-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-io-spark2_2.12: I/O utils 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-io-spark2_2.12 ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-io-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-io-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 8 Scala sources to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/2.12.6/classes ...
[INFO] Done compiling.
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-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) @ utils-io-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-io-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-io-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 1 Scala source to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/target/2.12.6/test-classes ...
[INFO] Done compiling.
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-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) @ utils-io-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark2_2.12 ---
Discovery starting.
Discovery completed in 110 milliseconds.
Run starting. Expected test count is: 7
ByteArrayLocatorSuite:
- byte access can be wrapped in a locator correctly
LocalFileLocatorSuite:
- parentLocator retrieves the parent directory
- relativeLocator retrieves a subdirectory
- bytes accesses the named underlying file
FileLocatorSuite:
- parseSlash can correctly parse a one-slash string
- parseSlash can correctly parse a two-slash string
- parseSlash can correctly parse a no-slash string
Run completed in 233 milliseconds.
Total number of tests run: 7
Suites: completed 4, aborted 0
Tests: succeeded 7, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-io-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-io-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-io-spark2_2.12 ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-io-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-io-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-io-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-io-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-io-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-io-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-io/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-io-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-io-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-io-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) @ utils-io-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-io-spark2_2.12 ---
Discovery starting.
Discovery completed in 118 milliseconds.
Run starting. Expected test count is: 7
ByteArrayLocatorSuite:
- byte access can be wrapped in a locator correctly
LocalFileLocatorSuite:
- parentLocator retrieves the parent directory
- relativeLocator retrieves a subdirectory
- bytes accesses the named underlying file
FileLocatorSuite:
- parseSlash can correctly parse a one-slash string
- parseSlash can correctly parse a two-slash string
- parseSlash can correctly parse a no-slash string
Run completed in 237 milliseconds.
Total number of tests run: 7
Suites: completed 4, aborted 0
Tests: succeeded 7, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-io-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-io-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-statistics-spark2_2.12: Spark code for fitting statistical models 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-statistics-spark2_2.12 ---
[INFO] Modified 0 of 6 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-statistics-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 4 Scala sources to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/2.12.6/classes ...
[INFO] Done compiling.
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-statistics-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) @ utils-statistics-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-statistics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-statistics-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 2 Scala sources to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/target/2.12.6/test-classes ...
[INFO] Done compiling.
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-statistics-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) @ utils-statistics-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-statistics-spark2_2.12 ---
Discovery starting.
Discovery completed in 130 milliseconds.
Run starting. Expected test count is: 6
PoissonMixtureModelSuite:
2019-03-21 09:27:29 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
2019-03-21 09:27:29 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:27:30 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- run the m step on a trivial example
2019-03-21 09:27:32 WARN  KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-03-21 09:27:33 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2019-03-21 09:27:33 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2019-03-21 09:27:34 WARN  KMeans:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- fit a poisson to several thousand points
ZScoreNormalizationSuite:
- compute mean of a set of samples
- compute variance of a set of samples
- variance should be 0 if all elements are the same
- check z-score for a varying rdd
Run completed in 6 seconds, 360 milliseconds.
Total number of tests run: 6
Suites: completed 3, aborted 0
Tests: succeeded 6, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-statistics-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-statistics-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-statistics-spark2_2.12 ---
[INFO] Modified 0 of 6 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-statistics-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-statistics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-statistics-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-statistics-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-statistics-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-statistics-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-statistics-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-statistics/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-statistics-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-statistics-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) @ utils-statistics-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-statistics-spark2_2.12 ---
Discovery starting.
Discovery completed in 116 milliseconds.
Run starting. Expected test count is: 6
PoissonMixtureModelSuite:
2019-03-21 09:27:37 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
2019-03-21 09:27:37 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:27:37 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- run the m step on a trivial example
2019-03-21 09:27:40 WARN  KMeans:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-03-21 09:27:40 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2019-03-21 09:27:40 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2019-03-21 09:27:41 WARN  KMeans:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- fit a poisson to several thousand points
ZScoreNormalizationSuite:
- compute mean of a set of samples
- compute variance of a set of samples
- variance should be 0 if all elements are the same
- check z-score for a varying rdd
Run completed in 6 seconds, 281 milliseconds.
Total number of tests run: 6
Suites: completed 3, aborted 0
Tests: succeeded 6, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-statistics-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-statistics-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-cli-spark2_2.12: utilities for building command line applications 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-cli-spark2_2.12 ---
[INFO] Modified 0 of 3 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-cli-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 3 Scala sources to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/target/2.12.6/classes ...
