AbortedConsole Output

Skipping 466 KB.. Full Log
 source files to /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/scala-2.11.12/classes at 1575391224868
[INFO] prepare-compile in 0 s
[INFO] compile in 8 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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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] /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/scala-2.11.12/test-classes at 1575391233920
[INFO] prepare-compile in 0 s
[INFO] compile in 7 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 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- sass-maven-plugin:3.7.1:update-stylesheets (default) @ mango-cli ---
[INFO] Checked 0 files for /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/sass
[INFO] Checked 0 filtered (**/*.css) files for /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.4-SNAPSHOT/css
[INFO] Compiling Sass templates
[INFO] Queueing Sass template for compile: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets => /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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-1.11.1 because its extensions are not built. Try: gem pristine ffi --version 1.11.1
Ignoring http_parser.rb-0.6.0 because its extensions are not built. Try: gem pristine http_parser.rb --version 0.6.0
[INFO]     >> /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets/main.scss => /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets/main.css
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (Run `npm install`) @ mango-cli ---
npm notice created a lockfile as package-lock.json. You should commit this file.
npm WARN mango-cli@0.0.2 No repository field.

audited 140 packages in 1.093s
found 0 vulnerabilities

[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 8761 resources
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-cli ---
[INFO] Building jar: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar to /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.8.0/convert-0.8.0.jar
[INFO] Installing artifact /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar to /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 '/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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] /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/scala-2.11.12/classes at 1575391263525
[INFO] prepare-compile in 0 s
[INFO] compile in 2 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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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 '/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] adam-cli-spark2_2.11-0.29.0.jar, mango-cli-0.0.4-SNAPSHOT.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[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 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar with /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/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: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
[INFO] Building tar: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  5.208 s]
[INFO] mango: CORE ........................................ SUCCESS [ 40.077 s]
[INFO] Mango: Python APIs ................................. SUCCESS [02:06 min]
[INFO] mango: CLI ......................................... SUCCESS [ 37.343 s]
[INFO] Mango: Assembly .................................... SUCCESS [ 26.700 s]
[INFO] mango: Distribution ................................ SUCCESS [ 33.985 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 04:29 min
[INFO] Finished at: 2019-12-03T08:42:02-08:00
[INFO] Final Memory: 88M/1499M
[INFO] ------------------------------------------------------------------------
+ pushd mango-python
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ make clean
pip uninstall -y bdgenomics.mango
Uninstalling bdgenomics.mango-0.0.6a2:
  Successfully uninstalled bdgenomics.mango-0.0.6a2
rm -rf src/*.egg-info
rm -rf build/
+ popd
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ pushd mango-viz
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ make prepare
pip install -r requirements.txt
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (1.0.0)
Requirement already satisfied: ipywidgets==7.0.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from -r requirements.txt (line 2)) (7.0.0)
Collecting six==1.11.0
  Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Requirement already satisfied: modin[ray]==0.6.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from -r requirements.txt (line 4)) (0.6.1)
Requirement already satisfied: pytest==2.8.3 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from -r requirements.txt (line 5)) (2.8.3)
Requirement already satisfied: jupyter_contrib_nbextensions==0.5.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from -r requirements.txt (line 6)) (0.5.1)
Requirement already satisfied: qtconsole in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (4.6.0)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (5.1.3)
Requirement already satisfied: jupyter-console in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (6.0.0)
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (6.0.2)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 1)) (5.6.1)
Requirement already satisfied: ipython>=4.0.0; python_version >= "3.3" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 2)) (7.8.0)
Requirement already satisfied: traitlets>=4.3.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 2)) (4.3.3)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 2)) (4.4.0)
Requirement already satisfied: widgetsnbextension~=3.0.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 2)) (3.0.8)
Requirement already satisfied: pandas==0.25.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from modin[ray]==0.6.1->-r requirements.txt (line 4)) (0.25.1)
Requirement already satisfied: ray==0.7.3; extra == "ray" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from modin[ray]==0.6.1->-r requirements.txt (line 4)) (0.7.3)
Requirement already satisfied: py>=1.4.29 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from pytest==2.8.3->-r requirements.txt (line 5)) (1.8.0)
Requirement already satisfied: jupyter-latex-envs>=1.3.8 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (1.4.6)
Requirement already satisfied: lxml in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (4.4.2)
Requirement already satisfied: jupyter-nbextensions-configurator>=0.4.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (0.4.1)
Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (4.6.1)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (0.2.0)
Requirement already satisfied: jupyter-highlight-selected-word>=0.1.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (0.2.0)
Requirement already satisfied: pyyaml in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (5.2)
Requirement already satisfied: jupyter-contrib-core>=0.3.3 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (0.3.3)
Requirement already satisfied: tornado in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (6.0.3)
Requirement already satisfied: jupyter-client>=4.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 1)) (5.3.4)
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 1)) (2.5.2)
Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter-console->jupyter==1.0.0->-r requirements.txt (line 1)) (2.0.10)
Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (0.8.3)
Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (2.10.3)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (1.5.0)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (0.7.1)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (18.1.1)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.8.4)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.4.4)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (1.4.2)
Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (3.1.0)
Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.6.0)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.3)
Requirement already satisfied: backcall in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.1.0)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (42.0.1.post20191125)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.7.5)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.15.1)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (4.4.1)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (4.7.0)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (3.2.0)
Requirement already satisfied: pytz>=2017.2 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->-r requirements.txt (line 4)) (2019.3)
Requirement already satisfied: numpy>=1.13.3 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->-r requirements.txt (line 4)) (1.17.4)
Requirement already satisfied: python-dateutil>=2.6.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->-r requirements.txt (line 4)) (2.8.1)
Requirement already satisfied: funcsigs in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (1.0.2)
Requirement already satisfied: redis in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (3.3.11)
Requirement already satisfied: colorama in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (0.4.1)
Requirement already satisfied: click in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (7.0)
Requirement already satisfied: filelock in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (3.0.12)
Requirement already satisfied: protobuf>=3.8.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->-r requirements.txt (line 4)) (3.11.1)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->jupyter-console->jupyter==1.0.0->-r requirements.txt (line 1)) (0.1.7)
Requirement already satisfied: ptyprocess; os_name != "nt" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from terminado>=0.8.1->notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (0.6.0)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jinja2->notebook->jupyter==1.0.0->-r requirements.txt (line 1)) (1.1.1)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 1)) (0.5.1)
Requirement already satisfied: parso>=0.5.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.5.1)
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (1.1.0)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (19.3.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.15.6)
Requirement already satisfied: zipp>=0.5 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (0.6.0)
Requirement already satisfied: more-itertools in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from zipp>=0.5->importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 2)) (8.0.0)
Installing collected packages: six
  Found existing installation: six 1.13.0
    Uninstalling six-1.13.0:
      Successfully uninstalled six-1.13.0
Successfully installed six-1.11.0
# install node_modules
cd bdgenomics/mango/js; \
	npm install
npm WARN deprecated browserslist@1.7.7: Browserslist 2 could fail on reading Browserslist >3.0 config used in other tools.
npm WARN deprecated core-js@1.2.7: core-js@<2.6.8 is no longer maintained. Please, upgrade to core-js@3 or at least to actual version of core-js@2.
npm WARN deprecated minimatch@2.0.10: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated natives@1.1.6: This module relies on Node.js's internals and will break at some point. Do not use it, and update to graceful-fs@4.x.
npm WARN deprecated minimatch@0.2.14: Please update to minimatch 3.0.2 or higher to avoid a RegExp DoS issue
npm WARN deprecated graceful-fs@1.2.3: please upgrade to graceful-fs 4 for compatibility with current and future versions of Node.js

