SuccessConsole Output

Skipping 6,429 KB.. Full Log
x/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/mangoTest0FQ1kTn/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-spark3_2.12/0.32.0/adam-core-spark3_2.12-0.32.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core-spark3_2.12/0.32.0/adam-core-spark3_2.12-0.32.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar to /tmp/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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_2.12/1.3.4/grizzled-slf4j_2.12-1.3.4.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/clapper/grizzled-slf4j_2.12/1.3.4/grizzled-slf4j_2.12-1.3.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar to /tmp/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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-spark3_2.12/0.32.0/adam-codegen-spark3_2.12-0.32.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-codegen-spark3_2.12/0.32.0/adam-codegen-spark3_2.12-0.32.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.15.0/bdg-formats-0.15.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.15.0/bdg-formats-0.15.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark3_2.12/0.3.0/utils-cli-spark3_2.12-0.3.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli-spark3_2.12/0.3.0/utils-cli-spark3_2.12-0.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark3_2.12/0.3.0/utils-misc-spark3_2.12-0.3.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc-spark3_2.12/0.3.0/utils-misc-spark3_2.12-0.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.3.0/utils-intervalrdd-spark3_2.12-0.3.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-intervalrdd-spark3_2.12/0.3.0/utils-intervalrdd-spark3_2.12-0.3.0.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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/scalatra/scalatra_2.12/2.5.0/scalatra_2.12-2.5.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalatra_2.12/2.5.0/scalatra_2.12-2.5.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra-common_2.12/2.5.0/scalatra-common_2.12-2.5.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalatra-common_2.12/2.5.0/scalatra-common_2.12-2.5.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar to /tmp/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/org/scala-lang/modules/scala-parser-combinators_2.12/1.0.4/scala-parser-combinators_2.12-1.0.4.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-parser-combinators_2.12/1.0.4/scala-parser-combinators_2.12-1.0.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-core_2.12/1.9.1/scalate-core_2.12-1.9.1.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-core_2.12/1.9.1/scalate-core_2.12-1.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-compiler/2.12.8/scala-compiler-2.12.8.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scala-compiler/2.12.8/scala-compiler-2.12.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-util_2.12/1.9.1/scalate-util_2.12-1.9.1.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-util_2.12/1.9.1/scalate-util_2.12-1.9.1.jar
[INFO] Installing artifact /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core-spark3_2.12/0.0.6-SNAPSHOT/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark3_2.12/0.3.0/utils-io-spark3_2.12-0.3.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark3_2.12/0.3.0/utils-io-spark3_2.12-0.3.0.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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/mangoTest0FQ1kTn/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/0.9.0/convert-ga4gh-0.9.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.9.0/convert-ga4gh-0.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.9.0/convert-htsjdk-0.9.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.9.0/convert-htsjdk-0.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/extensions/guice-assistedinject/4.2.2/guice-assistedinject-4.2.2.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/inject/extensions/guice-assistedinject/4.2.2/guice-assistedinject-4.2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.9.0/convert-0.9.0.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.9.0/convert-0.9.0.jar
[INFO] Installing artifact /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli-spark3_2.12/0.0.6-SNAPSHOT/mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] 
[INFO] ----------< org.bdgenomics.mango:mango-assembly-spark3_2.12 >-----------
[INFO] Building Mango_2.12: Assembly 0.0.6-SNAPSHOT                       [4/6]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/mangoTest0FQ1kTn/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-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly-spark3_2.12 ---
[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-spark3_2.12 ---
[INFO] Test Source directory: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[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-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/mangoTest0FQ1kTn/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-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ mango-assembly-spark3_2.12 ---
[INFO] Including org.bdgenomics.mango:mango-cli-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.12:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.6 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.12.6 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-spark3_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12: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:2.12.6 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-spark3_2.12:jar:0.32.0 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_2.12:jar:1.3.4 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-spark3_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_2.12:jar:0.3.0 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_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.12:jar:2.5.0 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 org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.12:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.12:jar:1.0.6 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.12.8 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark3_2.12:jar:0.3.0 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:0.9.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.9.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-assistedinject:jar:4.2.2 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.9.0 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar, adam-cli-spark3_2.12-0.32.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar with /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-shaded.jar
[INFO] 
[INFO] --------< org.bdgenomics.mango:mango-distribution-spark3_2.12 >---------
[INFO] Building mango_2.12: Distribution 0.0.6-SNAPSHOT                   [5/6]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.2-beta-5:single (default) @ mango-distribution-spark3_2.12 ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building tar : /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.bz2
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building zip: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.zip
[INFO] 
[INFO] -----------< org.bdgenomics.mango:mango-parent-spark3_2.12 >------------
[INFO] Building mango_2.12 0.0.6-SNAPSHOT                                 [6/6]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent-spark3_2.12 ---
[INFO] Modified 147 of 236 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.12 0.0.6-SNAPSHOT:
[INFO] 
[INFO] mango_2.12: CORE ................................... SUCCESS [ 21.466 s]
[INFO] Mango_2.12: Python APIs ............................ SUCCESS [01:57 min]
[INFO] mango_2.12: CLI .................................... SUCCESS [ 20.537 s]
[INFO] Mango_2.12: Assembly ............................... SUCCESS [ 23.983 s]
[INFO] mango_2.12: Distribution ........................... SUCCESS [ 57.164 s]
[INFO] mango_2.12 ......................................... SUCCESS [  2.489 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  04:03 min
[INFO] Finished at: 2020-08-19T13:34:24Z
[INFO] ------------------------------------------------------------------------
+ pushd mango-python
+ make clean
/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded /home
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
+ pushd mango-pileup
+ make prepare
/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded /home
/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded /home
pip install -r requirements.txt
Collecting ipywidgets>=7.5.0
  Downloading https://files.pythonhosted.org/packages/56/a0/dbcf5881bb2f51e8db678211907f16ea0a182b232c591a6d6f276985ca95/ipywidgets-7.5.1-py2.py3-none-any.whl (121kB)
Collecting six==1.11.0
  Downloading https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Requirement already satisfied: pytest==3.9.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from -r requirements.txt (line 3)) (3.9.1)
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from -r requirements.txt (line 4)) (1.0.0)
Collecting modin[ray]==0.8.0
  Downloading https://files.pythonhosted.org/packages/e9/7c/7ff264198ce393153f75ad6fce9fef9eb7624602776ea9854e4f067712d8/modin-0.8.0-py3-none-manylinux1_x86_64.whl (387kB)
Requirement already satisfied: jupyter_contrib_nbextensions==0.5.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from -r requirements.txt (line 6)) (0.5.1)
Collecting widgetsnbextension~=3.5.0
  Downloading https://files.pythonhosted.org/packages/6c/7b/7ac231c20d2d33c445eaacf8a433f4e22c60677eb9776c7c5262d7ddee2d/widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2MB)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipywidgets>=7.5.0->-r requirements.txt (line 1)) (5.0.7)
Requirement already satisfied: traitlets>=4.3.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipywidgets>=7.5.0->-r requirements.txt (line 1)) (4.3.3)
Requirement already satisfied: ipython>=4.0.0; python_version >= "3.3" in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipywidgets>=7.5.0->-r requirements.txt (line 1)) (7.8.0)
Requirement already satisfied: ipykernel>=4.5.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipywidgets>=7.5.0->-r requirements.txt (line 1)) (5.3.4)
Requirement already satisfied: setuptools in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pytest==3.9.1->-r requirements.txt (line 3)) (49.6.0.post20200814)
