Console Output

Skipping 6,543 KB.. Full Log
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/findbugs/jsr305/3.0.0/jsr305-3.0.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/code/findbugs/jsr305/3.0.0/jsr305-3.0.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-xml_2.12/1.2.0/scala-xml_2.12-1.2.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-xml_2.12/1.2.0/scala-xml_2.12-1.2.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-reflect/2.12.10/scala-reflect-2.12.10.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scala-reflect/2.12.10/scala-reflect-2.12.10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli-spark3_2.12/0.35.0/adam-cli-spark3_2.12-0.35.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli-spark3_2.12/0.35.0/adam-cli-spark3_2.12-0.35.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-apis-spark3_2.12/0.35.0/adam-apis-spark3_2.12-0.35.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis-spark3_2.12/0.35.0/adam-apis-spark3_2.12-0.35.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/args4j/args4j/2.33/args4j-2.33.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/args4j/args4j/2.33/args4j-2.33.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/net/codingwell/scala-guice_2.12/5.0.0/scala-guice_2.12-5.0.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/net/codingwell/scala-guice_2.12/5.0.0/scala-guice_2.12-5.0.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/guice/5.0.1/guice-5.0.1.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/inject/guice/5.0.1/guice-5.0.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/javax/inject/javax.inject/1/javax.inject-1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar to /tmp/mangoTestk9kRHJh/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_2.12/0.35.0/adam-core-spark3_2.12-0.35.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core-spark3_2.12/0.35.0/adam-core-spark3_2.12-0.35.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar to /tmp/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/2.8.0/commons-io-2.8.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/commons-io/commons-io/2.8.0/commons-io-2.8.0.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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/4.5.13/httpclient-4.5.13.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.5.13/httpclient-4.5.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpcore/4.4.13/httpcore-4.4.13.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.4.13/httpcore-4.4.13.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/guava/30.1.1-jre/guava-30.1.1-jre.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/guava/guava/30.1.1-jre/guava-30.1.1-jre.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/failureaccess/1.0.1/failureaccess-1.0.1.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/guava/failureaccess/1.0.1/failureaccess-1.0.1.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/mangoTestk9kRHJh/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/3.8.0/checker-qual-3.8.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/checkerframework/checker-qual/3.8.0/checker-qual-3.8.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/errorprone/error_prone_annotations/2.5.1/error_prone_annotations-2.5.1.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/errorprone/error_prone_annotations/2.5.1/error_prone_annotations-2.5.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/j2objc/j2objc-annotations/1.3/j2objc-annotations-1.3.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/j2objc/j2objc-annotations/1.3/j2objc-annotations-1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-codegen-spark3_2.12/0.35.0/adam-codegen-spark3_2.12-0.35.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-codegen-spark3_2.12/0.35.0/adam-codegen-spark3_2.12-0.35.0.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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/9.4.41.v20210516/jetty-server-9.4.41.v20210516.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-server/9.4.41.v20210516/jetty-server-9.4.41.v20210516.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-http/9.4.41.v20210516/jetty-http-9.4.41.v20210516.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-http/9.4.41.v20210516/jetty-http-9.4.41.v20210516.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-util/9.4.41.v20210516/jetty-util-9.4.41.v20210516.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util/9.4.41.v20210516/jetty-util-9.4.41.v20210516.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-io/9.4.41.v20210516/jetty-io-9.4.41.v20210516.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-io/9.4.41.v20210516/jetty-io-9.4.41.v20210516.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.41.v20210516/jetty-webapp-9.4.41.v20210516.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-webapp/9.4.41.v20210516/jetty-webapp-9.4.41.v20210516.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.41.v20210516/jetty-xml-9.4.41.v20210516.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-xml/9.4.41.v20210516/jetty-xml-9.4.41.v20210516.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.41.v20210516/jetty-servlet-9.4.41.v20210516.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-servlet/9.4.41.v20210516/jetty-servlet-9.4.41.v20210516.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-security/9.4.41.v20210516/jetty-security-9.4.41.v20210516.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-security/9.4.41.v20210516/jetty-security-9.4.41.v20210516.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-util-ajax/9.4.41.v20210516/jetty-util-ajax-9.4.41.v20210516.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util-ajax/9.4.41.v20210516/jetty-util-ajax-9.4.41.v20210516.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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/0.11.0/convert-ga4gh-0.11.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.11.0/convert-ga4gh-0.11.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.11.0/convert-htsjdk-0.11.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.11.0/convert-htsjdk-0.11.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/extensions/guice-assistedinject/5.0.1/guice-assistedinject-5.0.1.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/inject/extensions/guice-assistedinject/5.0.1/guice-assistedinject-5.0.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.11.0/convert-0.11.0.jar to /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.11.0/convert-0.11.0.jar
[INFO] Installing artifact /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTestk9kRHJh/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:1.2:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:4.0.3: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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:compile (scala-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiler bridge file: /home/jenkins/.sbt/1.0/zinc/org.scala-sbt/org.scala-sbt-compiler-bridge_2.12-1.4.4-bin_2.12.10__52.0-1.4.4_20201220T223045.jar
[INFO] compile in 0.1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1: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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1: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:3.2.0:jar (default-jar) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar-no-fork (attach-sources) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.2.0:jar (attach-javadocs) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:4.0.3: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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[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: 2.12.10