> spawn-sync@1.0.15 postinstall /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js/node_modules/spawn-sync
> node postinstall


> flow-bin@0.21.0 postinstall /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js/node_modules/flow-bin
> node lib/install.js

  ✔ flow binary test passed successfully
npm WARN prepublish-on-install As of npm@5, `prepublish` scripts are deprecated.
npm WARN prepublish-on-install Use `prepare` for build steps and `prepublishOnly` for upload-only.
npm WARN prepublish-on-install See the deprecation note in `npm help scripts` for more information.

> bdgenomics.mango.pileup@0.0.3-a0 prepublish /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js
> webpack

Hash: cc5171780dfef6f8f819330a8086a7bb1904b41b59f9ab4563f109013ebc
Version: webpack 1.15.0
Child
    Hash: cc5171780dfef6f8f819
    Version: webpack 1.15.0
    Time: 98ms
           Asset     Size  Chunks             Chunk Names
    extension.js  1.96 kB       0  [emitted]  main
       [0] ./src/extension.js 525 bytes {0} [built]
Child
    Hash: 330a8086a7bb1904b41b
    Version: webpack 1.15.0
    Time: 6391ms
           Asset     Size  Chunks             Chunk Names
        index.js  2.34 MB       0  [emitted]  main
    index.js.map   2.8 MB       0  [emitted]  main
       [0] ./src/index.js 957 bytes {0} [built]
       [7] ./src/pileupViewer.js 4.04 kB {0} [built]
     [526] ./src/utils.js 303 bytes {0} [built]
        + 525 hidden modules
Child
    Hash: 59f9ab4563f109013ebc
    Version: webpack 1.15.0
    Time: 6391ms
           Asset     Size  Chunks             Chunk Names
        index.js  2.32 MB       0  [emitted]  main
    index.js.map  2.77 MB       0  [emitted]  main
       [0] ./src/embed.js 576 bytes {0} [built]
       [1] ./src/pileupViewer.js 4.04 kB {0} [built]
     [520] ./src/utils.js 303 bytes {0} [built]
        + 519 hidden modules
npm notice created a lockfile as package-lock.json. You should commit this file.
npm WARN bdgenomics.mango.pileup@0.0.3-a0 No license field.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@1.2.9 (node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.9: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