Requirement already satisfied: more-itertools>=4.0.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pytest==3.9.1->-r requirements.txt (line 3)) (8.4.0)
Requirement already satisfied: py>=1.5.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pytest==3.9.1->-r requirements.txt (line 3)) (1.9.0)
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Requirement already satisfied: qtconsole in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (4.7.6)
Requirement already satisfied: nbconvert in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.6.1)
Requirement already satisfied: notebook in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (6.1.3)
Requirement already satisfied: jupyter-console in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (6.1.0)
Requirement already satisfied: packaging in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from modin[ray]==0.8.0->-r requirements.txt (line 5)) (20.4)
Collecting pandas==1.0.5
  Downloading https://files.pythonhosted.org/packages/c0/95/cb9820560a2713384ef49060b0087dfa2591c6db6f240215c2bce1f4211c/pandas-1.0.5-cp36-cp36m-manylinux1_x86_64.whl (10.1MB)
Collecting ray==0.8.6; extra == "ray"
  Downloading https://files.pythonhosted.org/packages/ea/0b/f253e92aee1225d9d0ef21dd15514352ce87f6dbc55de70707bc9d52477f/ray-0.8.6-cp36-cp36m-manylinux1_x86_64.whl (21.9MB)
Collecting pyarrow<0.17; extra == "ray"
  Downloading https://files.pythonhosted.org/packages/00/d2/695bab1e1e7a4554b6dbd287d55cca096214bd441037058a432afd724bb1/pyarrow-0.16.0-cp36-cp36m-manylinux2014_x86_64.whl (63.1MB)
Requirement already satisfied: tornado in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (6.0.4)
Requirement already satisfied: jupyter-core in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (4.6.3)
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Requirement already satisfied: pyyaml in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (5.3.1)
Requirement already satisfied: jupyter-highlight-selected-word>=0.1.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (0.2.0)
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Requirement already satisfied: lxml in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->-r requirements.txt (line 6)) (4.5.2)
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Requirement already satisfied: qtpy in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (1.9.0)
Requirement already satisfied: bleach in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.1.5)
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Requirement already satisfied: testpath in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.4.4)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.4.2)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.4)
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Requirement already satisfied: jinja2>=2.4 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (2.11.2)
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Requirement already satisfied: Send2Trash in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.5.0)
Requirement already satisfied: terminado>=0.8.3 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.3)
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Requirement already satisfied: numpy>=1.13.3 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pandas==1.0.5->modin[ray]==0.8.0->-r requirements.txt (line 5)) (1.19.1)
Requirement already satisfied: python-dateutil>=2.6.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pandas==1.0.5->modin[ray]==0.8.0->-r requirements.txt (line 5)) (2.8.1)
Requirement already satisfied: pytz>=2017.2 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pandas==1.0.5->modin[ray]==0.8.0->-r requirements.txt (line 5)) (2020.1)
Collecting google
  Downloading https://files.pythonhosted.org/packages/ac/35/17c9141c4ae21e9a29a43acdfd848e3e468a810517f862cad07977bf8fe9/google-3.0.0-py2.py3-none-any.whl (45kB)
Collecting redis<3.5.0,>=3.3.2
  Downloading https://files.pythonhosted.org/packages/f0/05/1fc7feedc19c123e7a95cfc9e7892eb6cdd2e5df4e9e8af6384349c1cc3d/redis-3.4.1-py2.py3-none-any.whl (71kB)
Requirement already satisfied: colorama in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->-r requirements.txt (line 5)) (0.4.3)
Requirement already satisfied: filelock in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->-r requirements.txt (line 5)) (3.0.12)
Collecting msgpack<2.0.0,>=0.6.0
  Downloading https://files.pythonhosted.org/packages/c9/35/33aa1af0700d21beabdf74373f31c52c048be8ee082f98edbc37ba3ae956/msgpack-1.0.0-cp36-cp36m-manylinux1_x86_64.whl (274kB)
Collecting grpcio
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Requirement already satisfied: click>=7.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->-r requirements.txt (line 5)) (7.1.2)
Collecting aiohttp
  Downloading https://files.pythonhosted.org/packages/7c/39/7eb5f98d24904e0f6d3edb505d4aa60e3ef83c0a58d6fe18244a51757247/aiohttp-3.6.2-cp36-cp36m-manylinux1_x86_64.whl (1.2MB)
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Collecting py-spy>=0.2.0
  Downloading https://files.pythonhosted.org/packages/8e/a7/ab45c9ee3c4654edda3efbd6b8e2fa4962226718a7e3e3be6e3926bf3617/py_spy-0.3.3-py2.py3-none-manylinux1_x86_64.whl (2.9MB)
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Requirement already satisfied: parso<0.8.0,>=0.7.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->-r requirements.txt (line 1)) (0.7.1)
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Requirement already satisfied: webencodings in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5.1)
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Requirement already satisfied: cffi>=1.0.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.14.1)
Collecting beautifulsoup4
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Collecting multidict<5.0,>=4.5
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Collecting async-timeout<4.0,>=3.0
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Collecting typing-extensions>=3.6.5; python_version < "3.7"
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Collecting yarl<2.0,>=1.0
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Collecting idna-ssl>=1.0; python_version < "3.7"
  Downloading https://files.pythonhosted.org/packages/46/03/07c4894aae38b0de52b52586b24bf189bb83e4ddabfe2e2c8f2419eec6f4/idna-ssl-1.1.0.tar.gz
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Collecting soupsieve>1.2
  Downloading https://files.pythonhosted.org/packages/6f/8f/457f4a5390eeae1cc3aeab89deb7724c965be841ffca6cfca9197482e470/soupsieve-2.0.1-py3-none-any.whl
Requirement already satisfied: idna>=2.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from yarl<2.0,>=1.0->aiohttp->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->-r requirements.txt (line 5)) (2.10)
Building wheels for collected packages: idna-ssl
  Building wheel for idna-ssl (setup.py): started
  Building wheel for idna-ssl (setup.py): finished with status 'done'
  Created wheel for idna-ssl: filename=idna_ssl-1.1.0-cp36-none-any.whl size=3161 sha256=9e48303b4af75af28d618e15956edb5a758b8bbee8596e40f24c4ee40fe9fcae
  Stored in directory: /home/jenkins/.cache/pip/wheels/d3/00/b3/32d613e19e08a739751dd6bf998cfed277728f8b2127ad4eb7
Successfully built idna-ssl
ERROR: jupyterlab 2.0.1 has requirement jupyterlab_server~=1.0.0, but you'll have jupyterlab-server 1.2.0 which is incompatible.
ERROR: bdgenomics-mango-pileup 0.0.6a0 has requirement ipywidgets==7.0.0, but you'll have ipywidgets 7.5.1 which is incompatible.
ERROR: bdgenomics-mango-pileup 0.0.6a0 has requirement modin[ray]==0.6.1, but you'll have modin 0.8.0 which is incompatible.
ERROR: bdgenomics-mango-pileup 0.0.6a0 has requirement pytest==2.8.3, but you'll have pytest 3.9.1 which is incompatible.
Installing collected packages: widgetsnbextension, ipywidgets, six, pandas, soupsieve, beautifulsoup4, google, redis, msgpack, grpcio, multidict, async-timeout, typing-extensions, yarl, idna-ssl, aiohttp, py-spy, ray, pyarrow, modin
  Found existing installation: widgetsnbextension 3.0.8
    Uninstalling widgetsnbextension-3.0.8:
      Successfully uninstalled widgetsnbextension-3.0.8
  Found existing installation: ipywidgets 7.0.0
    Uninstalling ipywidgets-7.0.0:
      Successfully uninstalled ipywidgets-7.0.0
  Found existing installation: six 1.15.0
    Uninstalling six-1.15.0:
      Successfully uninstalled six-1.15.0
  Found existing installation: pandas 0.25.1
    Uninstalling pandas-0.25.1:
      Successfully uninstalled pandas-0.25.1
  Found existing installation: redis 3.5.3
    Uninstalling redis-3.5.3:
      Successfully uninstalled redis-3.5.3
  Found existing installation: ray 0.7.3
    Uninstalling ray-0.7.3:
      Successfully uninstalled ray-0.7.3
  Found existing installation: modin 0.6.1
    Uninstalling modin-0.6.1:
      Successfully uninstalled modin-0.6.1
Successfully installed aiohttp-3.6.2 async-timeout-3.0.1 beautifulsoup4-4.9.1 google-3.0.0 grpcio-1.31.0 idna-ssl-1.1.0 ipywidgets-7.5.1 modin-0.8.0 msgpack-1.0.0 multidict-4.7.6 pandas-1.0.5 py-spy-0.3.3 pyarrow-0.16.0 ray-0.8.6 redis-3.4.1 six-1.11.0 soupsieve-2.0.1 typing-extensions-3.7.4.2 widgetsnbextension-3.5.1 yarl-1.5.1
# install node_modules
cd bdgenomics/mango/js; \
	npm install
npm WARN deprecated mkdirp@0.5.1: Legacy versions of mkdirp are no longer supported. Please update to mkdirp 1.x. (Note that the API surface has changed to use Promises in 1.x.)
npm WARN deprecated request@2.88.2: request has been deprecated, see https://github.com/request/request/issues/3142
npm WARN deprecated browserslist@1.7.7: Browserslist 2 could fail on reading Browserslist >3.0 config used in other tools.
npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node v14+. Upgrade to chokidar 3 with 15x less dependencies.
npm WARN deprecated har-validator@5.1.5: this library is no longer supported
npm WARN deprecated core-js@1.2.7: core-js@<3 is no longer maintained and not recommended for usage due to the number of issues. Please, upgrade your dependencies to the actual version of core-js@3.
npm WARN deprecated resolve-url@0.2.1: https://github.com/lydell/resolve-url#deprecated
npm WARN deprecated urix@0.1.0: Please see https://github.com/lydell/urix#deprecated
npm WARN deprecated fsevents@1.2.13: fsevents 1 will break on node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
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@0.0.5-beta.1 prepublish /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
> npm run build


