FailedConsole Output

Skipping 126 KB.. Full Log
me/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/classes at 1576021620105
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes at 1576021627543
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
Discovery starting.
Discovery completed in 562 milliseconds.
Run starting. Expected test count is: 31
MangoMainSuite:
- default command groups is non empty
- module provides default command groups
- inject default command groups when called via main
- command groups is empty when called via apply
- single command group
- add new command group to default command groups
- module restores default command groups when called via apply
- custom module with single command group
- custom module with new command group added to default command groups
VizReadsSuite:
2019-12-10 15:47:16 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2019-12-10 15:47:16 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-10 15:47:17 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-10 15:47:19 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
2019-12-10 15:47:19 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx...
2019-12-10 15:47:19 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx...
- Should pass for discovery mode
Could not load resource: [/WEB-INF/layouts/browser.ssp]
Could not load resource: [/WEB-INF/layouts/overall.ssp]
- Should get browser and overall template information
- should return reads
- Should throw error when reads do not exist
- Reads should throw NotFound error on invalid reference
- should not return reads with invalid key
- /variants/:key/:ref
- should not return variants with invalid key
- Should throw error when variants do not exist
- /features/:key/:ref
- should not return features with invalid key
- Should throw error when features do not exist
- Features should throw out of bounds error on invalid reference
- gets coverage from feature endpoint
- should not return coverage with invalid key
- Should return coverage and features
- gets genes
- Coverage should throw out of bounds error on invalid reference
- Should trigger requests for http files
2019-12-10 15:47:58 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.idx...
- should run example files
MakeGenomeSuite:
Exception in thread "Thread-125" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-137" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
2019-12-10 15:48:04 WARN  GenomeConfig:141 - No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1
- creates genome
- fails with invalid genome
Run completed in 52 seconds, 379 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 @ mango-cli >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-cli ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/scoverage-classes at 1576021687987
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [895 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
Discovery starting.
Discovery completed in 569 milliseconds.
Run starting. Expected test count is: 31
MangoMainSuite:
- default command groups is non empty
- module provides default command groups
- inject default command groups when called via main
- command groups is empty when called via apply
- single command group
- add new command group to default command groups
- module restores default command groups when called via apply
- custom module with single command group
- custom module with new command group added to default command groups
VizReadsSuite:
2019-12-10 15:48:18 WARN  Utils:66 - Your hostname, research-jenkins-worker-07 resolves to a loopback address: 127.0.1.1; using 192.168.10.27 instead (on interface eth0)
2019-12-10 15:48:18 WARN  Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address
2019-12-10 15:48:18 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2019-12-10 15:48:21 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx...
2019-12-10 15:48:22 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx...
2019-12-10 15:48:22 WARN  BedReader:158 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx...
- Should pass for discovery mode
Could not load resource: [/WEB-INF/layouts/browser.ssp]
Could not load resource: [/WEB-INF/layouts/overall.ssp]
- Should get browser and overall template information
- should return reads
- Should throw error when reads do not exist
- Reads should throw NotFound error on invalid reference
- should not return reads with invalid key
- /variants/:key/:ref
- should not return variants with invalid key
- Should throw error when variants do not exist
- /features/:key/:ref
- should not return features with invalid key
- Should throw error when features do not exist
- Features should throw out of bounds error on invalid reference
- gets coverage from feature endpoint
- should not return coverage with invalid key
- Should return coverage and features
- gets genes
- Coverage should throw out of bounds error on invalid reference
- Should trigger requests for http files
2019-12-10 15:49:34 WARN  VcfReader:205 - No index file for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf found. Generating /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.idx...
- should run example files
MakeGenomeSuite:
Exception in thread "Thread-123" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-135" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492)
	at java.net.URL.openStream(URL.java:1045)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45)
	at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58)
	at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23)
2019-12-10 15:49:41 WARN  GenomeConfig:141 - No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1
- creates genome
- fails with invalid genome
Run completed in 1 minute, 29 seconds.
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 @ mango-cli <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-cli ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Assembly 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scala-2.11.12/classes at 1576021788130
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-assembly >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-assembly ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scala-2.11.12/scoverage-classes at 1576021789930
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [0 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-assembly ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-assembly <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-assembly ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ mango-parent ---
[INFO] Starting Coveralls job for jenkins (4540 / https://amplab.cs.berkeley.edu/jenkins/job/mango/HADOOP_VERSION=2.7.5,SCALAVER=2.11,SPARK_VERSION=2.4.4,label=ubuntu/4540/)
[INFO] Using repository token <secret>
[INFO] Git commit 126d6b2 in master
[INFO] Writing Coveralls data to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/target/coveralls.json...
[INFO] Processing coverage report from /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 110ms
[INFO] Gathered code coverage metrics for 21 source files with 4008 lines of code:
[INFO] - 1110 relevant lines
[INFO] - 890 covered lines
[INFO] - 220 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 1516ms for Job #4540.1
[INFO] https://coveralls.io/jobs/56711101
[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] mango .............................................. SUCCESS [  1.971 s]
[INFO] mango: CORE ........................................ SUCCESS [02:51 min]
[INFO] mango: CLI ......................................... SUCCESS [02:46 min]
[INFO] Mango: Assembly .................................... SUCCESS [  6.527 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 05:50 min
[INFO] Finished at: 2019-12-10T15:49:54-08:00
[INFO] Final Memory: 63M/1474M
[INFO] ------------------------------------------------------------------------