[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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.4: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:0.35.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.35.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:5.0.0 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:5.0.1 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:2.12.13 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:3.0.2 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark3_2.12:jar:0.35.0 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:2.8.0 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:4.5.13 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.13 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:30.1.1-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0.1 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:3.8.0 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.5.1 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.3 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark3_2.12:jar:0.35.0 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:9.4.41.v20210516 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:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util-ajax:jar:9.4.41.v20210516 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:0.11.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.11.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-assistedinject:jar:5.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.11.0 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$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar, adam-cli-spark3_2.12-0.35.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar with /tmp/mangoTestk9kRHJh/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:1.2:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2: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:4.4.1:compile (scala-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar-no-fork (attach-sources) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.2.0:jar (attach-javadocs) @ mango-distribution-spark3_2.12 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] >>> scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1: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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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:1.2:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2: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:4.4.1:compile (scala-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar-no-fork (attach-sources) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.2.0:jar (attach-javadocs) @ mango-parent-spark3_2.12 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] >>> scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) > generate-sources @ mango-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) < generate-sources @ mango-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1: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 [ 53.109 s]
[INFO] Mango_2.12: Python APIs ............................ SUCCESS [02:36 min]
[INFO] mango_2.12: CLI .................................... SUCCESS [01:05 min]
[INFO] Mango_2.12: Assembly ............................... SUCCESS [ 35.099 s]
[INFO] mango_2.12: Distribution ........................... SUCCESS [01:54 min]
[INFO] mango_2.12 ......................................... SUCCESS [  4.824 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  07:09 min
[INFO] Finished at: 2021-06-29T19:03:49Z
[INFO] ------------------------------------------------------------------------
+ pushd mango-python
+ make clean
/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestk9kRHJh/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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded /home
/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded /home
pip install -r requirements.txt
Collecting ipywidgets>=7.5.0
  Downloading https://files.pythonhosted.org/packages/11/53/084940a83a8158364e630a664a30b03068c25ab75243224d6b488800d43a/ipywidgets-7.6.3-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
Collecting pytest>=5.3.2
  Downloading https://files.pythonhosted.org/packages/a1/59/6821e900592fbe261f19d67e4def0cb27e52ef8ed16d9922c144961cc1ee/pytest-6.2.4-py3-none-any.whl (280kB)
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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)
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Collecting jupyterlab-widgets>=1.0.0; python_version >= "3.6"
  Downloading https://files.pythonhosted.org/packages/18/b5/3473d275e3b2359efdf5768e9df95537308b93a31ad94fa92814ac565826/jupyterlab_widgets-1.0.0-py3-none-any.whl (243kB)
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Collecting widgetsnbextension~=3.5.0
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Collecting toml
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Collecting iniconfig
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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)
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Collecting grpcio
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Collecting google
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Collecting msgpack<2.0.0,>=0.6.0
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Collecting aiohttp
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Collecting py-spy>=0.2.0
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Collecting redis<3.5.0,>=3.3.2
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Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython>=4.0.0; python_version >= "3.3"->ipywidgets>=7.5.0->-r requirements.txt (line 1)) (0.7.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets>=7.5.0->-r requirements.txt (line 1)) (0.17.3)
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Requirement already satisfied: MarkupSafe>=2.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from jinja2>=2.4->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (2.0.1)
Requirement already satisfied: cffi>=1.0.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.14.5)
Collecting beautifulsoup4
  Downloading https://files.pythonhosted.org/packages/d1/41/e6495bd7d3781cee623ce23ea6ac73282a373088fcd0ddc809a047b18eae/beautifulsoup4-4.9.3-py3-none-any.whl (115kB)
Collecting multidict<7.0,>=4.5
  Downloading https://files.pythonhosted.org/packages/a1/35/b22524d6b9cacfb4c5eff413a069bbc17c6ea628e54da5c6c989998ced5f/multidict-5.1.0-cp36-cp36m-manylinux2014_x86_64.whl (141kB)
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
Collecting async-timeout<4.0,>=3.0
  Downloading https://files.pythonhosted.org/packages/e1/1e/5a4441be21b0726c4464f3f23c8b19628372f606755a9d2e46c187e65ec4/async_timeout-3.0.1-py3-none-any.whl
Requirement already satisfied: chardet<5.0,>=2.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from aiohttp->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->-r requirements.txt (line 5)) (4.0.0)
Collecting yarl<2.0,>=1.0
  Downloading https://files.pythonhosted.org/packages/da/08/52b26b44bce7b818b410aee37c5e424c9ea420c557bca97dc2adac29b151/yarl-1.6.3-cp36-cp36m-manylinux2014_x86_64.whl (293kB)
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Collecting soupsieve>1.2; python_version >= "3.0"
  Downloading https://files.pythonhosted.org/packages/36/69/d82d04022f02733bf9a72bc3b96332d360c0c5307096d76f6bb7489f7e57/soupsieve-2.2.1-py3-none-any.whl
Requirement already satisfied: idna>=2.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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->-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=3163 sha256=3c1a015eb35bc36dbe3795ce2a22faead25dc57fc5503b78e394fdf712cd402d
  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 7.6.3 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 6.2.4 which is incompatible.
Installing collected packages: jupyterlab-widgets, widgetsnbextension, ipywidgets, six, toml, iniconfig, pytest, pandas, grpcio, soupsieve, beautifulsoup4, google, msgpack, multidict, idna-ssl, async-timeout, yarl, aiohttp, py-spy, redis, 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 1.16.0
    Uninstalling six-1.16.0:
      Successfully uninstalled six-1.16.0
  Found existing installation: pytest 3.9.1
    Uninstalling pytest-3.9.1:
      Successfully uninstalled pytest-3.9.1
  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-3.7.4.post0 async-timeout-3.0.1 beautifulsoup4-4.9.3 google-3.0.0 grpcio-1.38.1 idna-ssl-1.1.0 iniconfig-1.1.1 ipywidgets-7.6.3 jupyterlab-widgets-1.0.0 modin-0.8.0 msgpack-1.0.2 multidict-5.1.0 pandas-1.0.5 py-spy-0.3.7 pyarrow-0.16.0 pytest-6.2.4 ray-0.8.6 redis-3.4.1 six-1.11.0 soupsieve-2.2.1 toml-0.10.2 widgetsnbextension-3.5.1 yarl-1.6.3
# 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 debug@4.1.1: Debug versions >=3.2.0 <3.2.7 || >=4 <4.3.1 have a low-severity ReDos regression when used in a Node.js environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (https://github.com/visionmedia/debug/issues/797)
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 uuid@3.4.0: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
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@<3.3 is no longer maintained and not recommended for usage due to the number of issues. Because of the V8 engine whims, feature detection in old core-js versions could cause a slowdown up to 100x even if nothing is polyfilled. Please, upgrade your dependencies to the actual version of core-js.
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@0.0.6-beta.1 prepublish /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
> npm run build