> bdgenomics.mango.pileup@0.0.5-beta.1 build /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
> npm run build:js && webpack


> bdgenomics.mango.pileup@0.0.5-beta.1 build:js /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
> tsc

Hash: fbf91a448a06ec206a44d127a74126237adb3d40d2ec58c120501036ff2f
Version: webpack 4.44.1
Child
    Hash: fbf91a448a06ec206a44
    Time: 2174ms
    Built at: 08/19/2020 1:35:26 PM
           Asset      Size  Chunks             Chunk Names
    extension.js  1.16 KiB       0  [emitted]  main
    Entrypoint main = extension.js
    [0] ./lib/extension.js 1.19 KiB {0} [built]
Child
    Hash: d127a74126237adb3d40
    Time: 19017ms
    Built at: 08/19/2020 1:35:43 PM
           Asset      Size  Chunks                          Chunk Names
        index.js   701 KiB       0  [emitted]        [big]  main
    index.js.map  3.15 MiB       0  [emitted] [dev]         main
    Entrypoint main [big] = index.js index.js.map
      [2] ./node_modules/underscore/modules/index-all.js + 1 modules 326 bytes {0} [built]
          |    2 modules
     [42] (webpack)/buildin/global.js 472 bytes {0} [built]
    [115] (webpack)/buildin/module.js 497 bytes {0} [built]
    [133] ./package.json 1.9 KiB {0} [built]
    [211] ./lib/index.js 2.18 KiB {0} [built]
    [212] ./css/index.css 899 bytes {0} [built]
    [213] ./node_modules/css-loader!./css/index.css 388 bytes {0} [built]
    [216] ./lib/pileupViewer.js 9.96 KiB {0} [built]
    [217] external "@jupyter-widgets/base" 42 bytes {0} [built]
    [521] ./lib/utils.js 703 bytes {0} [built]
        + 512 hidden modules
    
    WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB).
    This can impact web performance.
    Assets: 
      index.js (701 KiB)
    
    WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance.
    Entrypoints:
      main (701 KiB)
          index.js
    
    
    WARNING in webpack performance recommendations: 
    You can limit the size of your bundles by using import() or require.ensure to lazy load some parts of your application.
    For more info visit https://webpack.js.org/guides/code-splitting/
Child
    Hash: d2ec58c120501036ff2f
    Time: 21503ms
    Built at: 08/19/2020 1:35:46 PM
           Asset      Size  Chunks                          Chunk Names
        index.js   690 KiB       0  [emitted]        [big]  main
    index.js.map  3.12 MiB       0  [emitted] [dev]         main
    Entrypoint main [big] = index.js index.js.map
      [2] ./node_modules/underscore/modules/index-all.js + 1 modules 326 bytes {0} [built]
          |    2 modules
     [42] (webpack)/buildin/global.js 472 bytes {0} [built]
    [115] (webpack)/buildin/module.js 497 bytes {0} [built]
    [208] ./package.json 1.9 KiB {0} [built]
    [209] ./lib/embed.js 1.44 KiB {0} [built]
    [210] ./lib/pileupViewer.js 9.96 KiB {0} [built]
    [211] external "@jupyter-widgets/base" 42 bytes {0} [built]
    [515] ./lib/utils.js 703 bytes {0} [built]
        + 508 hidden modules
    
    WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB).
    This can impact web performance.
    Assets: 
      index.js (690 KiB)
    
    WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance.
    Entrypoints:
      main (690 KiB)
          index.js
    
    
    WARNING in webpack performance recommendations: 
    You can limit the size of your bundles by using import() or require.ensure to lazy load some parts of your application.
    For more info visit https://webpack.js.org/guides/code-splitting/
npm notice created a lockfile as package-lock.json. You should commit this file.
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@~2.1.2 (node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@2.1.3: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@^1.2.7 (node_modules/watchpack-chokidar2/node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.13: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
npm WARN @lumino/coreutils@1.5.3 requires a peer of crypto@1.0.1 but none is installed. You must install peer dependencies yourself.
npm WARN ws@7.3.1 requires a peer of bufferutil@^4.0.1 but none is installed. You must install peer dependencies yourself.
npm WARN ws@7.3.1 requires a peer of utf-8-validate@^5.0.2 but none is installed. You must install peer dependencies yourself.

added 1140 packages from 2002 contributors and audited 1143 packages in 54.662s
found 4 vulnerabilities (1 low, 2 moderate, 1 high)
  run `npm audit fix` to fix them, or `npm audit` for details
+ popd
+ mvn -P widgets test
/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded /home
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-pileup-spark3_2.12:jar:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-pileup-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/pom.xml, line 11, column 15
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-parent-spark3_${scala.version.prefix}:0.0.6-SNAPSHOT, /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pom.xml, line 13, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-parent-spark3_2.12:pom:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-parent-spark3_${scala.version.prefix}:0.0.6-SNAPSHOT, /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pom.xml, line 13, column 15
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Mango_2.12: Python visualization hooks                             [jar]
[INFO] mango_2.12                                                         [pom]
[INFO] 
[INFO] -----------< org.bdgenomics.mango:mango-pileup-spark3_2.12 >------------
[INFO] Building Mango_2.12: Python visualization hooks 0.0.6-SNAPSHOT     [1/2]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-pileup-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-pileup-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-pileup-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-pileup-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-pileup-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (dev-python) @ mango-pileup-spark3_2.12 ---
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/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pip-ephem-wheel-cache-enxxau0z
Created temporary directory: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-fk3ona18
Created requirements tracker '/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-fk3ona18'
Created temporary directory: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pip-install-7zsqaquv
Obtaining file:///tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
  Added file:///tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup to build tracker '/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-fk3ona18'
    Running setup.py (path:/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/setup.py) egg_info for package from file:///tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
    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@0.0.5-beta.1 prepublish /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
    > npm run build


    > bdgenomics.mango.pileup@0.0.5-beta.1 build /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
    > npm run build:js && webpack


    > bdgenomics.mango.pileup@0.0.5-beta.1 build:js /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
    > tsc

