FailedConsole Output

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Downloaded from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm-util/6.2/asm-util-6.2.jar (80 kB at 950 kB/s)
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Downloaded from central: https://repo.maven.apache.org/maven2/org/jdom/jdom2/2.0.6/jdom2-2.0.6.jar (305 kB at 3.2 MB/s)
[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-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar.
[INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.12:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.12:jar:1.0.6 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.12.8 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.9.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.9.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-assistedinject:jar:4.2.2 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.9.0 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] adam-cli-spark2_2.12-0.32.0.jar, mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] 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/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar with /tmp/mangoTestui3gp92/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                   [4/5]
[INFO] --------------------------------[ pom ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-plugins/16/maven-plugins-16.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.jar (209 kB at 7.7 MB/s)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution-spark3_2.12 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.2-beta-5:single (default) @ mango-distribution-spark3_2.12 ---
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/1.1/maven-common-artifact-filters-1.1.pom
Progress (1): 2.8 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/1.1/maven-common-artifact-filters-1.1.pom (2.8 kB at 346 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/10/maven-shared-components-10.pom
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/10/maven-shared-components-10.pom (8.4 kB at 1.1 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/9/maven-parent-9.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.0/maven-project-2.0.pom
Progress (1): 1.6 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.0/maven-project-2.0.pom (1.6 kB at 204 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven/2.0/maven-2.0.pom
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven/2.0/maven-2.0.pom (8.8 kB at 1.1 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0/maven-profile-2.0.pom
Progress (1): 1.4 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0/maven-profile-2.0.pom (1.4 kB at 196 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model/2.0/maven-model-2.0.pom
Progress (1): 2.4 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact-manager/2.0/maven-artifact-manager-2.0.pom
Progress (1): 1.3 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact-manager/2.0/maven-artifact-manager-2.0.pom (1.3 kB at 193 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.0/maven-repository-metadata-2.0.pom
Progress (1): 1.2 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.0/maven-repository-metadata-2.0.pom (1.2 kB at 153 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0/maven-artifact-2.0.pom
Progress (1): 723 B
                   
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0/maven-artifact-2.0.pom (723 B at 103 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-core/2.0/maven-core-2.0.pom
Progress (1): 4.1/5.6 kB
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-core/2.0/maven-core-2.0.pom (5.6 kB at 622 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/2.0/maven-settings-2.0.pom
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Progress (4): 70/109 kB | 30 kB | 20 kB | 12/222 kB 
                                                   
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0.4/maven-profile-2.0.4.jar (30 kB at 383 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model/2.0.4/maven-model-2.0.4.jar
Progress (3): 74/109 kB | 20 kB | 12/222 kB
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Progress (4): 86/109 kB | 20 kB | 25/222 kB | 4.1/80 kB
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Progress (4): 90/109 kB | 20 kB | 33/222 kB | 4.1/80 kB
Progress (4): 90/109 kB | 20 kB | 33/222 kB | 8.2/80 kB
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Progress (4): 98/109 kB | 20 kB | 33/222 kB | 12/80 kB
Progress (4): 98/109 kB | 20 kB | 33/222 kB | 16/80 kB
Progress (4): 98/109 kB | 20 kB | 37/222 kB | 16/80 kB
                                                      