> bdgenomics.mango.pileup@0.0.6-beta.1 build /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
> npm run build:js && webpack


> bdgenomics.mango.pileup@0.0.6-beta.1 build:js /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
> tsc

Hash: fbf91a448a06ec206a44bd27fedd62b484d5355d2fa11183ca4b226a5b67
Version: webpack 4.46.0
Child
    Hash: fbf91a448a06ec206a44
    Time: 3775ms
    Built at: 06/29/2021 7:05:50 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: bd27fedd62b484d5355d
    Time: 39391ms
    Built at: 06/29/2021 7:06:25 PM
           Asset      Size  Chunks                          Chunk Names
        index.js   706 KiB       0  [emitted]        [big]  main
    index.js.map  3.27 MiB       0  [emitted] [dev]         main
    Entrypoint main [big] = index.js index.js.map
      [4] ./node_modules/underscore/modules/index-all.js + 159 modules 81.3 KiB {0} [built]
          |    160 modules
     [34] (webpack)/buildin/global.js 472 bytes {0} [built]
    [109] (webpack)/buildin/module.js 497 bytes {0} [built]
    [124] (webpack)/buildin/harmony-module.js 573 bytes {0} [built]
    [128] ./package.json 1.99 KiB {0} [built]
    [201] ./lib/index.js 2.18 KiB {0} [built]
    [202] ./css/index.css 899 bytes {0} [built]
    [203] ./node_modules/css-loader!./css/index.css 333 bytes {0} [built]
    [206] ./lib/pileupViewer.js 10.6 KiB {0} [built]
    [207] external "@jupyter-widgets/base" 42 bytes {0} [built]
    [453] ./lib/utils.js 703 bytes {0} [built]
    [454] ./node_modules/react-color/es/index.js + 211 modules 268 KiB {0} [built]
          |    212 modules
        + 444 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 (706 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 (706 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: 2fa11183ca4b226a5b67
    Time: 43219ms
    Built at: 06/29/2021 7:06:29 PM
           Asset      Size  Chunks                          Chunk Names
        index.js   695 KiB       0  [emitted]        [big]  main
    index.js.map  3.24 MiB       0  [emitted] [dev]         main
    Entrypoint main [big] = index.js index.js.map
      [4] ./node_modules/underscore/modules/index-all.js + 159 modules 81.3 KiB {0} [built]
          |    160 modules
     [34] (webpack)/buildin/global.js 472 bytes {0} [built]
    [109] (webpack)/buildin/module.js 497 bytes {0} [built]
    [124] (webpack)/buildin/harmony-module.js 573 bytes {0} [built]
    [194] ./package.json 1.99 KiB {0} [built]
    [199] ./lib/embed.js 1.44 KiB {0} [built]
    [200] ./lib/pileupViewer.js 10.6 KiB {0} [built]
    [201] external "@jupyter-widgets/base" 42 bytes {0} [built]
    [447] ./lib/utils.js 703 bytes {0} [built]
    [448] ./node_modules/react-color/es/index.js + 211 modules 268 KiB {0} [built]
          |    212 modules
        + 440 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 (695 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 (695 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@~2.3.2 (node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@2.3.2: 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@1.8.0 requires a peer of crypto@1.0.1 but none is installed. You must install peer dependencies yourself.