added 759 packages from 697 contributors and audited 3136 packages in 36.464s
found 15 vulnerabilities (5 low, 2 moderate, 8 high)
  run `npm audit fix` to fix them, or `npm audit` for details
+ popd
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ mvn -P widgets test
OpenJDK 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: Python visualization hooks
[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 230 .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] ------------------------------------------------------------------------
[INFO] Building Mango: Python visualization hooks 0.0.4-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-viz ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-viz ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-viz ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-viz ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (dev-python) @ mango-viz ---
rm -rf bdgenomics/mango/pileup/static
rm -rf bdgenomics/mango/js/dist
rm -rf bdgenomics.mango.pileup.egg-info/
pip install -v -e .
Created temporary directory: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/pip-ephem-wheel-cache-d7_5gyua
Created temporary directory: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-0mwc7qzl
Created requirements tracker '/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-0mwc7qzl'
Created temporary directory: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/pip-install-gkxdxfg9
Obtaining file:///tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz
  Added file:///tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz to build tracker '/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-0mwc7qzl'
    Running setup.py (path:/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/setup.py) egg_info for package from file:///tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz
    Running command python setup.py egg_info
    running egg_info
    running jsdeps
    6.4.1
    6.4.1
    Installing build dependencies with npm.  This may take a while...
    npm WARN prepublish-on-install As of npm@5, `prepublish` scripts are deprecated.
    npm WARN prepublish-on-install Use `prepare` for build steps and `prepublishOnly` for upload-only.
    npm WARN prepublish-on-install See the deprecation note in `npm help scripts` for more information.

    > bdgenomics.mango.pileup@0.0.3-a0 prepublish /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js
    > webpack

    Hash: cc5171780dfef6f8f819330a8086a7bb1904b41b59f9ab4563f109013ebc
    Version: webpack 1.15.0
    Child
        Hash: cc5171780dfef6f8f819
        Version: webpack 1.15.0
        Time: 121ms
               Asset     Size  Chunks             Chunk Names
        extension.js  1.96 kB       0  [emitted]  main
           [0] ./src/extension.js 525 bytes {0} [built]
    Child
        Hash: 330a8086a7bb1904b41b
        Version: webpack 1.15.0
        Time: 6868ms
               Asset     Size  Chunks             Chunk Names
            index.js  2.34 MB       0  [emitted]  main
        index.js.map   2.8 MB       0  [emitted]  main
           [0] ./src/index.js 957 bytes {0} [built]
           [7] ./src/pileupViewer.js 4.04 kB {0} [built]
         [526] ./src/utils.js 303 bytes {0} [built]
            + 525 hidden modules
    Child
        Hash: 59f9ab4563f109013ebc
        Version: webpack 1.15.0
        Time: 6868ms
               Asset     Size  Chunks             Chunk Names
            index.js  2.32 MB       0  [emitted]  main
        index.js.map  2.77 MB       0  [emitted]  main
           [0] ./src/embed.js 576 bytes {0} [built]
           [1] ./src/pileupViewer.js 4.04 kB {0} [built]
         [520] ./src/utils.js 303 bytes {0} [built]
            + 519 hidden modules
    npm WARN bdgenomics.mango.pileup@0.0.3-a0 No license field.
    npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@1.2.9 (node_modules/fsevents):
    npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.9: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