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/2.4/maven-archiver-2.4.jar (20 kB at 234 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-repository-builder/1.0-alpha-2/maven-repository-builder-1.0-alpha-2.jar
Progress (3): 102/109 kB | 37/222 kB | 16/80 kB
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Progress (3): 102/109 kB | 41/222 kB | 20/80 kB
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Progress (3): 109 kB | 49/222 kB | 33/80 kB
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Progress (4): 109 kB | 49/222 kB | 33/80 kB | 8.2/80 kB
Progress (4): 109 kB | 49/222 kB | 37/80 kB | 8.2/80 kB
Progress (4): 109 kB | 49/222 kB | 37/80 kB | 12/80 kB 
Progress (4): 109 kB | 49/222 kB | 41/80 kB | 12/80 kB
Progress (4): 109 kB | 49/222 kB | 41/80 kB | 16/80 kB
Progress (4): 109 kB | 53/222 kB | 41/80 kB | 16/80 kB
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Progress (4): 109 kB | 57/222 kB | 49/80 kB | 20/80 kB
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Progress (5): 109 kB | 61/222 kB | 49/80 kB | 25/80 kB | 4.1/23 kB
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Progress (5): 109 kB | 66/222 kB | 49/80 kB | 29/80 kB | 8.2/23 kB
Progress (5): 109 kB | 66/222 kB | 53/80 kB | 29/80 kB | 8.2/23 kB
Progress (5): 109 kB | 66/222 kB | 53/80 kB | 29/80 kB | 12/23 kB 
Progress (5): 109 kB | 70/222 kB | 53/80 kB | 29/80 kB | 12/23 kB
Progress (5): 109 kB | 70/222 kB | 53/80 kB | 33/80 kB | 12/23 kB
Progress (5): 109 kB | 74/222 kB | 53/80 kB | 33/80 kB | 12/23 kB
Progress (5): 109 kB | 74/222 kB | 53/80 kB | 33/80 kB | 16/23 kB
Progress (5): 109 kB | 74/222 kB | 57/80 kB | 33/80 kB | 16/23 kB
Progress (5): 109 kB | 74/222 kB | 57/80 kB | 33/80 kB | 20/23 kB
                                                                 
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.0.4/maven-project-2.0.4.jar (109 kB at 1.2 MB/s)
Progress (4): 74/222 kB | 57/80 kB | 33/80 kB | 23 kB
Progress (4): 74/222 kB | 61/80 kB | 33/80 kB | 23 kB
Progress (4): 74/222 kB | 61/80 kB | 37/80 kB | 23 kB
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Progress (4): 78/222 kB | 61/80 kB | 41/80 kB | 23 kB
Progress (4): 78/222 kB | 66/80 kB | 41/80 kB | 23 kB
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Progress (4): 82/222 kB | 66/80 kB | 49/80 kB | 23 kB
Progress (4): 82/222 kB | 70/80 kB | 49/80 kB | 23 kB
Progress (4): 82/222 kB | 70/80 kB | 53/80 kB | 23 kB
Progress (4): 82/222 kB | 74/80 kB | 53/80 kB | 23 kB
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Progress (4): 90/222 kB | 78/80 kB | 57/80 kB | 23 kB
Progress (4): 94/222 kB | 78/80 kB | 57/80 kB | 23 kB
                                                     
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-repository-builder/1.0-alpha-2/maven-repository-builder-1.0-alpha-2.jar (23 kB at 244 kB/s)
Progress (3): 94/222 kB | 78/80 kB | 61/80 kB
Progress (3): 98/222 kB | 78/80 kB | 61/80 kB
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Progress (3): 164/222 kB | 80 kB | 80 kB
                                        
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0.4/maven-artifact-2.0.4.jar (80 kB at 795 kB/s)
Progress (2): 168/222 kB | 80 kB
                                
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model/2.0.4/maven-model-2.0.4.jar (80 kB at 786 kB/s)
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Progress (1): 222 kB    
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/2.0.1/plexus-utils-2.0.1.jar (222 kB at 2.1 MB/s)
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /tmp/mangoTestui3gp92/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-sources.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-javadoc.jar longer than 100 characters.
[INFO] Building tar : /tmp/mangoTestui3gp92/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-sources.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-javadoc.jar longer than 100 characters.
[INFO] Building zip: /tmp/mangoTestui3gp92/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                                 [5/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent-spark3_2.12 ---
[INFO] Modified 0 of 41 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.12 0.0.6-SNAPSHOT:
[INFO] 
[INFO] mango_2.12: CORE ................................... SUCCESS [ 24.419 s]
[INFO] mango_2.12: CLI .................................... SUCCESS [ 28.372 s]
[INFO] Mango_2.12: Assembly ............................... SUCCESS [ 22.081 s]
[INFO] mango_2.12: Distribution ........................... SUCCESS [ 53.758 s]
[INFO] mango_2.12 ......................................... SUCCESS [  0.746 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:09 min
[INFO] Finished at: 2020-08-19T02:26:50Z
[INFO] ------------------------------------------------------------------------