[WARNING] [Warn] : there was one deprecation warning
[WARNING] [Warn] : there was one deprecation warning (since 2.12.0)
[WARNING] [Warn] : there were two deprecation warnings in total; re-run with -deprecation for details
[WARNING] three warnings found
[INFO] Done compiling.
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-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) @ utils-cli-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-cli-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-cli-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-cli-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-cli-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-cli-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-cli-spark2_2.12 ---
[INFO] Modified 0 of 3 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-cli-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-cli-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-cli-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-cli-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-cli-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-cli-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-cli-spark2_2.12 ---
[INFO] No sources to compile
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[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-cli-spark2_2.12 ---
[INFO] No sources to compile
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[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-cli-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-cli-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-cli-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-serialization-spark2_2.12: tools for serializing data 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-serialization-spark2_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-serialization-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-serialization-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 1 Scala source to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/target/2.12.6/classes ...
[INFO] Done compiling.
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-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) @ utils-serialization-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-serialization-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-serialization-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-serialization-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-serialization-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-serialization-spark2_2.12 ---
Discovery starting.
Discovery completed in 128 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 172 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-serialization-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-serialization-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-serialization-spark2_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-serialization-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-serialization-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-serialization-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-serialization-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-serialization-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-serialization-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-serialization-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-serialization/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-serialization-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-serialization-spark2_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ utils-serialization-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-serialization-spark2_2.12 ---
Discovery starting.
Discovery completed in 74 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 120 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-serialization-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-serialization-spark2_2.12 ---
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 5 Scala sources to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/2.12.6/classes ...
[WARNING] [Warn] : there were two deprecation warnings (since 2.0.0); re-run with -deprecation for details
[WARNING] one warning found
[INFO] Done compiling.
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-intervalrdd-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) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiling 3 Scala sources to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/target/2.12.6/test-classes ...
[INFO] Done compiling.
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-intervalrdd-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) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-intervalrdd-spark2_2.12 ---
Discovery starting.
Discovery completed in 156 milliseconds.
Run starting. Expected test count is: 31
IntervalRDDSuite:
2019-03-21 09:28:11 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
2019-03-21 09:28:11 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:28:11 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- create IntervalRDD from RDD of datatype string
- merge new values into existing IntervalRDD
- call put multiple times on data with same interval
- test filterByInterval
- verify no data is lost in conversion from rdd to intervalrdd
- count data where chromosome partitions overlap
- get data where chromosome partitions overlap
- apply predicate to the RDD
- testing collect
- test before and after toRDD sizes are the same
- testing mapValues
- Attempt to access data from non existing key
- Delete values from rdd
- Repartitions IntervalRDD
IntervalPartitionSuite:
- create new partition
- create partition from iterator
- get values from iterator-created partition
- correctly fetches data that is initially unsorted
- put some for iterator of intervals and key-values
- get some for iterator of intervals
- selectively getting intervals
- putting differing number of reads into different regions
- putting then getting a region that overlaps 3 regions
- applying a predicate
- applying a map
IntervalArraySuite:
- succeeds in searching empty IntervalArray
- build a IntervalArray with a single item and retrieve data
- build a IntervalArray out of multiple datapoints and retrieve data
- verify get with requireOverlap set to false on IntervalArray retrieves nearest data
- verify IntervalArray fetches all valid ranges
- inserts new elements into IntervalArray
Run completed in 6 seconds, 295 milliseconds.
Total number of tests run: 31
Suites: completed 4, aborted 0
Tests: succeeded 31, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ utils-intervalrdd-spark2_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.6"
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:compile (scala-compile-first) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Test Source directory: /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/utils-intervalrdd/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.0.1:testCompile (scala-test-compile-first) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Using incremental compilation using Mixed compile order
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ utils-intervalrdd-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) @ utils-intervalrdd-spark2_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ utils-intervalrdd-spark2_2.12 ---
Discovery starting.
Discovery completed in 153 milliseconds.