    audited 3136 packages in 13.798s
    found 15 vulnerabilities (5 low, 2 moderate, 8 high)
      run `npm audit fix` to fix them, or `npm audit` for details
    creating bdgenomics.mango.pileup.egg-info
    writing bdgenomics.mango.pileup.egg-info/PKG-INFO
    writing dependency_links to bdgenomics.mango.pileup.egg-info/dependency_links.txt
    writing requirements to bdgenomics.mango.pileup.egg-info/requires.txt
    writing top-level names to bdgenomics.mango.pileup.egg-info/top_level.txt
    writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    reading manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
    warning: no previously-included files matching '__pycache__' found anywhere in distribution
    warning: no previously-included files matching '.DS_Store' found anywhere in distribution
    warning: no files found matching 'version.py'
    warning: no files found matching '*.*' under directory 'pileup/static'
    writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
  Source in /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz has version 0.0.6a1, which satisfies requirement bdgenomics.mango.pileup==0.0.6a1 from file:///tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz
  Removed bdgenomics.mango.pileup==0.0.6a1 from file:///tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz from build tracker '/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-0mwc7qzl'
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (1.0.0)
Requirement already satisfied: ipywidgets==7.0.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (7.0.0)
Requirement already satisfied: six==1.11.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (1.11.0)
Requirement already satisfied: modin[ray]==0.6.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (0.6.1)
  Installing extra requirements: 'ray'
Requirement already satisfied: pytest==2.8.3 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (2.8.3)
Requirement already satisfied: jupyter_contrib_nbextensions==0.5.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
Requirement already satisfied: qtconsole in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.6.0)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (5.1.3)
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (6.0.2)
Requirement already satisfied: jupyter-console in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (6.0.0)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (5.6.1)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.4.0)
Requirement already satisfied: ipython>=4.0.0; python_version >= "3.3" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (7.8.0)
Requirement already satisfied: widgetsnbextension~=3.0.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (3.0.8)
Requirement already satisfied: traitlets>=4.3.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.3.3)
Requirement already satisfied: pandas==0.25.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (0.25.1)
Requirement already satisfied: ray==0.7.3; extra == "ray" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (0.7.3)
Requirement already satisfied: py>=1.4.29 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from pytest==2.8.3->bdgenomics.mango.pileup==0.0.6a1) (1.8.0)
Requirement already satisfied: jupyter-contrib-core>=0.3.3 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.3.3)
Requirement already satisfied: jupyter-latex-envs>=1.3.8 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (1.4.6)
Requirement already satisfied: tornado in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (6.0.3)
Requirement already satisfied: pyyaml in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (5.2)
Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (4.6.1)
Requirement already satisfied: lxml in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (4.4.2)
Requirement already satisfied: jupyter-nbextensions-configurator>=0.4.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.4.1)
Requirement already satisfied: jupyter-highlight-selected-word>=0.1.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.2.0)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.2.0)
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (2.5.2)
Requirement already satisfied: jupyter-client>=4.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (5.3.4)
Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.8.3)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.5.0)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (18.1.1)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.7.1)
Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (2.10.3)
Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jupyter-console->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (2.0.10)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.4.2)
Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.6.0)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.4.4)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.8.4)
Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (3.1.0)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.3)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (3.2.0)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.15.1)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.4.1)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.7.5)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.7.0)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (42.0.1.post20191125)
Requirement already satisfied: backcall in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.1.0)
Requirement already satisfied: pytz>=2017.2 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (2019.3)
Requirement already satisfied: numpy>=1.13.3 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (1.17.4)
Requirement already satisfied: python-dateutil>=2.6.1 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from pandas==0.25.1->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (2.8.1)
Requirement already satisfied: filelock in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (3.0.12)
Requirement already satisfied: colorama in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (0.4.1)
Requirement already satisfied: redis in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (3.3.11)
Requirement already satisfied: funcsigs in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (1.0.2)
Requirement already satisfied: click in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (7.0)
Requirement already satisfied: protobuf>=3.8.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a1) (3.11.1)
Requirement already satisfied: ptyprocess; os_name != "nt" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from terminado>=0.8.1->notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.6.0)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jinja2->notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.1.1)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->jupyter-console->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.1.7)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.1.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.15.6)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (19.3.0)
Requirement already satisfied: parso>=0.5.0 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0; python_version >= "3.3"->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
Requirement already satisfied: zipp>=0.5 in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.6.0)
Requirement already satisfied: more-itertools in /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages (from zipp>=0.5->importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango.pileup==0.0.6a1) (8.0.0)
Installing collected packages: bdgenomics.mango.pileup
  Found existing installation: bdgenomics.mango.pileup 0.0.6a0
    Uninstalling bdgenomics.mango.pileup-0.0.6a0:
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages/~dgenomics.mango.pileup-0.0.6a0.dist-info
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages/bdgenomics.mango.pileup-0.0.6a0.dist-info/
      Created temporary directory: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/pip-uninstall-5lnftvwr
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages/bdgenomics/__init__.py
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages/bdgenomics/~_pycache__
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages/bdgenomics/__pycache__/
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages/bdgenomics/~ango
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages/bdgenomics/mango/
      Created temporary directory: /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/share/jupyter/nbextensions/~ileup
      Removing file or directory /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/share/jupyter/nbextensions/pileup/
      Successfully uninstalled bdgenomics.mango.pileup-0.0.6a0
  Running setup.py develop for bdgenomics.mango.pileup
    Running command /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/setup.py'"'"'; __file__='"'"'/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
    running develop
    running egg_info
    writing bdgenomics.mango.pileup.egg-info/PKG-INFO
    writing dependency_links to bdgenomics.mango.pileup.egg-info/dependency_links.txt
    writing requirements to bdgenomics.mango.pileup.egg-info/requires.txt
    writing top-level names to bdgenomics.mango.pileup.egg-info/top_level.txt
    reading manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
    warning: no previously-included files matching '__pycache__' found anywhere in distribution
    warning: no previously-included files matching '.DS_Store' found anywhere in distribution
    warning: no files found matching 'version.py'
    warning: no files found matching '*.*' under directory 'pileup/static'
    writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
    running build_ext
    Creating /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/lib/python3.6/site-packages/bdgenomics.mango.pileup.egg-link (link to .)
    Adding bdgenomics.mango.pileup 0.0.6a1 to easy-install.pth file

    Installed /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz
Successfully installed bdgenomics.mango.pileup
Cleaning up...
Removed build tracker '/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-0mwc7qzl'
jupyter nbextension uninstall pileup
No installed extension 'pileup' found.
jupyter nbextension enable --py widgetsnbextension
Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: OK
jupyter nbextension install --py --symlink --user bdgenomics.mango.pileup
Installing /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/pileup/static -> pileup
Symlinking: /home/jenkins/.local/share/jupyter/nbextensions/pileup -> /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/pileup/static
- Validating: OK