    Hash: fbf91a448a06ec206a44d127a74126237adb3d40d2ec58c120501036ff2f
    Version: webpack 4.44.1
    Child
        Hash: fbf91a448a06ec206a44
        Time: 217ms
        Built at: 08/19/2020 1:36:09 PM
               Asset      Size  Chunks             Chunk Names
        extension.js  1.16 KiB       0  [emitted]  main
        Entrypoint main = extension.js
        [0] ./lib/extension.js 1.19 KiB {0} [built]
    Child
        Hash: d127a74126237adb3d40
        Time: 10052ms
        Built at: 08/19/2020 1:36:19 PM
               Asset      Size  Chunks                          Chunk Names
            index.js   701 KiB       0  [emitted]        [big]  main
        index.js.map  3.15 MiB       0  [emitted] [dev]         main
        Entrypoint main [big] = index.js index.js.map
          [2] ./node_modules/underscore/modules/index-all.js + 1 modules 326 bytes {0} [built]
              |    2 modules
         [42] (webpack)/buildin/global.js 472 bytes {0} [built]
        [115] (webpack)/buildin/module.js 497 bytes {0} [built]
        [133] ./package.json 1.9 KiB {0} [built]
        [211] ./lib/index.js 2.18 KiB {0} [built]
        [212] ./css/index.css 899 bytes {0} [built]
        [213] ./node_modules/css-loader!./css/index.css 388 bytes {0} [built]
        [216] ./lib/pileupViewer.js 9.96 KiB {0} [built]
        [217] external "@jupyter-widgets/base" 42 bytes {0} [built]
        [521] ./lib/utils.js 703 bytes {0} [built]
            + 512 hidden modules

        WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB).
        This can impact web performance.
        Assets:
          index.js (701 KiB)

        WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance.
        Entrypoints:
          main (701 KiB)
              index.js


        WARNING in webpack performance recommendations:
        You can limit the size of your bundles by using import() or require.ensure to lazy load some parts of your application.
        For more info visit https://webpack.js.org/guides/code-splitting/
    Child
        Hash: d2ec58c120501036ff2f
        Time: 10008ms
        Built at: 08/19/2020 1:36:19 PM
               Asset      Size  Chunks                          Chunk Names
            index.js   690 KiB       0  [emitted]        [big]  main
        index.js.map  3.12 MiB       0  [emitted] [dev]         main
        Entrypoint main [big] = index.js index.js.map
          [2] ./node_modules/underscore/modules/index-all.js + 1 modules 326 bytes {0} [built]
              |    2 modules
         [42] (webpack)/buildin/global.js 472 bytes {0} [built]
        [115] (webpack)/buildin/module.js 497 bytes {0} [built]
        [208] ./package.json 1.9 KiB {0} [built]
        [209] ./lib/embed.js 1.44 KiB {0} [built]
        [210] ./lib/pileupViewer.js 9.96 KiB {0} [built]
        [211] external "@jupyter-widgets/base" 42 bytes {0} [built]
        [515] ./lib/utils.js 703 bytes {0} [built]
            + 508 hidden modules

        WARNING in asset size limit: The following asset(s) exceed the recommended size limit (244 KiB).
        This can impact web performance.
        Assets:
          index.js (690 KiB)

        WARNING in entrypoint size limit: The following entrypoint(s) combined asset size exceeds the recommended limit (244 KiB). This can impact web performance.
        Entrypoints:
          main (690 KiB)
              index.js


        WARNING in webpack performance recommendations:
        You can limit the size of your bundles by using import() or require.ensure to lazy load some parts of your application.
        For more info visit https://webpack.js.org/guides/code-splitting/
    npm WARN @lumino/coreutils@1.5.3 requires a peer of crypto@1.0.1 but none is installed. You must install peer dependencies yourself.
    npm WARN ws@7.3.1 requires a peer of bufferutil@^4.0.1 but none is installed. You must install peer dependencies yourself.
    npm WARN ws@7.3.1 requires a peer of utf-8-validate@^5.0.2 but none is installed. You must install peer dependencies yourself.
    npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@2.1.3 (node_modules/fsevents):
    npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@2.1.3: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
    npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@1.2.13 (node_modules/watchpack-chokidar2/node_modules/fsevents):
    npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@1.2.13: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