Run starting. Expected test count is: 31
IntervalRDDSuite:
2019-03-21 09:28:19 WARN  Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1)
2019-03-21 09:28:19 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-03-21 09:28:19 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- create IntervalRDD from RDD of datatype string
- merge new values into existing IntervalRDD
- call put multiple times on data with same interval
- test filterByInterval
- verify no data is lost in conversion from rdd to intervalrdd
- count data where chromosome partitions overlap
- get data where chromosome partitions overlap
- apply predicate to the RDD
- testing collect
- test before and after toRDD sizes are the same
- testing mapValues
- Attempt to access data from non existing key
- Delete values from rdd
- Repartitions IntervalRDD
IntervalPartitionSuite:
- create new partition
- create partition from iterator
- get values from iterator-created partition
- correctly fetches data that is initially unsorted
- put some for iterator of intervals and key-values
- get some for iterator of intervals
- selectively getting intervals
- putting differing number of reads into different regions
- putting then getting a region that overlaps 3 regions
- applying a predicate
- applying a map
IntervalArraySuite:
- succeeds in searching empty IntervalArray
- build a IntervalArray with a single item and retrieve data
- build a IntervalArray out of multiple datapoints and retrieve data
- verify get with requireOverlap set to false on IntervalArray retrieves nearest data
- verify IntervalArray fetches all valid ranges
- inserts new elements into IntervalArray
Run completed in 6 seconds, 392 milliseconds.
Total number of tests run: 31
Suites: completed 4, aborted 0
Tests: succeeded 31, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ utils-intervalrdd-spark2_2.12 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ utils-intervalrdd-spark2_2.12 ---
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO] Skipping SCoverage report generation
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building utils 0.2.15-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ utils-parent-spark2_2.12 ---
[INFO] Starting Coveralls job for jenkins (143 / https://amplab.cs.berkeley.edu/jenkins/job/bdg-utils-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=2.4.0,label=ubuntu/143/)
[INFO] Using repository token <secret>
[INFO] Git commit 3030c52 in pr/134/merge
[INFO] Writing Coveralls data to /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/target/coveralls.json...
[INFO] Processing coverage report from /home/jenkins/workspace/bdg-utils-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.0/label/ubuntu/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 73ms
[INFO] Gathered code coverage metrics for 0 source files with 0 lines of code:
[INFO] - 0 relevant lines
[INFO] - 0 covered lines
[INFO] - 0 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 1496ms for Job #143.1
[INFO] https://coveralls.io/jobs/46448449
[INFO] *** It might take hours for Coveralls to update the actual coverage numbers for a job
[INFO]     If you see question marks in the report, please be patient
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] utils .............................................. SUCCESS [  2.012 s]
[INFO] utils-misc-spark2_2.12: Miscellaneous Spark utility code SUCCESS [ 25.574 s]
[INFO] utils-minhash-spark2_2.12: MinHash-based Jaccard similarity estimator SUCCESS [ 24.730 s]
[INFO] utils-metrics-spark2_2.12: tools for collecting metrics on top of RDDs SUCCESS [ 41.937 s]
[INFO] utils-io-spark2_2.12: I/O utils .................... SUCCESS [ 12.574 s]
[INFO] utils-statistics-spark2_2.12: Spark code for fitting statistical models SUCCESS [ 28.249 s]
[INFO] utils-cli-spark2_2.12: utilities for building command line applications SUCCESS [  4.941 s]
[INFO] utils-serialization-spark2_2.12: tools for serializing data SUCCESS [  5.609 s]
[INFO] utils-intervalrdd-spark2_2.12: IntervalRDD based on interval tree SUCCESS [ 31.462 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:01 min
[INFO] Finished at: 2019-03-21T09:28:27-07:00
[INFO] Final Memory: 50M/1365M
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${UTILS_MVN_TMP_DIR}
+ find /tmp/utilsTestMvnnRuhZyP
/tmp/utilsTestMvnnRuhZyP
/tmp/utilsTestMvnnRuhZyP/LocalFileLocatorSuite6555632222376391776test
/tmp/utilsTestMvnnRuhZyP/test.txt2936026961704558175.txt
/tmp/utilsTestMvnnRuhZyP/test.txt5430526890565532402.txt
/tmp/utilsTestMvnnRuhZyP/LocalFileLocatorSuite7781547774417600189test
/tmp/utilsTestMvnnRuhZyP/LocalFileLocatorSuite2390283777130051063test
/tmp/utilsTestMvnnRuhZyP/LocalFileLocatorSuite3290247828129259926test
/tmp/utilsTestMvnnRuhZyP/LocalFileLocatorSuite7904596056681886122test
/tmp/utilsTestMvnnRuhZyP/LocalFileLocatorSuite4108251440441507371test
rm -rf ${UTILS_MVN_TMP_DIR}
+ rm -rf /tmp/utilsTestMvnnRuhZyP

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

Recording test results
Setting commit status on GitHub for https://github.com/bigdatagenomics/utils/commit/3030c52ab8de8e063586e81e0c73991dd4286e91
Finished: SUCCESS