added 1141 packages from 2058 contributors and audited 1144 packages in 114.142s

51 packages are looking for funding
  run `npm fund` for details

found 6 vulnerabilities (1 low, 3 moderate, 2 high)
  run `npm audit fix` to fix them, or `npm audit` for details
/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded /home
+ popd
+ mvn -P widgets test
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_${scala.version.prefix}:[unknown-version], /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/pom.xml, line 11, column 15
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-parent-spark3_${scala.version.prefix}:0.0.6-SNAPSHOT, /tmp/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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:1.2:enforce (enforce-versions) @ mango-pileup-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2: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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:compile (scala-compile-first) @ mango-pileup-spark3_2.12 ---
[INFO] compile in 0.0 s
[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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/pip-ephem-wheel-cache-2ibiwpkf
Created temporary directory: /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9p4581jv
Created requirements tracker '/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9p4581jv'
Created temporary directory: /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/pip-install-vg1zfsq9
Obtaining file:///tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
  Added file:///tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup to build tracker '/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9p4581jv'
    Running setup.py (path:/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/setup.py) egg_info for package from file:///tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
    Running command python setup.py egg_info
    running egg_info
    running jsdeps
    6.14.7
    6.14.7
    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@0.0.6-beta.1 prepublish /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
    > npm run build


    > bdgenomics.mango.pileup@0.0.6-beta.1 build /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
    > npm run build:js && webpack


    > bdgenomics.mango.pileup@0.0.6-beta.1 build:js /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
    > tsc

    Hash: fbf91a448a06ec206a44bd27fedd62b484d5355d2fa11183ca4b226a5b67
    Version: webpack 4.46.0
    Child
        Hash: fbf91a448a06ec206a44
        Time: 331ms
        Built at: 06/29/2021 7:07:08 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: bd27fedd62b484d5355d
        Time: 16204ms
        Built at: 06/29/2021 7:07:24 PM
               Asset      Size  Chunks                          Chunk Names
            index.js   706 KiB       0  [emitted]        [big]  main
        index.js.map  3.27 MiB       0  [emitted] [dev]         main
        Entrypoint main [big] = index.js index.js.map
          [4] ./node_modules/underscore/modules/index-all.js + 159 modules 81.3 KiB {0} [built]
              |    160 modules
         [34] (webpack)/buildin/global.js 472 bytes {0} [built]
        [109] (webpack)/buildin/module.js 497 bytes {0} [built]
        [124] (webpack)/buildin/harmony-module.js 573 bytes {0} [built]
        [128] ./package.json 1.99 KiB {0} [built]
        [201] ./lib/index.js 2.18 KiB {0} [built]
        [202] ./css/index.css 899 bytes {0} [built]
        [203] ./node_modules/css-loader!./css/index.css 333 bytes {0} [built]
        [206] ./lib/pileupViewer.js 10.6 KiB {0} [built]
        [207] external "@jupyter-widgets/base" 42 bytes {0} [built]
        [453] ./lib/utils.js 703 bytes {0} [built]
        [454] ./node_modules/react-color/es/index.js + 211 modules 268 KiB {0} [built]
              |    212 modules
            + 444 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 (706 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 (706 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: 2fa11183ca4b226a5b67
        Time: 19869ms
        Built at: 06/29/2021 7:07:27 PM
               Asset      Size  Chunks                          Chunk Names
            index.js   695 KiB       0  [emitted]        [big]  main
        index.js.map  3.24 MiB       0  [emitted] [dev]         main
        Entrypoint main [big] = index.js index.js.map
          [4] ./node_modules/underscore/modules/index-all.js + 159 modules 81.3 KiB {0} [built]
              |    160 modules
         [34] (webpack)/buildin/global.js 472 bytes {0} [built]
        [109] (webpack)/buildin/module.js 497 bytes {0} [built]
        [124] (webpack)/buildin/harmony-module.js 573 bytes {0} [built]
        [194] ./package.json 1.99 KiB {0} [built]
        [199] ./lib/embed.js 1.44 KiB {0} [built]
        [200] ./lib/pileupViewer.js 10.6 KiB {0} [built]
        [201] external "@jupyter-widgets/base" 42 bytes {0} [built]
        [447] ./lib/utils.js 703 bytes {0} [built]
        [448] ./node_modules/react-color/es/index.js + 211 modules 268 KiB {0} [built]
              |    212 modules
            + 440 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 (695 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 (695 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@1.8.0 requires a peer of crypto@1.0.1 but none is installed. You must install peer dependencies yourself.
    npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents@2.3.2 (node_modules/fsevents):
    npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents@2.3.2: 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 1144 packages in 43.733s