# if those pass, build the distribution package
mvn -U \
    -P distribution \
    package \
    -DskipTests \
    -Dhadoop.version=${HADOOP_VERSION} \
    -Dspark.version=${SPARK_VERSION} \
    -DargLine=${MANGO_MVN_TMP_DIR}
+ mvn -U -P distribution package -DskipTests -Dhadoop.version=2.7.5 -Dspark.version=2.4.4 -DargLine=/tmp/mangoTestMvn6zaF3VM
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] mango
[INFO] mango: CORE
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO] mango: Distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent ---
[INFO] Modified 0 of 39 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CORE 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-core ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-core ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-core >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-core <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class AlignmentRecordMaterialization(@transient sc: SparkContext,
                                      ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class FeatureMaterialization(@transient sc: SparkContext,
                              ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
                                                             @transient sc: SparkContext,
                                                              ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class VariantContextMaterialization(@transient sc: SparkContext,
                                     ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
    try {
    ^
warning: there were four feature warnings; re-run with -feature for details
model contains 42 documentable templates
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/RefSeq.scala:29: warning: Variable GENOME undefined in comment for object RefSeqFile in object RefSeqFile
 * Processes refSeq file, downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                     ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                  ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                                    ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:51: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz
                                                                                   ^
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:52: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - refSeq.txt file: downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                 ^
11 warnings found
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CLI 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli ---
[INFO] Modified 0 of 8 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-cli ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- sass-maven-plugin:3.7.1:update-stylesheets (default) @ mango-cli ---
[INFO] Checked 0 files for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/sass
[INFO] Checked 0 filtered (**/*.css) files for /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT/css
[INFO] Compiling Sass templates
[INFO] Queueing Sass template for compile: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets => /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets
Ignoring eventmachine-1.2.7 because its extensions are not built. Try: gem pristine eventmachine --version 1.2.7
Ignoring ffi-1.9.25 because its extensions are not built. Try: gem pristine ffi --version 1.9.25
Ignoring http_parser.rb-0.6.0 because its extensions are not built. Try: gem pristine http_parser.rb --version 0.6.0
[INFO]     >> /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.scss => /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.css
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (Run `npm install`) @ mango-cli ---
npm WARN mango-cli@0.0.2 No repository field.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:copy-resources (copy-resources) @ mango-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 8760 resources
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-cli ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-cli ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-cli ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-cli >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-cli <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
model contains 26 documentable templates
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- appassembler-maven-plugin:1.10:assemble (default) @ mango-cli ---