# make sure that the distribution package contains an assembly jar
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzf mango-distribution/target/mango-distribution*-bin.tar.gz | \
    grep mango-assembly | \
    grep jar | \
    grep -v -e sources -e javadoc
+ grep mango-assembly
+ tar tzf mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
+ grep jar
+ grep -v -e sources -e javadoc
mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvnpf7AADR
/tmp/mangoTestMvnpf7AADR
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/._SUCCESS.crc
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/_processingSteps.avro
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=2
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=2/positionBin=189/part-00000-ee938b83-5972-4d74-bc7c-ada2fa67c8fb.c000.snappy.parquet
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=2/positionBin=189/.part-00000-ee938b83-5972-4d74-bc7c-ada2fa67c8fb.c000.snappy.parquet.crc
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/_partitionedByStartPos
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/._references.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/_SUCCESS
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/_references.avro
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/_readGroups.avro
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/._readGroups.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=1
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=1/positionBin=240/part-00000-ee938b83-5972-4d74-bc7c-ada2fa67c8fb.c000.snappy.parquet
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=1/positionBin=240/.part-00000-ee938b83-5972-4d74-bc7c-ada2fa67c8fb.c000.snappy.parquet.crc
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=1/positionBin=26/part-00000-ee938b83-5972-4d74-bc7c-ada2fa67c8fb.c000.snappy.parquet
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146.adam/referenceName=1/positionBin=26/.part-00000-ee938b83-5972-4d74-bc7c-ada2fa67c8fb.c000.snappy.parquet.crc
/tmp/mangoTestMvnpf7AADR/invalidBuild.genome2033986753349626621
/tmp/mangoTestMvnpf7AADR/invalidBuild.genome2033986753349626621/properties.txt
/tmp/mangoTestMvnpf7AADR/fake-631591864976688328.txt
/tmp/mangoTestMvnpf7AADR/genomes5518473330574374790
/tmp/mangoTestMvnpf7AADR/genomes5518473330574374790/hg19.genome
/tmp/mangoTestMvnpf7AADR/genomes4916239476446380182
/tmp/mangoTestMvnpf7AADR/genomes4916239476446380182/hg19.genome
/tmp/mangoTestMvnpf7AADR/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/._samples.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/._SUCCESS.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/_partitionedByStartPos
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/._references.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/_SUCCESS
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/_references.avro
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/._header.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/_samples.avro
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/referenceName=1
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/referenceName=1/positionBin=0/part-00000-e0dfc14d-c845-4533-b6b0-a0f3dc9a5be5.c000.snappy.parquet
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/referenceName=1/positionBin=0/.part-00000-e0dfc14d-c845-4533-b6b0-a0f3dc9a5be5.c000.snappy.parquet.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984.adam/_header
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/._SUCCESS.crc
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/_processingSteps.avro
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=2
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=2/positionBin=189/part-00000-5abe57f5-6369-4e9a-9d39-dba1d1cdd1c0.c000.snappy.parquet
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=2/positionBin=189/.part-00000-5abe57f5-6369-4e9a-9d39-dba1d1cdd1c0.c000.snappy.parquet.crc
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/_partitionedByStartPos
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/._references.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/_SUCCESS
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/_references.avro
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/_readGroups.avro
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/._readGroups.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=1
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=1/positionBin=240/part-00000-5abe57f5-6369-4e9a-9d39-dba1d1cdd1c0.c000.snappy.parquet
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=1/positionBin=240/.part-00000-5abe57f5-6369-4e9a-9d39-dba1d1cdd1c0.c000.snappy.parquet.crc
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=1/positionBin=26/part-00000-5abe57f5-6369-4e9a-9d39-dba1d1cdd1c0.c000.snappy.parquet
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481.adam/referenceName=1/positionBin=26/.part-00000-5abe57f5-6369-4e9a-9d39-dba1d1cdd1c0.c000.snappy.parquet.crc
/tmp/mangoTestMvnpf7AADR/43327242389538389
/tmp/mangoTestMvnpf7AADR/mmbroken7149799192843763273.genome
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890
/tmp/mangoTestMvnpf7AADR/fake-1724088129492833423.txt
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/._samples.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/._SUCCESS.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/_partitionedByStartPos
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/._references.avro.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/_SUCCESS
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/_references.avro
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/._header.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/_samples.avro
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/referenceName=1
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/referenceName=1/positionBin=0/.part-00000-c53fe3fa-0a41-4221-b9f4-0e4e4b239fdc.c000.snappy.parquet.crc
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/referenceName=1/positionBin=0/part-00000-c53fe3fa-0a41-4221-b9f4-0e4e4b239fdc.c000.snappy.parquet
/tmp/mangoTestMvnpf7AADR/TempSuite5144198934842824890.adam/_header
/tmp/mangoTestMvnpf7AADR/4998012860386797328
/tmp/mangoTestMvnpf7AADR/TempSuite1640742239984440146
/tmp/mangoTestMvnpf7AADR/mmbroken3864772897455127049.genome
/tmp/mangoTestMvnpf7AADR/5814917961451509326
/tmp/mangoTestMvnpf7AADR/5814917961451509326/anoGam1.genome
/tmp/mangoTestMvnpf7AADR/2850612827622584322
/tmp/mangoTestMvnpf7AADR/2850612827622584322/anoGam1.genome
/tmp/mangoTestMvnpf7AADR/invalidBuild.genome1147281899141122531
/tmp/mangoTestMvnpf7AADR/invalidBuild.genome1147281899141122531/properties.txt
/tmp/mangoTestMvnpf7AADR/fake-4322842083850864066.sh
/tmp/mangoTestMvnpf7AADR/fake-3744620089664928958.sh
/tmp/mangoTestMvnpf7AADR/TempSuite2118866166837857481
/tmp/mangoTestMvnpf7AADR/TempSuite5494978589739327984
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvnpf7AADR