    To initialize this nbextension in the browser every time the notebook (or other app) loads:
    
          jupyter nbextension enable bdgenomics.mango.pileup --user --py
    
jupyter nbextension enable bdgenomics.mango.pileup --py --user
Enabling notebook extension pileup/extension...
      - Validating: OK
python setup.py sdist bdist_egg
running sdist
running egg_info
writing bdgenomics.mango.pileup.egg-info/PKG-INFO
writing dependency_links to bdgenomics.mango.pileup.egg-info/dependency_links.txt
writing requirements to bdgenomics.mango.pileup.egg-info/requires.txt
writing top-level names to bdgenomics.mango.pileup.egg-info/top_level.txt
reading manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no files found matching 'version.py'
warning: no files found matching '*.*' under directory 'pileup/static'
writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
running check
creating bdgenomics.mango.pileup-0.0.6a1
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io/test
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/static
creating bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying files to bdgenomics.mango.pileup-0.0.6a1...
copying MANIFEST.in -> bdgenomics.mango.pileup-0.0.6a1
copying README.md -> bdgenomics.mango.pileup-0.0.6a1
copying requirements.txt -> bdgenomics.mango.pileup-0.0.6a1
copying setup.py -> bdgenomics.mango.pileup-0.0.6a1
copying bdgenomics/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics
copying bdgenomics.mango.pileup.egg-info/PKG-INFO -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/SOURCES.txt -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/dependency_links.txt -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/not-zip-safe -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/requires.txt -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics.mango.pileup.egg-info/top_level.txt -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics.mango.pileup.egg-info
copying bdgenomics/mango/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango
copying bdgenomics/mango/io/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/bedfile.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/genomicfile.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/readers.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/utils.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
copying bdgenomics/mango/io/test/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io/test
copying bdgenomics/mango/io/test/test_bed.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io/test
copying bdgenomics/mango/pileup/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/_version.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/pileupViewer.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/sources.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/track.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/static/extension.js -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js.map -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/test/__init__.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_application.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_embed.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_notebook.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_types.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/pileup/test
Writing bdgenomics.mango.pileup-0.0.6a1/setup.cfg
creating dist
Creating tar archive
removing 'bdgenomics.mango.pileup-0.0.6a1' (and everything under it)
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/mango
copying bdgenomics/mango/__init__.py -> build/lib/bdgenomics/mango
creating build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/readers.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/genomicfile.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/__init__.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/utils.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/bedfile.py -> build/lib/bdgenomics/mango/io
creating build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/pileupViewer.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/_version.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/__init__.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/track.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/sources.py -> build/lib/bdgenomics/mango/pileup
creating build/lib/bdgenomics/mango/io/test
copying bdgenomics/mango/io/test/test_bed.py -> build/lib/bdgenomics/mango/io/test
copying bdgenomics/mango/io/test/__init__.py -> build/lib/bdgenomics/mango/io/test
creating build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_application.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_notebook.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_types.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_embed.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/__init__.py -> build/lib/bdgenomics/mango/pileup/test
creating build/lib/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/extension.js -> build/lib/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js -> build/lib/bdgenomics/mango/pileup/static
copying bdgenomics/mango/pileup/static/index.js.map -> build/lib/bdgenomics/mango/pileup/static
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/mango
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/io/readers.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/io/genomicfile.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/io/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/io/test/test_bed.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/io/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/io/utils.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/io/bedfile.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/pileupViewer.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/_version.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/track.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_application.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_notebook.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_types.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_embed.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/static/index.js -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/static/index.js.map -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/static/extension.js -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/sources.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/readers.py to readers.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/genomicfile.py to genomicfile.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test/test_bed.py to test_bed.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/utils.py to utils.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/bedfile.py to bedfile.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/pileupViewer.py to pileupViewer.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/_version.py to _version.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/track.py to track.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/test_application.py to test_application.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/test_notebook.py to test_notebook.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/test_types.py to test_types.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/test_embed.py to test_embed.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/sources.py to sources.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.cpython-36.pyc
installing package data to build/bdist.linux-x86_64/egg
running install_data
creating build/bdist.linux-x86_64/egg/share
creating build/bdist.linux-x86_64/egg/share/jupyter
creating build/bdist.linux-x86_64/egg/share/jupyter/nbextensions
creating build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
copying bdgenomics/mango/pileup/static/extension.js -> build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
copying bdgenomics/mango/pileup/static/index.js -> build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
copying bdgenomics/mango/pileup/static/index.js.map -> build/bdist.linux-x86_64/egg/share/jupyter/nbextensions/pileup
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.pileup.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/bdgenomics.mango.pileup-0.0.6a1-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-viz ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (test-python) @ mango-viz ---
pushd examples \
	&& jupyter nbconvert --to python pileup-tutorial.ipynb
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/examples /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz
[NbConvertApp] Converting notebook pileup-tutorial.ipynb to python
[NbConvertApp] Writing 2872 bytes to pileup-tutorial.py
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics/mango/
============================= test session starts ==============================
platform linux -- Python 3.6.9, pytest-2.8.3, py-1.8.0, pluggy-0.3.1 -- /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/bin/python
cachedir: .cache
rootdir: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz, inifile: 
collecting ... collected 28 items

bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_column_type PASSED
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_required_columns PASSED
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_to_json PASSED
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_validate_num_rows PASSED
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_visualization PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_features PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_genes PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_genotypes PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_pileup PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_toSVG PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_variants PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_zoomIn PASSED
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_zoomOut PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_embed_pileup PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_embed_data_two_widgets PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_snippet PASSED
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_minimal_pileup_html PASSED
bdgenomics/mango/pileup/test/test_notebook.py::MangoVizExampleTest::test_notebook_example PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_coverage PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_features PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_genes PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_genome PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_location PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_pileup PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_scale PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_variants PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_serialization PASSED
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_tracks_serialization PASSED