    audited 1143 packages in 25.266s
    found 4 vulnerabilities (1 low, 2 moderate, 1 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/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup has version 0.0.6a1, which satisfies requirement bdgenomics.mango.pileup==0.0.6a1 from file:///tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
  Removed bdgenomics.mango.pileup==0.0.6a1 from file:///tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup from build tracker '/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-fk3ona18'
Requirement already satisfied: ipywidgets>=7.5.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (7.5.1)
Requirement already satisfied: six==1.11.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (1.11.0)
Requirement already satisfied: pytest==3.9.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (3.9.1)
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (1.0.0)
Requirement already satisfied: modin[ray]==0.8.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (0.8.0)
  Installing extra requirements: 'ray'
Requirement already satisfied: jupyter_contrib_nbextensions==0.5.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
Requirement already satisfied: traitlets>=4.3.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (4.3.3)
Requirement already satisfied: ipython>=4.0.0; python_version >= "3.3" in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (7.8.0)
Requirement already satisfied: ipykernel>=4.5.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (5.3.4)
Requirement already satisfied: widgetsnbextension~=3.5.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (3.5.1)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (5.0.7)
Requirement already satisfied: pluggy>=0.7 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango.pileup==0.0.6a1) (0.13.1)
Requirement already satisfied: setuptools in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango.pileup==0.0.6a1) (49.6.0.post20200814)
Requirement already satisfied: atomicwrites>=1.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango.pileup==0.0.6a1) (1.4.0)
Requirement already satisfied: more-itertools>=4.0.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango.pileup==0.0.6a1) (8.4.0)
Requirement already satisfied: py>=1.5.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango.pileup==0.0.6a1) (1.9.0)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pytest==3.9.1->bdgenomics.mango.pileup==0.0.6a1) (19.3.0)
Requirement already satisfied: nbconvert in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (5.6.1)
Requirement already satisfied: qtconsole in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (4.7.6)
Requirement already satisfied: notebook in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (6.1.3)
Requirement already satisfied: jupyter-console in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (6.1.0)
Requirement already satisfied: packaging in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (20.4)
Requirement already satisfied: pandas==1.0.5 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.0.5)
Requirement already satisfied: ray==0.8.6; extra == "ray" in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (0.8.6)
Requirement already satisfied: pyarrow<0.17; extra == "ray" in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (0.16.0)
Requirement already satisfied: ipython-genutils in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.2.0)
Requirement already satisfied: jupyter-latex-envs>=1.3.8 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (1.4.6)
Requirement already satisfied: jupyter-core in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (4.6.3)
Requirement already satisfied: jupyter-nbextensions-configurator>=0.4.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.4.1)
Requirement already satisfied: tornado in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (6.0.4)
Requirement already satisfied: lxml in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (4.5.2)
Requirement already satisfied: pyyaml in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (5.3.1)
Requirement already satisfied: jupyter-contrib-core>=0.3.3 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/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-highlight-selected-word>=0.1.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jupyter_contrib_nbextensions==0.5.1->bdgenomics.mango.pileup==0.0.6a1) (0.2.0)
Requirement already satisfied: decorator in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from traitlets>=4.3.1->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (4.4.2)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (4.8.0)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (0.17.2)
Requirement already satisfied: prompt-toolkit<2.1.0,>=2.0.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (2.0.10)
Requirement already satisfied: pickleshare in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (0.7.5)
Requirement already satisfied: backcall in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (0.2.0)
Requirement already satisfied: pygments in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (2.6.1)
Requirement already satisfied: jupyter-client in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ipykernel>=4.5.1->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (6.1.6)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (3.2.0)
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pluggy>=0.7->pytest==3.9.1->bdgenomics.mango.pileup==0.0.6a1) (1.7.0)
Requirement already satisfied: jinja2>=2.4 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (2.11.2)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/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/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (3.1.5)
Requirement already satisfied: testpath in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.4.4)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.4.2)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.3)
Requirement already satisfied: defusedxml in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.6.0)
Requirement already satisfied: qtpy in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.9.0)
Requirement already satisfied: pyzmq>=17.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (19.0.2)
Requirement already satisfied: terminado>=0.8.3 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/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/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.5.0)
Requirement already satisfied: prometheus-client in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.8.0)
Requirement already satisfied: argon2-cffi in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (20.1.0)
Requirement already satisfied: pyparsing>=2.0.2 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from packaging->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (2.4.7)
Requirement already satisfied: pytz>=2017.2 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pandas==1.0.5->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (2020.1)
Requirement already satisfied: python-dateutil>=2.6.1 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pandas==1.0.5->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (2.8.1)
Requirement already satisfied: numpy>=1.13.3 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pandas==1.0.5->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.19.1)
Requirement already satisfied: grpcio in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.31.0)
Requirement already satisfied: colorama in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (0.4.3)
Requirement already satisfied: protobuf>=3.8.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (3.13.0)
Requirement already satisfied: click>=7.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (7.1.2)
Requirement already satisfied: filelock in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (3.0.12)
Requirement already satisfied: py-spy>=0.2.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (0.3.3)
Requirement already satisfied: msgpack<2.0.0,>=0.6.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.0.0)
Requirement already satisfied: redis<3.5.0,>=3.3.2 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (3.4.1)
Requirement already satisfied: aiohttp in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (3.6.2)
Requirement already satisfied: google in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (3.0.0)
Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (0.6.0)
Requirement already satisfied: parso<0.8.0,>=0.7.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jedi>=0.10->ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (0.7.1)
Requirement already satisfied: wcwidth in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (0.2.5)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7.5.0->bdgenomics.mango.pileup==0.0.6a1) (0.16.0)
Requirement already satisfied: zipp>=0.5 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pluggy>=0.7->pytest==3.9.1->bdgenomics.mango.pileup==0.0.6a1) (3.1.0)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from jinja2>=2.4->nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.1.1)
Requirement already satisfied: webencodings in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
Requirement already satisfied: cffi>=1.0.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.14.1)
Requirement already satisfied: idna-ssl>=1.0; python_version < "3.7" in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from aiohttp->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.1.0)
Requirement already satisfied: yarl<2.0,>=1.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from aiohttp->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.5.1)
Requirement already satisfied: typing-extensions>=3.6.5; python_version < "3.7" in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from aiohttp->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (3.7.4.2)
Requirement already satisfied: async-timeout<4.0,>=3.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from aiohttp->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (3.0.1)
Requirement already satisfied: multidict<5.0,>=4.5 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from aiohttp->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (4.7.6)
Requirement already satisfied: chardet<4.0,>=2.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from aiohttp->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (3.0.4)
Requirement already satisfied: beautifulsoup4 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from google->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (4.9.1)
Requirement already satisfied: pycparser in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (2.20)
Requirement already satisfied: idna>=2.0 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from idna-ssl>=1.0; python_version < "3.7"->aiohttp->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (2.10)
Requirement already satisfied: soupsieve>1.2 in /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages (from beautifulsoup4->google->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (2.0.1)
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/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages/~dgenomics.mango.pileup-0.0.6a0.dist-info
      Removing file or directory /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages/bdgenomics.mango.pileup-0.0.6a0.dist-info/
      Created temporary directory: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pip-uninstall-sktv8hbe
      Removing file or directory /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages/bdgenomics/__init__.py
      Created temporary directory: /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages/bdgenomics/~_pycache__
      Removing file or directory /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages/bdgenomics/__pycache__/
      Created temporary directory: /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages/bdgenomics/~ango
      Removing file or directory /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/lib/python3.6/site-packages/bdgenomics/mango/
      Created temporary directory: /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/share/jupyter/nbextensions/~ileup
      Removing file or directory /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/share/jupyter/nbextensions/pileup/
      Successfully uninstalled bdgenomics.mango.pileup-0.0.6a0
  Running setup.py develop for bdgenomics.mango.pileup
    Running command /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/setup.py'"'"'; __file__='"'"'/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/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/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/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/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
Successfully installed bdgenomics.mango.pileup
Cleaning up...
Removed build tracker '/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-fk3ona18'
jupyter nbextension uninstall bdgenomics.mango.pileup
No installed extension 'bdgenomics.mango.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/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/pileup/static -> bdgenomics.mango.pileup
Symlinking: /home/jenkins/.local/share/jupyter/nbextensions/bdgenomics.mango.pileup -> /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/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 bdgenomics.mango.pileup/extension...
      - Validating: OK
jupyter labextension install bdgenomics/mango/js/ # install widget for jupyter lab
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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/VCFfile.py -> bdgenomics.mango.pileup-0.0.6a1/bdgenomics/mango/io
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/io/test/test_vcf.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/pileup
copying bdgenomics/mango/pileup/sources.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/track.py -> 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
creating build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/readers.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/VCFfile.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/bedfile.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
creating 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/__init__.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_application.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_embed.py -> build/lib/bdgenomics/mango/pileup/test
creating build/lib/bdgenomics/mango/io/test
copying bdgenomics/mango/io/test/test_vcf.py -> 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/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/pileup
copying build/lib/bdgenomics/mango/pileup/sources.py -> 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
creating 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_notebook.py -> 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/__init__.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
creating 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/static/index.js -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/static
copying build/lib/bdgenomics/mango/pileup/track.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/__init__.py -> 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/VCFfile.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/io/__init__.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/utils.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_vcf.py -> 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/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
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/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/test/test_types.py to test_types.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_application.py to test_application.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/test/test_embed.py to test_embed.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/__init__.py to __init__.cpython-36.pyc
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/VCFfile.py to VCFfile.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/io/__init__.py to __init__.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/utils.py to utils.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test/test_vcf.py to test_vcf.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/__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-pileup-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-pileup-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-pileup-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (test-python) @ mango-pileup-spark3_2.12 ---
pushd examples \
	&& jupyter nbconvert --to python pileup-tutorial.ipynb
/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/examples /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
[NbConvertApp] Converting notebook pileup-tutorial.ipynb to python
[NbConvertApp] Writing 2970 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 3.6.11, pytest-3.9.1, py-1.9.0, pluggy-0.13.1 -- /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/bin/python
cachedir: .pytest_cache
rootdir: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup, inifile:
collecting ... collected 32 items

bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_column_type PASSED [  3%]
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_required_columns PASSED [  6%]
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_to_json PASSED   [  9%]
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_validate_num_rows PASSED [ 12%]
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_visualization PASSED [ 15%]
bdgenomics/mango/io/test/test_vcf.py::VCFFileTest::test_column_type PASSED [ 18%]
bdgenomics/mango/io/test/test_vcf.py::VCFFileTest::test_required_columns PASSED [ 21%]
bdgenomics/mango/io/test/test_vcf.py::VCFFileTest::test_to_json PASSED   [ 25%]
bdgenomics/mango/io/test/test_vcf.py::VCFFileTest::test_visualization PASSED [ 28%]
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_features PASSED [ 31%]
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_genes PASSED [ 34%]
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_genotypes PASSED [ 37%]
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_pileup PASSED [ 40%]
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_toSVG PASSED [ 43%]
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_variants PASSED [ 46%]
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_zoomIn PASSED [ 50%]
bdgenomics/mango/pileup/test/test_application.py::MangoVizTest::test_zoomOut PASSED [ 53%]
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_embed_pileup PASSED [ 56%]
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_embed_data_two_widgets PASSED [ 59%]
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_snippet PASSED [ 62%]
bdgenomics/mango/pileup/test/test_embed.py::TestEmbed::test_minimal_pileup_html PASSED [ 65%]
bdgenomics/mango/pileup/test/test_notebook.py::MangoVizExampleTest::test_notebook_example PASSED [ 68%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_coverage PASSED [ 71%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_features PASSED [ 75%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_genes PASSED [ 78%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_genome PASSED [ 81%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_location PASSED [ 84%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_pileup PASSED [ 87%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_scale PASSED [ 90%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_invalid_viz_variants PASSED [ 93%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_track_serialization PASSED [ 96%]
bdgenomics/mango/pileup/test/test_types.py::TestTypes::test_tracks_serialization PASSED [100%]

- generated xml file: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/target/pytest-reports/tests.xml -
=============================== warnings summary ===============================
DeprecationWarning: Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator.