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${MANGO_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/mangoTestMvnpf7AADR:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# set spark artifact string for downloading assembly
SPARK=spark-${SPARK_VERSION}
+ SPARK=spark-2.4.6

# what hadoop version are we on? format string for downloading spark assembly
if [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
    HADOOP=hadoop2.7
else
    echo "Unknown Hadoop version."
    exit 1
fi
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7

# Spark 2.4.3+ and less than 3.0.0 needs special case for Scala 2.12
if [ ${SCALAVER} == 2.12 ] && [ ${SPARK_VERSION} == 2.4.6 ]
then
    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-without-hadoop-scala-2.12.tgz" \
        -o ${MANGO_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12.tgz

    tar xzf ${MANGO_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12.tgz --directory ${MANGO_TMP_DIR}
    export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-without-hadoop-scala-2.12

    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=hadoop/core/hadoop-2.7.7/hadoop-2.7.7.tar.gz" \
        -o ${MANGO_TMP_DIR}/hadoop-2.7.7.tar.gz

    tar xzf ${MANGO_TMP_DIR}/hadoop-2.7.7.tar.gz --directory ${MANGO_TMP_DIR}

    # remove references to avro 1.7.x
    find ${MANGO_TMP_DIR}/hadoop-2.7.7 -name *.jar | grep avro | xargs rm

    export SPARK_DIST_CLASSPATH=$(${MANGO_TMP_DIR}/hadoop-2.7.7/bin/hadoop classpath)
else
    curl \
        -v \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
        -o ${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}.tgz

    tar xzf ${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}.tgz --directory ${MANGO_TMP_DIR}
    export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}
fi
+ '[' 2.12 == 2.12 ']'
+ '[' 2.4.6 == 2.4.6 ']'
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.6/spark-2.4.6-bin-without-hadoop-scala-2.12.tgz' -o /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12.tgz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

  0  139M    0  896k    0     0  1104k      0  0:02:09 --:--:--  0:02:09 1104k
 79  139M   79  111M    0     0  61.6M      0  0:00:02  0:00:01  0:00:01  110M
100  139M  100  139M    0     0  67.6M      0  0:00:02  0:00:02 --:--:--  110M
+ tar xzf /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12.tgz --directory /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded
+ export SPARK_HOME=/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12
+ SPARK_HOME=/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=hadoop/core/hadoop-2.7.7/hadoop-2.7.7.tar.gz' -o /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