    51 packages are looking for funding
      run `npm fund` for details

    found 6 vulnerabilities (1 low, 3 moderate, 2 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
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    writing manifest file 'bdgenomics.mango.pileup.egg-info/SOURCES.txt'
  Source in /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup has version 0.0.6a1, which satisfies requirement bdgenomics.mango.pileup==0.0.6a1 from file:///tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
  Removed bdgenomics.mango.pileup==0.0.6a1 from file:///tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup from build tracker '/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9p4581jv'
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Requirement already satisfied: six==1.11.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (1.11.0)
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  Installing extra requirements: 'ray'
Requirement already satisfied: jupyter_contrib_nbextensions==0.5.1 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
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Requirement already satisfied: pandas==1.0.5 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.0.5)
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Requirement already satisfied: numpy>=1.13.3 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from pandas==1.0.5->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.19.5)
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Requirement already satisfied: grpcio in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.38.1)
Requirement already satisfied: google in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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: msgpack<2.0.0,>=0.6.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (1.0.2)
Requirement already satisfied: py-spy>=0.2.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (0.3.7)
Requirement already satisfied: filelock in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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: redis<3.5.0,>=3.3.2 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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: click>=7.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (8.0.1)
Requirement already satisfied: colorama in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (0.4.4)
Requirement already satisfied: aiohttp in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (3.7.4.post0)
Requirement already satisfied: wcwidth in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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: parso<0.8.0,>=0.7.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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: ptyprocess>=0.5 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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) (0.7.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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) (0.17.3)
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Requirement already satisfied: async-generator in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.10)
Requirement already satisfied: nest-asyncio in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from nbclient<0.6.0,>=0.5.0->nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (1.5.1)
Requirement already satisfied: webencodings in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango.pileup==0.0.6a1) (0.5.1)
Requirement already satisfied: beautifulsoup4 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages (from google->ray==0.8.6; extra == "ray"->modin[ray]==0.8.0->bdgenomics.mango.pileup==0.0.6a1) (4.9.3)
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Requirement already satisfied: idna>=2.0 in /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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)
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-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages/~dgenomics.mango.pileup-0.0.6a0.dist-info
      Removing file or directory /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages/bdgenomics.mango.pileup-0.0.6a0.dist-info/
      Created temporary directory: /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/pip-uninstall-vixbk5cg
      Removing file or directory /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages/bdgenomics/__init__.py
      Created temporary directory: /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages/bdgenomics/~_pycache__
      Removing file or directory /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages/bdgenomics/__pycache__/
      Created temporary directory: /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages/bdgenomics/~ango
      Removing file or directory /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages/bdgenomics/mango/
      Created temporary directory: /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/share/jupyter/nbextensions/~ileup
      Removing file or directory /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/setup.py'"'"'; __file__='"'"'/tmp/mangoTestk9kRHJh/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-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
Successfully installed bdgenomics.mango.pileup
Cleaning up...
Removed build tracker '/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/pip-req-tracker-9p4581jv'
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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/pileup/static -> bdgenomics.mango.pileup
Symlinking: /home/jenkins/.local/share/jupyter/nbextensions/bdgenomics.mango.pileup -> /tmp/mangoTestk9kRHJh/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
-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/Building jupyterlab assets (build:dev:minimize)
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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/pileupViewer.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/__init__.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/sources.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/_version.py -> build/lib/bdgenomics/mango/pileup
copying bdgenomics/mango/pileup/track.py -> build/lib/bdgenomics/mango/pileup
creating build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/genomicfile.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/bedfile.py -> 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/utils.py -> build/lib/bdgenomics/mango/io
copying bdgenomics/mango/io/__init__.py -> build/lib/bdgenomics/mango/io
creating build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_embed.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_notebook.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_application.py -> build/lib/bdgenomics/mango/pileup/test
copying bdgenomics/mango/pileup/test/test_types.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
copying build/lib/bdgenomics/__init__.py -> 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/_version.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_application.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/test_embed.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
copying build/lib/bdgenomics/mango/pileup/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test
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/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/track.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
copying build/lib/bdgenomics/mango/pileup/sources.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
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/index.js -> 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/pileupViewer.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup
creating 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/utils.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/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
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/io/test/test_bed.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/io/test/test_vcf.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/io/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io/test
copying build/lib/bdgenomics/mango/io/bedfile.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/io
copying build/lib/bdgenomics/mango/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.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/test/test_application.py to test_application.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/test_embed.py to test_embed.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/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/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/track.py to track.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/pileup/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/io/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/utils.py to utils.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/genomicfile.py to genomicfile.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/test/test_bed.py to test_bed.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/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/io/bedfile.py to bedfile.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/__init__.py to __init__.cpython-36.pyc
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:3.8.1: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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-pileup-spark3_2.12 ---
[INFO] compile in 0.0 s
[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/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/examples /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
[NbConvertApp] Converting notebook pileup-tutorial.ipynb to python
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics/mango/
============================= test session starts ==============================
platform linux -- Python 3.6.13, pytest-6.2.4, py-1.10.0, pluggy-0.13.1 -- /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/bin/python
cachedir: .pytest_cache
rootdir: /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup
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%]