[INFO] Installing artifact /home/jenkins/.m2/repository/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro/1.8.2/avro-1.8.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro/1.8.2/avro-1.8.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/tukaani/xz/1.5/xz-1.5.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-codec/commons-codec/1.4/commons-codec-1.4.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-pool/commons-pool/1.6/commons-pool-1.6.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-pool/commons-pool/1.6/commons-pool-1.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli-spark2_2.11/0.29.0/adam-cli-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli-spark2_2.11/0.29.0/adam-cli-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-apis-spark2_2.11/0.29.0/adam-apis-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis-spark2_2.11/0.29.0/adam-apis-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/args4j/args4j/2.33/args4j-2.33.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/args4j/args4j/2.33/args4j-2.33.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/guice/4.2.0/guice-4.2.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/inject/guice/4.2.0/guice-4.2.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/javax/inject/javax.inject/1/javax.inject-1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/aopalliance/aopalliance/1.0/aopalliance-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-core-spark2_2.11/0.29.0/adam-core-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core-spark2_2.11/0.29.0/adam-core-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/objenesis/objenesis/2.1/objenesis-2.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/objenesis/objenesis/2.1/objenesis-2.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-io/commons-io/2.6/commons-io-2.6.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/commons-io/commons-io/2.6/commons-io-2.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.29.0/adam-codegen-spark2_2.11-0.29.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.29.0/adam-codegen-spark2_2.11-0.29.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.14.0/bdg-formats-0.14.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.14.0/bdg-formats-0.14.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar
[INFO] Installing artifact /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-ga4gh/0.8.0/convert-ga4gh-0.8.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.8.0/convert-ga4gh-0.8.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.8.0/convert-htsjdk-0.8.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.8.0/convert-htsjdk-0.8.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.8.0/convert-0.8.0.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.8.0/convert-0.8.0.jar
[INFO] Installing artifact /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar to /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli/0.0.4-SNAPSHOT/mango-cli-0.0.4-SNAPSHOT.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Assembly 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly ---
[INFO] Test Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly ---
[INFO] Source directory: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ mango-assembly ---
[INFO] Including org.bdgenomics.mango:mango-cli:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.3 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 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 com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.29.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.14.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
[INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra.rl:rl_2.11:jar:0.4.10 in the shaded jar.
[INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar.
[INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar.
[INFO] Including joda-time:joda-time:jar:2.9.1 in the shaded jar.
[INFO] Including org.joda:joda-convert:jar:1.8.1 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.5 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.11.12 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.8.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.8.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.8.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.8.1 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] mango-cli-0.0.4-SNAPSHOT.jar, adam-cli-spark2_2.11-0.29.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar with /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: Distribution 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.4.1:single (default) @ mango-distribution ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
[INFO] Building tar: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  3.247 s]
[INFO] mango: CORE ........................................ SUCCESS [ 15.824 s]
[INFO] mango: CLI ......................................... SUCCESS [ 19.135 s]
[INFO] Mango: Assembly .................................... SUCCESS [ 21.137 s]
[INFO] mango: Distribution ................................ SUCCESS [ 27.724 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 01:27 min
[INFO] Finished at: 2019-12-10T15:51:23-08:00
[INFO] Final Memory: 89M/1486M
[INFO] ------------------------------------------------------------------------