  0  208M    0  396k    0     0   291k      0  0:12:12  0:00:01  0:12:11  291k
  0  208M    0  400k    0     0   176k      0  0:20:13  0:00:02  0:20:11  4781
  0  208M    0  417k    0     0   130k      0  0:27:15  0:00:03  0:27:12 11915
  2  208M    2 5921k    0     0  1425k      0  0:02:29  0:00:04  0:02:25 1977k
  5  208M    5 11.4M    0     0  2283k      0  0:01:33  0:00:05  0:01:28 2997k
  8  208M    8 17.5M    0     0  2914k      0  0:01:13  0:00:06  0:01:07 3657k
 11  208M   11 23.5M    0     0  3368k      0  0:01:03  0:00:07  0:00:56 4857k
 14  208M   14 29.8M    0     0  3747k      0  0:00:56  0:00:08  0:00:48 6077k
 17  208M   17 35.7M    0     0  3999k      0  0:00:53  0:00:09  0:00:44 6137k
 20  208M   20 42.1M    0     0  4249k      0  0:00:50  0:00:10  0:00:40 6276k
 22  208M   22 47.5M    0     0  4366k      0  0:00:48  0:00:11  0:00:37 6154k
 25  208M   25 53.3M    0     0  4498k      0  0:00:47  0:00:12  0:00:35 6114k
 28  208M   28 59.1M    0     0  4600k      0  0:00:46  0:00:13  0:00:33 5991k
 30  208M   30 64.1M    0     0  4640k      0  0:00:46  0:00:14  0:00:32 5813k
 33  208M   33 70.1M    0     0  4740k      0  0:00:45  0:00:15  0:00:30 5737k
 36  208M   36 76.2M    0     0  4835k      0  0:00:44  0:00:16  0:00:28 5880k
 39  208M   39 81.5M    0     0  4865k      0  0:00:43  0:00:17  0:00:26 5759k
 41  208M   41 85.5M    0     0  4820k      0  0:00:44  0:00:18  0:00:26 5399k
 41  208M   41 86.5M    0     0  4621k      0  0:00:46  0:00:19  0:00:27 4567k
 41  208M   41 87.5M    0     0  4444k      0  0:00:48  0:00:20  0:00:28 3551k
 45  208M   45 93.9M    0     0  4548k      0  0:00:46  0:00:21  0:00:25 3621k
 47  208M   47 99.6M    0     0  4607k      0  0:00:46  0:00:22  0:00:24 3719k
 50  208M   50  105M    0     0  4686k      0  0:00:45  0:00:23  0:00:22 4195k
 53  208M   53  111M    0     0  4723k      0  0:00:45  0:00:24  0:00:21 5119k
 56  208M   56  116M    0     0  4758k      0  0:00:44  0:00:25  0:00:19 6031k
 58  208M   58  122M    0     0  4798k      0  0:00:44  0:00:26  0:00:18 5848k
 61  208M   61  127M    0     0  4814k      0  0:00:44  0:00:27  0:00:17 5729k
 64  208M   64  133M    0     0  4871k      0  0:00:43  0:00:28  0:00:15 5728k
 66  208M   66  139M    0     0  4901k      0  0:00:43  0:00:29  0:00:14 5756k
 69  208M   69  145M    0     0  4936k      0  0:00:43  0:00:30  0:00:13 5836k
 72  208M   72  151M    0     0  4966k      0  0:00:43  0:00:31  0:00:12 5848k
 74  208M   74  156M    0     0  4982k      0  0:00:42  0:00:32  0:00:10 5892k
 77  208M   77  162M    0     0  5018k      0  0:00:42  0:00:33  0:00:09 5845k
 80  208M   80  168M    0     0  5048k      0  0:00:42  0:00:34  0:00:08 5905k
 83  208M   83  174M    0     0  5078k      0  0:00:42  0:00:35  0:00:07 5936k
 86  208M   86  180M    0     0  5101k      0  0:00:41  0:00:36  0:00:05 5947k
 89  208M   89  186M    0     0  5131k      0  0:00:41  0:00:37  0:00:04 6090k
 92  208M   92  192M    0     0  5157k      0  0:00:41  0:00:38  0:00:03 6075k
 94  208M   94  196M    0     0  5137k      0  0:00:41  0:00:39  0:00:02 5749k