=============================== warnings summary ===============================
../../../../home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/lib/python3.6/site-packages/ipywidgets/widgets/widget.py:282
  DeprecationWarning: Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator.

bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_column_type
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_required_columns
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_to_json
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_validate_num_rows
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_visualization
  UserWarning: User-defined function verification is still under development in Modin. The function provided is not verified.

bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_column_type
  UserWarning: `Series.<lambda>` defaulting to pandas implementation.
  To request implementation, send an email to feature_requests@modin.org.

bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_required_columns
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_to_json
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_validate_num_rows
bdgenomics/mango/io/test/test_bed.py::BedFileTest::test_visualization
  UserWarning: `Series.<lambda>` defaulting to pandas implementation.

bdgenomics/mango/io/test/test_vcf.py::VCFFileTest::test_column_type
bdgenomics/mango/io/test/test_vcf.py::VCFFileTest::test_required_columns
bdgenomics/mango/io/test/test_vcf.py::VCFFileTest::test_to_json
bdgenomics/mango/io/test/test_vcf.py::VCFFileTest::test_visualization
bdgenomics/mango/pileup/test/test_notebook.py::MangoVizExampleTest::test_notebook_example
  UserWarning: Parameters provided defaulting to pandas implementation.

bdgenomics/mango/pileup/test/test_notebook.py::MangoVizExampleTest::test_notebook_example
  FutureWarning: the 'numpy' keyword is deprecated and will be removed in a future version. Please take steps to stop the use of 'numpy'

bdgenomics/mango/pileup/test/test_notebook.py::MangoVizExampleTest::test_notebook_example
  UserWarning: `DataFrame.to_json` defaulting to pandas implementation.

-- Docs: https://docs.pytest.org/en/stable/warnings.html
- generated xml file: /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/target/pytest-reports/tests.xml -
======================= 32 passed, 18 warnings in 30.62s =======================
# run lint and flow for js
pushd bdgenomics/mango/js \
	&& npm run test
/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup

> bdgenomics.mango.pileup@0.0.6-beta.1 test /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup/bdgenomics/mango/js
> karma start --single-run --browsers ChromeHeadlessNoSandbox