- generated xml file: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/target/pytest-reports/tests.xml -
========================== 28 passed in 9.80 seconds ===========================
# run lint and flow for js
pushd bdgenomics/mango/js \
	&& npm run lint
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz

> bdgenomics.mango.pileup@0.0.3-a0 lint /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz/bdgenomics/mango/js
> ./scripts/lint.sh

[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-viz ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-viz ---
[INFO] Tests are skipped.
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  4.552 s]
[INFO] Mango: Python visualization hooks .................. SUCCESS [ 39.326 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 44.059 s
[INFO] Finished at: 2019-12-03T08:43:28-08:00
[INFO] Final Memory: 23M/1044M
[INFO] ------------------------------------------------------------------------
+ pushd mango-viz
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-viz /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ make clean
rm -rf bdgenomics/mango/js/dist
rm -rf bdgenomics.mango.pileup.egg-info/
rm -rf bdgenomics/mango/pileup/static/
rm -rf dist/
rm -rf bdgenomics/mango/js/node_modules
jupyter nbextension uninstall pileup
Removing: /home/jenkins/.local/share/jupyter/nbextensions/pileup
+ popd
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ tar tzvf mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
+ grep bdgenomics.mango
+ grep egg
drwxr-xr-x 0/0                    0 2019-12-03 08:38 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/
-rwxr-xr-x jenkins/jenkins      827 2019-12-03 08:38 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/SOURCES.txt
-rwxr-xr-x jenkins/jenkins      798 2019-12-03 08:38 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/PKG-INFO
-rwxr-xr-x jenkins/jenkins       11 2019-12-03 08:38 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/top_level.txt
-rwxr-xr-x jenkins/jenkins       46 2019-12-03 08:38 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/dependency_links.txt
-rwxr-xr-x jenkins/jenkins      145 2019-12-03 08:38 mango-distribution-0.0.4-SNAPSHOT/bdgenomics.mango.egg-info/requires.txt
-rw-r--r-- jenkins/jenkins    51416 2019-12-03 08:38 mango-distribution-0.0.4-SNAPSHOT/repo/bdgenomics.mango-0.0.6a2-py3.6.egg
+ MANGO_NOTEBOOK_LOGS=/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-notebook.log
+ sleep 2
+ bash -xv /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/mango-notebook
+ kill 35885
+ echo 'Mango Notebook Succeeded'
Mango Notebook Succeeded
+ cp -r mango-python/target /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../mango-python/
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test: line 177: 35885 Terminated              bash -xv ${PROJECT_ROOT}/bin/mango-notebook &> ${MANGO_NOTEBOOK_LOGS}
+ 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/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/bin/deactivate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/bin/deactivate
++ _CONDA_DIR=/home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/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 /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ]]

if (( $? == 0 )); then
    # Inverse of activation: run deactivate scripts prior to deactivating env
    _CONDA_D="${CONDA_PREFIX}/etc/conda/deactivate.d"
    if [[ -d $_CONDA_D ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi

#    # get the activation path that would have been provided for this prefix
#    _LAST_ACTIVATE_PATH=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$CONDA_PREFIX")
#
#    # in activate, we replace a placeholder so that conda keeps its place in the PATH order
#    # The activate script sets _CONDA_HOLD here to activate that behavior.
#    #   Otherwise, PATH is simply removed.
#    if [ -n "$_CONDA_HOLD" ]; then
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'CONDA_PATH_PLACEHOLDER\1', '$PATH', 1))")"
#    else
#        export PATH="$($_CONDA_PYTHON2 -c "import re; print(re.sub(r'$_LAST_ACTIVATE_PATH(:?)', r'', '$PATH', 1))")"
#    fi
#
#    unset _LAST_ACTIVATE_PATH

    export PATH=$("$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX")

    unset CONDA_DEFAULT_ENV
    unset CONDA_PREFIX
    unset CONDA_PATH_BACKUP
    export PS1="$CONDA_PS1_BACKUP"
    unset CONDA_PS1_BACKUP
    unset _CONDA_PYTHON2
else
    unset _CONDA_PYTHON2
    return $?
fi
++ ((  0 == 0  ))
++ _CONDA_D=/home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/etc/conda/deactivate.d
++ [[ -d /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/etc/conda/deactivate.d ]]
"$_CONDA_DIR/conda" ..deactivate.path $_SHELL$EXT "$CONDA_PREFIX"
+++ /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643/bin/conda ..deactivate.path bash /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643
++ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ unset CONDA_DEFAULT_ENV
++ unset CONDA_PREFIX
++ unset CONDA_PATH_BACKUP
++ export PS1=
++ PS1=
++ unset CONDA_PS1_BACKUP
++ unset _CONDA_PYTHON2