 94  208M   94  198M    0     0  5019k      0  0:00:42  0:00:40  0:00:02 4627k
 96  208M   96  200M    0     0  4991k      0  0:00:42  0:00:41  0:00:01 4197k
 97  208M   97  202M    0     0  4918k      0  0:00:43  0:00:42  0:00:01 3371k
 97  208M   97  203M    0     0  4822k      0  0:00:44  0:00:43  0:00:01 2300k
 97  208M   97  204M    0     0  4729k      0  0:00:45  0:00:44  0:00:01 1567k
 98  208M   98  205M    0     0  4644k      0  0:00:45  0:00:45 --:--:-- 1470k
 98  208M   98  206M    0     0  4576k      0  0:00:46  0:00:46 --:--:-- 1164k
 99  208M   99  207M    0     0  4511k      0  0:00:47  0:00:47 --:--:--  992k
100  208M  100  208M    0     0  4512k      0  0:00:47  0:00:47 --:--:-- 1243k
+ tar xzf /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7.tar.gz --directory /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded
+ grep avro
+ find /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7 -name '*.jar'
+ xargs rm
++ /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/bin/hadoop classpath
+ export 'SPARK_DIST_CLASSPATH=/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/etc/hadoop:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/lib/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/lib/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/lib/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/lib/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/*:/contrib/capacity-scheduler/*.jar'
+ SPARK_DIST_CLASSPATH='/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/etc/hadoop:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/lib/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/lib/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/lib/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/lib/*:/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/*:/contrib/capacity-scheduler/*.jar'



# create a conda environment for python build, if necessary
pythons=( 3.6 )
+ pythons=(3.6)
for python in ${pythons[*]}
do
    set +x +v
    conda create -y -q -c conda-forge -n mango-build-${PYTHON_UUID} python=${python} pip=19.3.1 jupyterlab=2.0.1
    source activate mango-build-${PYTHON_UUID}
    set -x -v

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

    # prepare mango python
    pushd mango-python
    make prepare
    popd

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

    # clean mango python
    pushd mango-python
    make clean
    popd

    # prepare mango viz
    pushd mango-pileup
    make prepare
    popd

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

    # clean mango viz
    pushd mango-pileup
    make clean
    popd

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

    # test mango notebook, output to temporary log file
    MANGO_NOTEBOOK_LOGS=${MANGO_TMP_DIR}/mango-notebook.log

    # notebook args --ip=0.0.0.0 --no-browser --allow-root required for docker
    bash -xv ${PROJECT_ROOT}/bin/mango-notebook -- --ip=0.0.0.0 --no-browser --allow-root &> ${MANGO_NOTEBOOK_LOGS} &