UserWarning: User-defined function verification is still under development in Modin. The function provided is not verified.
UserWarning: `Series.<lambda>` defaulting to pandas implementation.
To request implementation, send an email to feature_requests@modin.org.

UserWarning: User-defined function verification is still under development in Modin. The function provided is not verified.
UserWarning: `Series.<lambda>` defaulting to pandas implementation.

UserWarning: User-defined function verification is still under development in Modin. The function provided is not verified.
UserWarning: `Series.<lambda>` defaulting to pandas implementation.

UserWarning: User-defined function verification is still under development in Modin. The function provided is not verified.
UserWarning: `Series.<lambda>` defaulting to pandas implementation.

UserWarning: User-defined function verification is still under development in Modin. The function provided is not verified.
UserWarning: `Series.<lambda>` defaulting to pandas implementation.

UserWarning: Parameters provided defaulting to pandas implementation.

UserWarning: Parameters provided defaulting to pandas implementation.

UserWarning: Parameters provided defaulting to pandas implementation.

UserWarning: Parameters provided defaulting to pandas implementation.

UserWarning: Parameters provided defaulting to pandas implementation.
FutureWarning: the 'numpy' keyword is deprecated and will be removed in a future version. Please take steps to stop the use of 'numpy'
UserWarning: `DataFrame.to_json` defaulting to pandas implementation.

-- Docs: https://docs.pytest.org/en/latest/warnings.html
=================== 32 passed, 18 warnings in 23.97 seconds ====================
# run lint and flow for js
pushd bdgenomics/mango/js \
	&& npm run test
/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup

> bdgenomics.mango.pileup@0.0.5-beta.1 test /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
> karma start --single-run --browsers ChromeHeadlessNoSandbox


START:
ℹ 「wdm」: Hash: 9d2c943b68425fd58dd0
Version: webpack 4.44.1
Time: 80ms
Built at: 08/19/2020 1:38:54 PM
ℹ 「wdm」: Compiled successfully.
ℹ 「wdm」: Compiling...
ℹ 「wdm」: Hash: 857ea458b38d857a1edf
Version: webpack 4.44.1
Time: 578ms
Built at: 08/19/2020 1:38:54 PM
            Asset     Size          Chunks             Chunk Names
lib/test/index.js  926 KiB  lib/test/index  [emitted]  lib/test/index
Entrypoint lib/test/index = lib/test/index.js
[./lib/test/index.js] 478 bytes {lib/test/index} [built]
[./lib/test/utils.js] 1.05 KiB {lib/test/index} [built]
[./lib/test/widget-utils.js] 735 bytes {lib/test/index} [built]
[./lib/utils.js] 703 bytes {lib/test/index} [built]
[./node_modules/assertion-error/index.js] 2.37 KiB {lib/test/index} [built]
[./node_modules/chai/index.js] 40 bytes {lib/test/index} [built]
[./node_modules/chai/lib/chai.js] 1.23 KiB {lib/test/index} [built]
[./node_modules/chai/lib/chai/assertion.js] 5.59 KiB {lib/test/index} [built]
[./node_modules/chai/lib/chai/config.js] 2.87 KiB {lib/test/index} [built]
[./node_modules/chai/lib/chai/core/assertions.js] 130 KiB {lib/test/index} [built]
[./node_modules/chai/lib/chai/interface/assert.js] 91.1 KiB {lib/test/index} [built]
[./node_modules/chai/lib/chai/interface/expect.js] 1.12 KiB {lib/test/index} [built]
[./node_modules/chai/lib/chai/interface/should.js] 6.01 KiB {lib/test/index} [built]
[./node_modules/chai/lib/chai/utils/addChainableMethod.js] 5.32 KiB {lib/test/index} [built]
[./node_modules/chai/lib/chai/utils/index.js] 2.4 KiB {lib/test/index} [built]
    + 28 hidden modules
ℹ 「wdm」: Compiled successfully.
19 08 2020 13:38:55.218:INFO [karma-server]: Karma v5.1.1 server started at http://localhost:9876/
19 08 2020 13:38:55.219:INFO [launcher]: Launching browsers ChromeHeadlessNoSandbox with concurrency unlimited
19 08 2020 13:38:55.227:INFO [launcher]: Starting browser ChromeHeadless
19 08 2020 13:38:56.663:INFO [Chrome Headless 84.0.4147.125 (Linux x86_64)]: Connected on socket agJEgQw-UItcnRLEAAAA with id 53822237
Chrome Headless 84.0.4147.125 (Linux x86_64): Executed 0 of 1 SUCCESS (0 secs / 0 secs)
Chrome Headless 84.0.4147.125 (Linux x86_64): Executed 1 of 1 SUCCESS (0 secs / 0.001 secs)
  utils >
    ✔ has valid genome builds
Chrome Headless 84.0.4147.125 (Linux x86_64): Executed 1 of 1 SUCCESS (0.005 secs / 0.001 secs)
TOTAL: 1 SUCCESS

Finished in 0.005 secs / 0.001 secs @ 13:38:56 GMT+0000 (Coordinated Universal Time)

SUMMARY:
✔ 1 test completed
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-pileup-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-pileup-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] -----------< org.bdgenomics.mango:mango-parent-spark3_2.12 >------------
[INFO] Building mango_2.12 0.0.6-SNAPSHOT                                 [2/2]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent-spark3_2.12 ---
[INFO] Modified 0 of 236 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.12 0.0.6-SNAPSHOT:
[INFO] 
[INFO] Mango_2.12: Python visualization hooks ............. SUCCESS [03:08 min]
[INFO] mango_2.12 ......................................... SUCCESS [  4.397 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  03:12 min
[INFO] Finished at: 2020-08-19T13:39:01Z
[INFO] ------------------------------------------------------------------------
+ pushd mango-pileup
+ make clean
/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-pileup /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded /home
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 bdgenomics.mango.pileup
Removing: /home/jenkins/.local/share/jupyter/nbextensions/bdgenomics.mango.pileup
jupyter labextension uninstall bdgenomics.mango.pileup
Uninstalling bdgenomics.mango.pileup from /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e/share/jupyter/lab/extensions
Building jupyterlab assets (build:prod:minimize)
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+ popd
+ grep bdgenomics.mango
+ grep egg
+ tar tzf mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/bdgenomics.mango.egg-info/
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/bdgenomics.mango.egg-info/top_level.txt
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/bdgenomics.mango.egg-info/dependency_links.txt
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/bdgenomics.mango.egg-info/PKG-INFO
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/bdgenomics.mango.egg-info/SOURCES.txt
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/bdgenomics.mango.egg-info/requires.txt
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/bdgenomics.mango-0.0.6a2-py3.6.egg
+ MANGO_NOTEBOOK_LOGS=/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-notebook.log
+ sleep 2
+ bash -xv /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/bin/mango-notebook -- --ip=0.0.0.0 --no-browser --allow-root
Mango Notebook Succeeded
+ kill 16881
+ echo 'Mango Notebook Succeeded'
+ set +e +x
/opt/conda/bin/deactivate: line 1: 16881 Terminated              bash -xv ${PROJECT_ROOT}/bin/mango-notebook -- --ip=0.0.0.0 --no-browser --allow-root &> ${MANGO_NOTEBOOK_LOGS}
#!/bin/sh
_CONDA_ROOT="/opt/conda"
# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
\echo >&2 "DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'."
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
\. "$_CONDA_ROOT/etc/profile.d/conda.sh" || return $?
export CONDA_EXE='/opt/conda/bin/conda'
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE='/opt/conda/bin/python'

# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause

__add_sys_prefix_to_path() {
    # In dev-mode CONDA_EXE is python.exe and on Windows
    # it is in a different relative location to condabin.
    if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then
        SYSP=$(\dirname "${CONDA_EXE}")
    else
        SYSP=$(\dirname "${CONDA_EXE}")
        SYSP=$(\dirname "${SYSP}")
    fi

    if [ -n "${WINDIR+x}" ]; then
        PATH="${SYSP}/bin:${PATH}"
        PATH="${SYSP}/Scripts:${PATH}"
        PATH="${SYSP}/Library/bin:${PATH}"
        PATH="${SYSP}/Library/usr/bin:${PATH}"
        PATH="${SYSP}/Library/mingw-w64/bin:${PATH}"
        PATH="${SYSP}:${PATH}"
    else
        PATH="${SYSP}/bin:${PATH}"
    fi
    \export PATH
}

__conda_hashr() {
    if [ -n "${ZSH_VERSION:+x}" ]; then
        \rehash
    elif [ -n "${POSH_VERSION:+x}" ]; then
        :  # pass
    else
        \hash -r
    fi
}

__conda_activate() {
    if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
        # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
        # after conda updated to >= 4.4. See issue #6173.
        PS1="$CONDA_PS1_BACKUP"
        \unset CONDA_PS1_BACKUP
    fi

    \local cmd="$1"
    shift
    \local ask_conda
    CONDA_INTERNAL_OLDPATH="${PATH}"
    __add_sys_prefix_to_path
    ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix "$cmd" "$@")" || \return $?
    rc=$?
    PATH="${CONDA_INTERNAL_OLDPATH}"
    \eval "$ask_conda"
    if [ $rc != 0 ]; then
        \export PATH
    fi
    __conda_hashr
}

__conda_reactivate() {
    \local ask_conda
    CONDA_INTERNAL_OLDPATH="${PATH}"
    __add_sys_prefix_to_path
    ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix reactivate)" || \return $?
    PATH="${CONDA_INTERNAL_OLDPATH}"
    \eval "$ask_conda"
    __conda_hashr
}

conda() {
    if [ "$#" -lt 1 ]; then
        "$CONDA_EXE" $_CE_M $_CE_CONDA
    else
        \local cmd="$1"
        shift
        case "$cmd" in
            activate|deactivate)
                __conda_activate "$cmd" "$@"
                ;;
            install|update|upgrade|remove|uninstall)
                CONDA_INTERNAL_OLDPATH="${PATH}"
                __add_sys_prefix_to_path
                "$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
                \local t1=$?
                PATH="${CONDA_INTERNAL_OLDPATH}"
                if [ $t1 = 0 ]; then
                    __conda_reactivate
                else
                    return $t1
                fi
                ;;
            *)
                CONDA_INTERNAL_OLDPATH="${PATH}"
                __add_sys_prefix_to_path
                "$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
                \local t1=$?
                PATH="${CONDA_INTERNAL_OLDPATH}"
                return $t1
                ;;
        esac
    fi
}

if [ -z "${CONDA_SHLVL+x}" ]; then
    \export CONDA_SHLVL=0
    # In dev-mode CONDA_EXE is python.exe and on Windows
    # it is in a different relative location to condabin.
    if [ -n "${_CE_CONDA+x}" ] && [ -n "${WINDIR+x}" ]; then
        PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
    else
        PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
    fi
    \export PATH

    # We're not allowing PS1 to be unbound. It must at least be set.
    # However, we're not exporting it, which can cause problems when starting a second shell
    # via a first shell (i.e. starting zsh from bash).
    if [ -z "${PS1+x}" ]; then
        PS1=
    fi
fi
conda deactivate
export PATH='/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
unset CONDA_PREFIX
unset CONDA_DEFAULT_ENV
unset CONDA_PROMPT_MODIFIER
PS1=''
export CONDA_SHLVL='0'
export CONDA_EXE='/opt/conda/bin/conda'
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE='/opt/conda/bin/python'

## Package Plan ##

  environment location: /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e


The following packages will be REMOVED:

  _libgcc_mutex-0.1-conda_forge
  _openmp_mutex-4.5-1_gnu
  argon2-cffi-20.1.0-py36h8c4c3a4_1
  attrs-19.3.0-py_0
  backcall-0.2.0-pyh9f0ad1d_0
  backports-1.0-py_2
  backports.functools_lru_cache-1.6.1-py_0
  bleach-3.1.5-pyh9f0ad1d_0
  brotlipy-0.7.0-py36h8c4c3a4_1000
  ca-certificates-2020.6.24-0
  certifi-2020.6.20-py36_0
  cffi-1.14.1-py36h0ff685e_0
  chardet-3.0.4-py36h9f0ad1d_1006
  cryptography-3.0-py36h45558ae_0
  decorator-4.4.2-py_0
  defusedxml-0.6.0-py_0
  entrypoints-0.3-py36h9f0ad1d_1001
  idna-2.10-pyh9f0ad1d_0
  importlib-metadata-1.7.0-py36h9f0ad1d_0
  importlib_metadata-1.7.0-0
  ipykernel-5.3.4-py36h95af2a2_0
  ipython-7.16.1-py36h95af2a2_0
  ipython_genutils-0.2.0-py_1
  jedi-0.17.2-py36h9f0ad1d_0
  jinja2-2.11.2-pyh9f0ad1d_0
  json5-0.9.4-pyh9f0ad1d_0
  jsonschema-3.2.0-py36h9f0ad1d_1
  jupyter_client-6.1.6-py_0
  jupyter_core-4.6.3-py36h9f0ad1d_1
  jupyterlab-2.0.1-py_0
  jupyterlab_server-1.2.0-py_0
  ld_impl_linux-64-2.34-hc38a660_9
  libffi-3.2.1-he1b5a44_1007
  libgcc-ng-9.3.0-h24d8f2e_15
  libgomp-9.3.0-h24d8f2e_15
  libsodium-1.0.18-h516909a_0
  libstdcxx-ng-9.3.0-hdf63c60_15
  markupsafe-1.1.1-py36h8c4c3a4_1
  mistune-0.8.4-py36h8c4c3a4_1001
  nbconvert-5.6.1-py36h9f0ad1d_1
  nbformat-5.0.7-py_0
  ncurses-6.2-he1b5a44_1
  nodejs-10.13.0-he6710b0_0
  notebook-6.1.3-py36h9f0ad1d_0
  openssl-1.1.1g-h7b6447c_0
  packaging-20.4-pyh9f0ad1d_0
  pandoc-2.10.1-h516909a_0
  pandocfilters-1.4.2-py_1
  parso-0.7.1-pyh9f0ad1d_0
  pexpect-4.8.0-py36h9f0ad1d_1
  pickleshare-0.7.5-py36h9f0ad1d_1001
  pip-19.3.1-py36_0
  prometheus_client-0.8.0-pyh9f0ad1d_0
  prompt-toolkit-3.0.6-py_0
  ptyprocess-0.6.0-py_1001
  pycparser-2.20-pyh9f0ad1d_2
  pygments-2.6.1-py_0
  pyopenssl-19.1.0-py_1
  pyparsing-2.4.7-pyh9f0ad1d_0
  pyrsistent-0.16.0-py36h8c4c3a4_0
  pysocks-1.7.1-py36h9f0ad1d_1
  python-3.6.11-h4d41432_2_cpython
  python-dateutil-2.8.1-py_0
  python_abi-3.6-1_cp36m
  pyzmq-19.0.2-py36h9947dbf_0
  readline-8.0-he28a2e2_2
  requests-2.24.0-pyh9f0ad1d_0
  send2trash-1.5.0-py_0
  setuptools-49.6.0-py36h9f0ad1d_0
  six-1.15.0-pyh9f0ad1d_0
  sqlite-3.33.0-h4cf870e_0
  terminado-0.8.3-py36h9f0ad1d_1
  testpath-0.4.4-py_0
  tk-8.6.10-hed695b0_0
  tornado-6.0.4-py36h8c4c3a4_1
  traitlets-4.3.3-py36h9f0ad1d_1
  urllib3-1.25.10-py_0
  wcwidth-0.2.5-pyh9f0ad1d_1
  webencodings-0.5.1-py_1
  wheel-0.35.1-pyh9f0ad1d_0
  xz-5.2.5-h516909a_1
  zeromq-4.3.2-he1b5a44_3
  zipp-3.1.0-py_0
  zlib-1.2.11-h516909a_1007