START:
ℹ 「wdm」: Hash: 9d2c943b68425fd58dd0
Version: webpack 4.46.0
Time: 128ms
Built at: 06/29/2021 7:12:31 PM
ℹ 「wdm」: Compiled successfully.
ℹ 「wdm」: Compiling...
ℹ 「wdm」: Hash: 1b5c8ace8c034b77d2a9
Version: webpack 4.46.0
Time: 9202ms
Built at: 06/29/2021 7:12:40 PM
            Asset      Size          Chunks             Chunk Names
lib/test/index.js  11.8 MiB  lib/test/index  [emitted]  lib/test/index
Entrypoint lib/test/index = lib/test/index.js
[./lib/pileupViewer.js] 10.6 KiB {lib/test/index} [built]
[./lib/test/dummy-manager.js] 6.38 KiB {lib/test/index} [built]
[./lib/test/index.js] 521 bytes {lib/test/index} [built]
[./lib/test/pileupViewer.js] 1.79 KiB {lib/test/index} [built]
[./lib/test/utils.js] 1.05 KiB {lib/test/index} [built]
[./lib/test/widget-utils.js] 2.78 KiB {lib/test/index} [built]
[./lib/utils.js] 703 bytes {lib/test/index} [built]
[./node_modules/@jupyter-widgets/base/lib/index.js] 367 bytes {lib/test/index} [built]
[./node_modules/@jupyter-widgets/base/lib/manager-base.js] 20.9 KiB {lib/test/index} [built]
[./node_modules/@jupyter-widgets/controls/lib/index.js] 780 bytes {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/pileup/dist/main/pileup.js] 10.7 KiB {lib/test/index} [built]
[./node_modules/underscore/modules/index-all.js] 809 bytes {lib/test/index} [built]
[./package.json] 1.99 KiB {lib/test/index} [built]
    + 931 hidden modules
ℹ 「wdm」: Compiled successfully.
29 06 2021 19:12:41.558:INFO [karma-server]: Karma v5.2.3 server started at http://localhost:9876/
29 06 2021 19:12:41.562:INFO [launcher]: Launching browsers ChromeHeadlessNoSandbox with concurrency unlimited
29 06 2021 19:12:41.789:INFO [launcher]: Starting browser ChromeHeadless
29 06 2021 19:12:44.161:INFO [Chrome Headless 84.0.4147.135 (Linux x86_64)]: Connected on socket Kt6mJwjr8BsFMMA5AAAA with id 14014436
Chrome Headless 84.0.4147.135 (Linux x86_64): Executed 0 of 2 SUCCESS (0 secs / 0 secs)
Chrome Headless 84.0.4147.135 (Linux x86_64): Executed 1 of 2 SUCCESS (0 secs / 0.002 secs)
  utils >
    ✔ has valid genome builds
Chrome Headless 84.0.4147.135 (Linux x86_64): Executed 2 of 2 SUCCESS (0 secs / 0.01 secs)
  pileupViewer
    ✔ has set correct parameters
Chrome Headless 84.0.4147.135 (Linux x86_64): Executed 2 of 2 SUCCESS (0.025 secs / 0.01 secs)
TOTAL: 2 SUCCESS

Finished in 0.025 secs / 0.01 secs @ 19:12:45 GMT+0000 (Coordinated Universal Time)

SUMMARY:
✔ 2 tests completed
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1: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:1.2:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2: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:4.4.1:compile (scala-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] compile in 0.0 s
[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 [06:09 min]
[INFO] mango_2.12 ......................................... SUCCESS [  8.942 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  06:18 min
[INFO] Finished at: 2021-06-29T19:12:54Z
[INFO] ------------------------------------------------------------------------
/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-pileup /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded /home
+ pushd mango-pileup
+ make clean
rm -rf bdgenomics/mango/js/dist
rm -rf bdgenomics.mango.pileup.egg-info/
rm -rf bdgenomics/mango/pileup/static/
rm -rf dist/
rm -rf bdgenomics/mango/js/node_modules
jupyter nbextension uninstall 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-1a4fca2b-84d7-4e30-8ff7-767adf5c512d/share/jupyter/lab/extensions
Building jupyterlab assets (build:prod:minimize)
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/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded /home
+ 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/dependency_links.txt
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/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/bdgenomics.mango.egg-info/PKG-INFO
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/bdgenomics.mango-0.0.6a2-py3.6.egg
+ MANGO_NOTEBOOK_LOGS=/tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/mango-notebook.log
+ sleep 2
+ bash -xv /tmp/mangoTestk9kRHJh/deleteMePleaseThisIsNoLongerNeeded/bin/mango-notebook -- --ip=0.0.0.0 --no-browser --allow-root
Mango Notebook Succeeded
+ kill 17463
+ echo 'Mango Notebook Succeeded'
+ set +e +x
#!/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
/opt/conda/bin/deactivate: line 7: 17463 Terminated              bash -xv ${PROJECT_ROOT}/bin/mango-notebook -- --ip=0.0.0.0 --no-browser --allow-root &> ${MANGO_NOTEBOOK_LOGS}
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-1a4fca2b-84d7-4e30-8ff7-767adf5c512d


The following packages will be REMOVED:

  _libgcc_mutex-0.1-conda_forge
  _openmp_mutex-4.5-1_gnu
  argon2-cffi-20.1.0-py36h8f6f2f9_2
  async_generator-1.10-py_0
  attrs-21.2.0-pyhd8ed1ab_0
  backcall-0.2.0-pyh9f0ad1d_0
  backports-1.0-py_2
  backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0
  bleach-3.3.0-pyh44b312d_0
  brotlipy-0.7.0-py36h8f6f2f9_1001
  ca-certificates-2021.5.25-h06a4308_1
  certifi-2021.5.30-py36h06a4308_0
  cffi-1.14.5-py36hc120d54_0
  chardet-4.0.0-py36h5fab9bb_1
  cryptography-3.4.7-py36hb60f036_0
  decorator-5.0.9-pyhd8ed1ab_0
  defusedxml-0.7.1-pyhd8ed1ab_0
  entrypoints-0.3-pyhd8ed1ab_1003
  icu-68.1-h2531618_0
  idna-2.10-pyh9f0ad1d_0
  importlib-metadata-4.6.0-py36h5fab9bb_0
  ipykernel-5.5.5-py36hcb3619a_0
  ipython-7.16.1-py36he448a4c_2
  ipython_genutils-0.2.0-py_1
  jedi-0.17.2-py36h5fab9bb_1
  jinja2-3.0.1-pyhd8ed1ab_0
  json5-0.9.5-pyh9f0ad1d_0
  jsonschema-3.2.0-pyhd8ed1ab_3
  jupyter_client-6.1.12-pyhd8ed1ab_0
  jupyter_core-4.7.1-py36h5fab9bb_0
  jupyterlab-2.0.1-py_0
  jupyterlab_pygments-0.1.2-pyh9f0ad1d_0
  jupyterlab_server-1.2.0-py_0
  ld_impl_linux-64-2.35.1-hea4e1c9_2
  libffi-3.3-h58526e2_2
  libgcc-ng-9.3.0-h2828fa1_19
  libgomp-9.3.0-h2828fa1_19
  libsodium-1.0.18-h36c2ea0_1
  libstdcxx-ng-9.3.0-h6de172a_19
  libuv-1.40.0-h7b6447c_0
  markupsafe-2.0.1-py36h8f6f2f9_0
  mistune-0.8.4-py36h8f6f2f9_1004
  nbclient-0.5.3-pyhd8ed1ab_0
  nbconvert-6.0.7-py36h5fab9bb_3
  nbformat-5.1.3-pyhd8ed1ab_0
  ncurses-6.2-h58526e2_4
  nest-asyncio-1.5.1-pyhd8ed1ab_0
  nodejs-14.8.0-hda19d22_0
  notebook-6.3.0-py36h5fab9bb_0
  openssl-1.1.1k-h27cfd23_0
  packaging-20.9-pyh44b312d_0
  pandoc-2.14.0.3-h7f98852_0
  pandocfilters-1.4.2-py_1
  parso-0.7.1-pyh9f0ad1d_0
  pexpect-4.8.0-pyh9f0ad1d_2
  pickleshare-0.7.5-py_1003
  pip-19.3.1-py36_0
  prometheus_client-0.11.0-pyhd8ed1ab_0
  prompt-toolkit-3.0.19-pyha770c72_0
  ptyprocess-0.7.0-pyhd3deb0d_0
  pycparser-2.20-pyh9f0ad1d_2
  pygments-2.9.0-pyhd8ed1ab_0
  pyopenssl-20.0.1-pyhd8ed1ab_0
  pyparsing-2.4.7-pyh9f0ad1d_0
  pyrsistent-0.17.3-py36h8f6f2f9_2
  pysocks-1.7.1-py36h5fab9bb_3
  python-3.6.13-hffdb5ce_0_cpython
  python-dateutil-2.8.1-py_0
  python_abi-3.6-2_cp36m
  pyzmq-22.1.0-py36h7068817_0
  readline-8.1-h46c0cb4_0
  requests-2.25.1-pyhd3deb0d_0
  send2trash-1.7.1-pyhd8ed1ab_0
  setuptools-49.6.0-py36h5fab9bb_3
  six-1.16.0-pyh6c4a22f_0
  sqlite-3.36.0-h9cd32fc_0
  terminado-0.10.1-py36h5fab9bb_0
  testpath-0.5.0-pyhd8ed1ab_0
  tk-8.6.10-h21135ba_1
  tornado-6.1-py36h8f6f2f9_1
  traitlets-4.3.3-py36h9f0ad1d_1
  typing_extensions-3.10.0.0-pyha770c72_0
  urllib3-1.26.6-pyhd8ed1ab_0
  wcwidth-0.2.5-pyh9f0ad1d_2
  webencodings-0.5.1-py_1
  wheel-0.36.2-pyhd3deb0d_0
  xz-5.2.5-h516909a_1
  zeromq-4.3.4-h9c3ff4c_0
  zipp-3.4.1-pyhd8ed1ab_0
  zlib-1.2.11-h516909a_1010


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

Remove all packages in environment /home/jenkins/.conda/envs/mango-build-1a4fca2b-84d7-4e30-8ff7-767adf5c512d:


# test mango submit
MANGO_BROWSER_LOGS=${MANGO_TMP_DIR}/mango-submit.log
+ MANGO_BROWSER_LOGS=/tmp/mangoTestk9kRHJh/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/mangoTestk9kRHJh/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
clean_up
+ clean_up
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
Build step 'Execute shell' marked build as failure
Finished: FAILURE