# make sure that the distribution package contains an assembly jar
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzvf mango-distribution/target/mango-distribution*-bin.tar.gz | \
    grep mango-assembly | \
    grep jar | \
    grep -v -e sources -e javadoc
+ grep mango-assembly
+ tar tzvf mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
+ grep jar
+ grep -v -e sources -e javadoc
-rw-r--r-- jenkins/jenkins 93389288 2019-12-10 15:50 mango-distribution-0.0.4-SNAPSHOT/repo/mango-assembly-0.0.4-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvn6zaF3VM
/tmp/mangoTestMvn6zaF3VM
/tmp/mangoTestMvn6zaF3VM/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvn6zaF3VM/genomes1436941980735878172
/tmp/mangoTestMvn6zaF3VM/genomes1436941980735878172/hg19.genome
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858
/tmp/mangoTestMvn6zaF3VM/mmbroken1381560712175240577.genome
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/_SUCCESS
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/._references.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=1
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=1/positionBin=26/part-00000-d9435ac0-5beb-4030-876a-2c8a255da134.c000.snappy.parquet
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=1/positionBin=26/.part-00000-d9435ac0-5beb-4030-876a-2c8a255da134.c000.snappy.parquet.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=1/positionBin=240/part-00000-d9435ac0-5beb-4030-876a-2c8a255da134.c000.snappy.parquet
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=1/positionBin=240/.part-00000-d9435ac0-5beb-4030-876a-2c8a255da134.c000.snappy.parquet.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/_readGroups.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/_partitionedByStartPos
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/_references.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/._SUCCESS.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/._readGroups.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=2
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=2/positionBin=189/part-00000-d9435ac0-5beb-4030-876a-2c8a255da134.c000.snappy.parquet
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/referenceName=2/positionBin=189/.part-00000-d9435ac0-5beb-4030-876a-2c8a255da134.c000.snappy.parquet.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301.adam/_processingSteps.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite2622696080051943301
/tmp/mangoTestMvn6zaF3VM/genomes6863544069141498919
/tmp/mangoTestMvn6zaF3VM/genomes6863544069141498919/hg19.genome
/tmp/mangoTestMvn6zaF3VM/1819279443244748926
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/_SUCCESS
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/._references.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=1
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=1/positionBin=26/.part-00000-df7132ad-5439-4c83-8c95-a4216c653e73.c000.snappy.parquet.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=1/positionBin=26/part-00000-df7132ad-5439-4c83-8c95-a4216c653e73.c000.snappy.parquet
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=1/positionBin=240/.part-00000-df7132ad-5439-4c83-8c95-a4216c653e73.c000.snappy.parquet.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=1/positionBin=240/part-00000-df7132ad-5439-4c83-8c95-a4216c653e73.c000.snappy.parquet
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/_readGroups.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/_partitionedByStartPos
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/_references.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/._SUCCESS.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/._readGroups.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=2
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=2/positionBin=189/.part-00000-df7132ad-5439-4c83-8c95-a4216c653e73.c000.snappy.parquet.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/referenceName=2/positionBin=189/part-00000-df7132ad-5439-4c83-8c95-a4216c653e73.c000.snappy.parquet
/tmp/mangoTestMvn6zaF3VM/TempSuite6601762701134427549.adam/_processingSteps.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/_SUCCESS
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/._references.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/referenceName=1
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/referenceName=1/positionBin=0/part-00000-79b38a93-a0b0-4f94-80d3-3407e73cbca2.c000.snappy.parquet
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/referenceName=1/positionBin=0/.part-00000-79b38a93-a0b0-4f94-80d3-3407e73cbca2.c000.snappy.parquet.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/._samples.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/_partitionedByStartPos
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/_references.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/._header.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/._SUCCESS.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/_samples.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite941067347233911232.adam/_header
/tmp/mangoTestMvn6zaF3VM/3327880250779410560
/tmp/mangoTestMvn6zaF3VM/3327880250779410560/anoGam1.genome
/tmp/mangoTestMvn6zaF3VM/1617924600804286571
/tmp/mangoTestMvn6zaF3VM/1617924600804286571/anoGam1.genome
/tmp/mangoTestMvn6zaF3VM/mmbroken6756330745059256820.genome
/tmp/mangoTestMvn6zaF3VM/8820625515792088546
/tmp/mangoTestMvn6zaF3VM/invalidBuild.genome6270406081662722
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/_SUCCESS
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/._references.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/referenceName=1
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/referenceName=1/positionBin=0/.part-00000-62f9491b-0824-40fb-a2ca-0d94be84a903.c000.snappy.parquet.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/referenceName=1/positionBin=0/part-00000-62f9491b-0824-40fb-a2ca-0d94be84a903.c000.snappy.parquet
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/._samples.avro.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/_partitionedByStartPos
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/_references.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/._header.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/._SUCCESS.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/_samples.avro
/tmp/mangoTestMvn6zaF3VM/TempSuite8538117789227157858.adam/_header
/tmp/mangoTestMvn6zaF3VM/invalidBuild.genome9086714111325996633
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvn6zaF3VM