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

Remove all packages in environment /home/jenkins/.conda/envs/mango-build-dc98cff5-ad82-4993-bf0f-227117d7539e:


# test mango submit
MANGO_BROWSER_LOGS=${MANGO_TMP_DIR}/mango-submit.log
+ MANGO_BROWSER_LOGS=/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-submit.log
bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS} &

# sleep for 10 seconds to let mango-browser start up
sleep 10
+ sleep 10
+ bash -xv /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/example-files/browser-scripts/run-example.sh

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

if [[ $? != 0 ]]; then
    echo
    exit 1
fi
+ [[ 0 != 0 ]]

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

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

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

# There should be processes running for mango-browser
if [ "${#PROCESSES[@]}" -gt 0 ] ; then
    echo "Mango Browser Succeeded"
    # kill all Mango Browser related processes
    kill ${PROCESSES};
else
    echo "Mango Browser failed with logs:"
    cat ${MANGO_BROWSER_LOGS}
    exit 1
fi
+ '[' 1 -gt 0 ']'
+ echo 'Mango Browser Succeeded'
Mango Browser Succeeded
+ kill 16989

# test genome builds
TEST_GENOME="anoGam1"
+ TEST_GENOME=anoGam1
bash -xv ${PROJECT_ROOT}/bin/make_genome ${TEST_GENOME} ${MANGO_TMP_DIR}
+ bash -xv /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/bin/make_genome anoGam1 /tmp/mangoTest0FQ1kTn/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 /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/bin/make_genome
+ SOURCE_DIR=/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/bin

# get Mango jar
MANGO_CLI_JAR=$(${SOURCE_DIR}/find-mango-assembly.sh)
++ /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/bin/find-mango-assembly.sh
+ MANGO_CLI_JAR=/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar

SPARK_SUBMIT=$(${SOURCE_DIR}/find-spark.sh)
++ /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/bin/find-spark.sh
+ SPARK_SUBMIT=/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-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/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.0-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 /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar MakeGenome anoGam1 /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded
20/08/19 13:40:41 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
20/08/19 13:40:41 INFO SparkContext: Running Spark version 3.0.0
20/08/19 13:40:41 INFO ResourceUtils: ==============================================================
20/08/19 13:40:41 INFO ResourceUtils: Resources for spark.driver:

20/08/19 13:40:41 INFO ResourceUtils: ==============================================================
20/08/19 13:40:41 INFO SparkContext: Submitted application: MakeGenome
20/08/19 13:40:42 INFO SecurityManager: Changing view acls to: jenkins
20/08/19 13:40:42 INFO SecurityManager: Changing modify acls to: jenkins
20/08/19 13:40:42 INFO SecurityManager: Changing view acls groups to: 
20/08/19 13:40:42 INFO SecurityManager: Changing modify acls groups to: 
20/08/19 13:40:42 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()
20/08/19 13:40:42 INFO Utils: Successfully started service 'sparkDriver' on port 42269.
20/08/19 13:40:42 INFO SparkEnv: Registering MapOutputTracker
20/08/19 13:40:42 INFO SparkEnv: Registering BlockManagerMaster
20/08/19 13:40:42 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/08/19 13:40:42 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/08/19 13:40:42 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
20/08/19 13:40:42 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-43134054-58d7-4d3a-887a-86d491f4b6f3
20/08/19 13:40:42 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
20/08/19 13:40:42 INFO SparkEnv: Registering OutputCommitCoordinator
20/08/19 13:40:42 WARN Utils: Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
20/08/19 13:40:42 INFO Utils: Successfully started service 'SparkUI' on port 4041.
20/08/19 13:40:43 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://c18570184018:4041
20/08/19 13:40:43 INFO SparkContext: Added JAR file:/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar at spark://c18570184018:42269/jars/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar with timestamp 1597844443093
20/08/19 13:40:43 INFO Executor: Starting executor ID driver on host c18570184018
20/08/19 13:40:43 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 36547.
20/08/19 13:40:43 INFO NettyBlockTransferService: Server created on c18570184018:36547
20/08/19 13:40:43 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/08/19 13:40:43 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, c18570184018, 36547, None)
20/08/19 13:40:43 INFO BlockManagerMasterEndpoint: Registering block manager c18570184018:36547 with 408.9 MiB RAM, BlockManagerId(driver, c18570184018, 36547, None)
20/08/19 13:40:43 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, c18570184018, 36547, None)
20/08/19 13:40:43 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, c18570184018, 36547, None)
20/08/19 13:40:45 WARN GenomeConfig$: No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoband.txt.gz for genome anoGam1
20/08/19 13:40:46 INFO MakeGenome: Saved genome anoGam1 to /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded
20/08/19 13:40:46 INFO SparkContext: Invoking stop() from shutdown hook
20/08/19 13:40:46 INFO SparkUI: Stopped Spark web UI at http://c18570184018:4041
20/08/19 13:40:46 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/08/19 13:40:46 INFO MemoryStore: MemoryStore cleared
20/08/19 13:40:46 INFO BlockManager: BlockManager stopped
20/08/19 13:40:46 INFO BlockManagerMaster: BlockManagerMaster stopped
20/08/19 13:40:46 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/08/19 13:40:46 INFO SparkContext: Successfully stopped SparkContext
20/08/19 13:40:46 INFO ShutdownHookManager: Shutdown hook called
20/08/19 13:40:46 INFO ShutdownHookManager: Deleting directory /tmp/spark-5504724c-4a03-4baa-a32d-5d131e9e1065
20/08/19 13:40:46 INFO ShutdownHookManager: Deleting directory /tmp/spark-5ac90a05-8d30-4165-9969-a78c0e24721d
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/3.0.0/label/ubuntu/scripts/jenkins-test: line 331: 16989 Terminated              bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS}

unzip ${MANGO_TMP_DIR}/${TEST_GENOME}.genome -d ${MANGO_TMP_DIR}/${TEST_GENOME}
+ unzip /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/anoGam1.genome -d /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/anoGam1
Archive:  /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/anoGam1.genome
  inflating: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/anoGam1/properties.txt  
  inflating: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/anoGam1/refGene.txt.gz  
  inflating: /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/anoGam1/anoGam1.chrom.sizes  

pushd ${MANGO_TMP_DIR}/${TEST_GENOME}
+ pushd /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/anoGam1
/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded/anoGam1 /tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded /home
cat properties.txt
+ cat properties.txt
sequenceLocation=http://hgdownload.cse.ucsc.edu/goldenPath/anoGam1/bigZips/anoGam1.2bit
chromSizes=anoGam1.chrom.sizes
refGene=refGene.txt.gz
cat ${TEST_GENOME}.chrom.sizes
+ cat anoGam1.chrom.sizes
chr2L	48795086
chr2R	62725911
chr3L	41284009
chr3R	53272125
chrM	15363
chrU	59568033
chrX	22145176
popd
+ popd
/tmp/mangoTest0FQ1kTn/deleteMePleaseThisIsNoLongerNeeded /home

# exist mango working directory
popd
+ popd
/home

echo
+ echo

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

+ echo
clean_up
+ clean_up
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
Finished: SUCCESS