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ conda remove -y --name mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643 --all

Package plan for package removal in environment /home/jenkins/anaconda2/envs/mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643:

The following packages will be REMOVED:

    _libgcc_mutex:   0.1-main               
    ca-certificates: 2019.10.16-0           
    certifi:         2019.9.11-py36_0       
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       9.1.0-hdf63c60_0       
    libstdcxx-ng:    9.1.0-hdf63c60_0       
    ncurses:         6.1-he6710b0_1         
    nodejs:          10.13.0-he6710b0_0     
    openssl:         1.1.1d-h7b6447c_3      
    pip:             19.3.1-py36_0          
    python:          3.6.9-h265db76_0       
    readline:        7.0-h7b6447c_5         
    setuptools:      42.0.1-py36_0          
    sqlite:          3.30.1-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.6-py36_0          
    xz:              5.2.4-h14c3975_4       
    zlib:            1.2.11-h7b6447c_3      

+ MANGO_BROWSER_LOGS=/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/mango-submit.log
+ sleep 10
+ bash -xv /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../example-files/browser-scripts/run-example.sh
+ 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
  "alignments": [],
+ [[ 0 != 0 ]]
+ grep variants
+ 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
  "variants": [{
+ [[ 0 != 0 ]]
+ PROCESSES=($(ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }'))
ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }'
++ ps aux
++ grep -F browser-scripts/run-example.sh
++ grep -v -F grep
++ awk '{ print $2 }'
+ '[' 1 -gt 0 ']'
+ echo 'Mango Browser Succeeded'
Mango Browser Succeeded
+ kill 41448
+ TEST_GENOME=anoGam1
+ bash -xv /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/make_genome anoGam1 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded
#!/usr/bin/env bash
#
# Licensed to Big Data Genomics (BDG) under one
# or more contributor license agreements.  See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership.  The BDG licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.  You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

# Runs MakeGenome, which generates a .genome file containing reference, genes, cytoband, and chromsizes.
# Requires 2 arguments: genome name and output file to save .genome file to.

SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})
dirname ${BASH_SOURCE[0]}
++ dirname /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/make_genome
+ SOURCE_DIR=/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin

# get Mango jar
MANGO_CLI_JAR=$(${SOURCE_DIR}/find-mango-assembly.sh)
${SOURCE_DIR}/find-mango-assembly.sh
++ /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/find-mango-assembly.sh
+ MANGO_CLI_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

SPARK_SUBMIT=$(${SOURCE_DIR}/find-spark.sh)
${SOURCE_DIR}/find-spark.sh
++ /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/../bin/find-spark.sh
+ SPARK_SUBMIT=/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit

# submit the job to Spark
"$SPARK_SUBMIT" \
  --class "org.bdgenomics.adam.cli.MangoMain" \
  --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
  --conf spark.kryo.registrator=org.bdgenomics.mango.serialization.MangoKryoRegistrator \
  $MANGO_CLI_JAR \
  "MakeGenome" "$@" \