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${MANGO_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/mangoTestMvn6zaF3VM:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# run integration tests
# prebuilt spark distributions are scala 2.11 for spark 2.x
if [[ ${SCALAVER} == 2.11 ]];
then

    # set the TMPDIR envar, which is used by python to choose where to make temp directories
    export TMPDIR=${MANGO_TMP_DIR}

    pushd $PROJECT_ROOT

    # Copy the jar into our temp space for testing
    cp -r . $MANGO_TMP_DIR
    popd

    pushd $MANGO_TMP_DIR

    # what hadoop version are we on? format string for downloading spark assembly
    if [[ $HADOOP_VERSION =~ ^2\.6 ]]; then
        HADOOP=hadoop2.6
    elif [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
        HADOOP=hadoop2.7
    else
        echo "Unknown Hadoop version."
        exit 1
    fi

    # set spark artifact string for downloading assembly
    SPARK=spark-${SPARK_VERSION}

    # download prepackaged spark assembly
    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
        -o ${SPARK}-bin-${HADOOP}.tgz

    tar xzvf ${SPARK}-bin-${HADOOP}.tgz
    export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}

    # create a conda environment for python build, if necessary
    pythons=( 3.6 )
    for python in ${pythons[*]}
    do
        conda create -y -q -n mango-build-${PYTHON_UUID} python=${python} pip
        source activate mango-build-${PYTHON_UUID}

        # install npm and node in the venv for mango-viz
        conda install -y nodejs

        # prepare mango python
        pushd mango-python
        make prepare
        popd

        # we can run the python build, now that we have a spark executable
        mvn -U \
            -P python,distribution \
            package \
            -DskipTests \
            -Dhadoop.version=${HADOOP_VERSION} \
            -Dspark.version=${SPARK_VERSION}

        # clean mango python
        pushd mango-python
        make clean
        popd

        # prepare mango viz
        pushd mango-viz
        make prepare
        popd

        # run the widgets tests (mango-viz)
        mvn -P widgets test

        # clean mango viz
        pushd mango-viz
        make clean
        popd

        # make sure that the distribution package contains an egg
        # if no assembly jar is found, this will exit with code 1 and fail the build
        tar tzvf mango-distribution/target/mango-distribution*-bin.tar.gz | \
            grep bdgenomics.mango | \
            grep egg

        # test mango notebook, output to temporary log file
        MANGO_NOTEBOOK_LOGS=${MANGO_TMP_DIR}/mango-notebook.log
        bash -xv ${PROJECT_ROOT}/bin/mango-notebook  &> ${MANGO_NOTEBOOK_LOGS} &

        # sleep for 2 seconds to let mango-notebook start up
        sleep 2

        # if mango-notebook fails, then trying to kill the process will fail
        if kill $! ; then
            echo "Mango Notebook Succeeded"
        else
            echo "Mango Notebook failed with logs:"
            cat ${MANGO_NOTEBOOK_LOGS}
            exit 1
        fi

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

        # deactivate and remove the conda env
        source deactivate
        conda remove -y --name mango-build-${PYTHON_UUID} --all

    done

    # test mango submit
    MANGO_BROWSER_LOGS=${MANGO_TMP_DIR}/mango-submit.log
    bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS} &