+ /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-hadoop2.7/bin/spark-submit --class org.bdgenomics.adam.cli.MangoMain --conf spark.serializer=org.apache.spark.serializer.KryoSerializer --conf spark.kryo.registrator=org.bdgenomics.mango.serialization.MangoKryoRegistrator /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 MakeGenome anoGam1 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded
19/12/03 08:43:48 WARN Utils: Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
19/12/03 08:43:48 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
19/12/03 08:43:48 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.MangoMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
19/12/03 08:43:49 INFO SparkContext: Running Spark version 2.4.4
19/12/03 08:43:49 INFO SparkContext: Submitted application: MakeGenome
19/12/03 08:43:49 INFO SecurityManager: Changing view acls to: jenkins
19/12/03 08:43:49 INFO SecurityManager: Changing modify acls to: jenkins
19/12/03 08:43:49 INFO SecurityManager: Changing view acls groups to: 
19/12/03 08:43:49 INFO SecurityManager: Changing modify acls groups to: 
19/12/03 08:43:49 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
19/12/03 08:43:49 INFO Utils: Successfully started service 'sparkDriver' on port 34165.
19/12/03 08:43:49 INFO SparkEnv: Registering MapOutputTracker
19/12/03 08:43:49 INFO SparkEnv: Registering BlockManagerMaster
19/12/03 08:43:49 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
19/12/03 08:43:49 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
19/12/03 08:43:49 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-70d86a7b-5cfa-4694-a33c-f6558bd3feb0
19/12/03 08:43:49 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
19/12/03 08:43:49 INFO SparkEnv: Registering OutputCommitCoordinator
19/12/03 08:43:50 WARN Utils: Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
19/12/03 08:43:50 INFO Utils: Successfully started service 'SparkUI' on port 4041.
19/12/03 08:43:50 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.10.31:4041
19/12/03 08:43:50 INFO SparkContext: Added JAR file:/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 at spark://192.168.10.31:34165/jars/mango-assembly-0.0.4-SNAPSHOT.jar with timestamp 1575391430222
19/12/03 08:43:50 INFO Executor: Starting executor ID driver on host localhost
19/12/03 08:43:50 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 32831.
19/12/03 08:43:50 INFO NettyBlockTransferService: Server created on 192.168.10.31:32831
19/12/03 08:43:50 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
19/12/03 08:43:50 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.10.31, 32831, None)
19/12/03 08:43:50 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.10.31:32831 with 366.3 MB RAM, BlockManagerId(driver, 192.168.10.31, 32831, None)
19/12/03 08:43:50 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.10.31, 32831, None)
19/12/03 08:43:50 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.10.31, 32831, None)
Exception in thread "Thread-28" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1896)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1498)
	at java.net.URL.openStream(URL.java:1057)
	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$1.run(ProcessImpl.scala:23)
Exception in thread "Thread-40" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1896)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1498)
	at java.net.URL.openStream(URL.java:1057)
	at scala.sys.process.ProcessBuilderImpl$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$1.run(ProcessImpl.scala:23)
19/12/03 08:43:54 WARN GenomeConfig: No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1
19/12/03 08:43:54 INFO MakeGenome: Saved genome anoGam1 to /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded
19/12/03 08:43:54 INFO MakeGenome: Overall Duration: 5.29 secs
19/12/03 08:43:54 INFO SparkContext: Invoking stop() from shutdown hook
19/12/03 08:43:54 INFO SparkUI: Stopped Spark web UI at http://192.168.10.31:4041
19/12/03 08:43:54 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
19/12/03 08:43:54 INFO MemoryStore: MemoryStore cleared
19/12/03 08:43:54 INFO BlockManager: BlockManager stopped
19/12/03 08:43:54 INFO BlockManagerMaster: BlockManagerMaster stopped
19/12/03 08:43:54 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
19/12/03 08:43:54 INFO SparkContext: Successfully stopped SparkContext
19/12/03 08:43:54 INFO ShutdownHookManager: Shutdown hook called
19/12/03 08:43:54 INFO ShutdownHookManager: Deleting directory /tmp/spark-97c76d36-53ff-4d20-849c-e57fce870ccc
19/12/03 08:43:54 INFO ShutdownHookManager: Deleting directory /tmp/spark-f39a2dff-b542-44c6-8b69-7904223d8041
/home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/scripts/jenkins-test: line 301: 41448 Terminated              bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS}
+ unzip /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/anoGam1.genome -d /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/anoGam1
Archive:  /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/anoGam1.genome
  inflating: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/anoGam1/refGene.txt.gz  
  inflating: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/anoGam1/cytoBand.txt.gz  
  inflating: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/anoGam1/properties.txt  
  inflating: /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/anoGam1/anoGam1.chrom.sizes  
+ pushd /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/anoGam1
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded/anoGam1 /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu
+ cat properties.txt
sequenceLocation=http://hgdownload.cse.ucsc.edu/goldenPath/anoGam1/bigZips/anoGam1.2bit
chromSizes=anoGam1.chrom.sizes
refGene=refGene.txt.gz
+ cat anoGam1.chrom.sizes
chr2L	48795086
chr2R	62725911
chr3L	41284009
chr3R	53272125
chrM	15363
chrU	59568033
chrX	22145176
+ popd
/tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu

echo
+ echo

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

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-b285eee5-9c61-41e5-bf1a-18f9d967e643 --all

CondaEnvironmentNotFoundError: Could not find environment: mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643 .
You can list all discoverable environments with `conda info --envs`.

+ echo 'conda ENV mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643 does not exist'
conda ENV mango-build-b285eee5-9c61-41e5-bf1a-18f9d967e643 does not exist
+ rm -rf /tmp/mangoTest06udJrN/deleteMePleaseThisIsNoLongerNeeded
+ rm -rf /tmp/mangoTestMvnZOZZ8yS
+ mvn --settings=/home/jenkins/workspace/settings.xml deploy -DskipTests -Pdistribution
[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] --- maven-license-plugin:1.10.b1:check (default) @ mango-parent ---
[INFO] Checking licenses...
[INFO] 
[INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ mango-parent ---
[INFO] Installing /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.4/label/ubuntu/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/mango-parent-0.0.4-SNAPSHOT.pom
[INFO] 
[INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ mango-parent ---
Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/maven-metadata.xml
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Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/maven-metadata.xml (613 B at 0.0 KB/sec)
Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/mango-parent-0.0.4-20191203.164538-177.pom
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Uploaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/mango-parent-0.0.4-20191203.164538-177.pom (28 KB at 0.2 KB/sec)
Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/maven-metadata.xml
432/432 B   
            
Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/maven-metadata.xml (432 B at 0.0 KB/sec)
Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/maven-metadata.xml
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Uploaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/0.0.4-SNAPSHOT/maven-metadata.xml (613 B at 0.0 KB/sec)
Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/mango/mango-parent/maven-metadata.xml
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[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,
                                     ^
Build timed out (after 30 minutes). Marking the build as aborted.
/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 {
    ^
Build was aborted
Finished: ABORTED