    # sleep for 10 seconds to let mango-browser start up
    sleep 10

    # make sure server responds to POST for reads and variants
    curl -s -N \
    --header "Content-type: application/json" \
    --request POST \
    --data "{\"pageToken\":null,\"pageSize\":200,\"readGroupIds\":[\"chr17_7500000-7515000_sam\"],\"referenceId\":\"chr17\",\"start\":1,\"end\":100}"  \
    http://localhost:8080/reads/search | grep alignments

    if [[ $? != 0 ]]; then
        echo "invalid alignments"
        exit 1
    fi

    curl -s -N \
        --header "Content-type: application/json" \
        --request POST \
        --data "{\"variantSetId\":\"ALL_chr17_7500000-7515000_phase3_shapeit2_mvncall_integrated_v5a_20130502_genotypes_vcf\",\"pageToken\":null,\"pageSize\":400,\"referenceName\":\"chr17\",\"callSetIds\":[],\"start\":7500000,\"end\":7515000}"  \
        http://localhost:8080/variants/search | grep variants

    if [[ $? != 0 ]]; then
        echo "invalid variants"
        exit 1
    fi

    # get processes with mango prefix
    PROCESSES=( $(ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }') )

    # There should be processes running for mango-browser
    if [ "${#PROCESSES[@]}" -gt 0 ] ; then
        echo "Mango Browser Succeeded"
        # kill all Mango Browser related processes
        kill ${PROCESSES}; 
    else
        echo "Mango Browser failed with logs:"
        cat ${MANGO_BROWSER_LOGS}
        exit 1
    fi

    # test genome builds
    TEST_GENOME="anoGam1"
    bash -xv ${PROJECT_ROOT}/bin/make_genome ${TEST_GENOME} ${MANGO_TMP_DIR}

    unzip ${MANGO_TMP_DIR}/${TEST_GENOME}.genome -d ${MANGO_TMP_DIR}/${TEST_GENOME}

    pushd ${MANGO_TMP_DIR}/${TEST_GENOME}
    cat properties.txt
    cat ${TEST_GENOME}.chrom.sizes
    popd
fi
+ [[ 2.11 == 2.11 ]]
+ export TMPDIR=/tmp/mangoTestBItaGEh/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/mangoTestBItaGEh/deleteMePleaseThisIsNoLongerNeeded
+ pushd /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/..
~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ cp -r . /tmp/mangoTestBItaGEh/deleteMePleaseThisIsNoLongerNeeded
+ popd
~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ pushd /tmp/mangoTestBItaGEh/deleteMePleaseThisIsNoLongerNeeded
/tmp/mangoTestBItaGEh/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ [[ 2.7.5 =~ ^2\.6 ]]
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7
+ SPARK=spark-2.4.4
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.4/spark-2.4.4-bin-hadoop2.7.tgz' -o spark-2.4.4-bin-hadoop2.7.tgz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0

  0     0    0     0    0     0      0      0 --:--:--  0:00:04 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:05 --:--:--     0
curl: (56) Recv failure: Connection reset by peer
clean_up
+ clean_up
+ source deactivate
#!/bin/bash

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

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
++ [[ -z '' ]]
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]
++ return 0
+ conda remove -y --force --name mango-build-c7970b7c-6da5-452f-8d93-6f2a55d5a699 --all

CondaEnvironmentNotFoundError: Could not find environment: mango-build-c7970b7c-6da5-452f-8d93-6f2a55d5a699 .
You can list all discoverable environments with `conda info --envs`.

+ echo 'conda ENV mango-build-c7970b7c-6da5-452f-8d93-6f2a55d5a699 does not exist'
conda ENV mango-build-c7970b7c-6da5-452f-8d93-6f2a55d5a699 does not exist
+ rm -rf /tmp/mangoTestBItaGEh/deleteMePleaseThisIsNoLongerNeeded
+ rm -rf /tmp/mangoTestMvn6zaF3VM
Build step 'Execute shell' marked build as failure
Sending e-mails to: akmorrow@berkeley.edu
Finished: FAILURE