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

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

    # deactivate and remove the conda env
    set +e +x
    source deactivate
    conda remove -y --name mango-build-${PYTHON_UUID} --all
    set -e -x
done
+ for python in ${pythons[*]}
+ set +x +v
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab

  added / updated specs:
    - jupyterlab=2.0.1
    - pip=19.3.1
    - python=3.6


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |            1_gnu          22 KB  conda-forge
    argon2-cffi-20.1.0         |   py36h8c4c3a4_1          47 KB  conda-forge
    attrs-19.3.0               |             py_0          35 KB  conda-forge
    backcall-0.2.0             |     pyh9f0ad1d_0          13 KB  conda-forge
    backports-1.0              |             py_2           4 KB  conda-forge
    backports.functools_lru_cache-1.6.1|             py_0           8 KB  conda-forge
    bleach-3.1.5               |     pyh9f0ad1d_0         112 KB  conda-forge
    brotlipy-0.7.0             |py36h8c4c3a4_1000         346 KB  conda-forge
    ca-certificates-2020.6.20  |       hecda079_0         145 KB  conda-forge
    certifi-2020.6.20          |   py36h9f0ad1d_0         151 KB  conda-forge
    cffi-1.14.1                |   py36h0ff685e_0         223 KB  conda-forge
    chardet-3.0.4              |py36h9f0ad1d_1006         188 KB  conda-forge
    cryptography-3.0           |   py36h45558ae_0         640 KB  conda-forge
    decorator-4.4.2            |             py_0          11 KB  conda-forge
    defusedxml-0.6.0           |             py_0          22 KB  conda-forge
    entrypoints-0.3            |py36h9f0ad1d_1001          12 KB  conda-forge
    idna-2.10                  |     pyh9f0ad1d_0          52 KB  conda-forge
    importlib-metadata-1.7.0   |   py36h9f0ad1d_0          44 KB  conda-forge
    importlib_metadata-1.7.0   |                0           3 KB  conda-forge
    ipykernel-5.3.4            |   py36h95af2a2_0         165 KB  conda-forge
    ipython-7.16.1             |   py36h95af2a2_0         1.1 MB  conda-forge
    ipython_genutils-0.2.0     |             py_1          21 KB  conda-forge
    jedi-0.17.2                |   py36h9f0ad1d_0         950 KB  conda-forge
    jinja2-2.11.2              |     pyh9f0ad1d_0          93 KB  conda-forge
    json5-0.9.4                |     pyh9f0ad1d_0          20 KB  conda-forge
    jsonschema-3.2.0           |   py36h9f0ad1d_1          89 KB  conda-forge
    jupyter_client-6.1.6       |             py_0          75 KB  conda-forge
    jupyter_core-4.6.3         |   py36h9f0ad1d_1          71 KB  conda-forge
    jupyterlab-2.0.1           |             py_0         5.7 MB  conda-forge
    jupyterlab_server-1.2.0    |             py_0          25 KB  conda-forge
    ld_impl_linux-64-2.34      |       hc38a660_9         612 KB  conda-forge
    libffi-3.2.1               |    he1b5a44_1007          47 KB  conda-forge
    libgcc-ng-9.3.0            |      h24d8f2e_15         7.8 MB  conda-forge
    libgomp-9.3.0              |      h24d8f2e_15         378 KB  conda-forge
    libsodium-1.0.18           |       h516909a_0         339 KB  conda-forge
    libstdcxx-ng-9.3.0         |      hdf63c60_15         4.0 MB  conda-forge
    markupsafe-1.1.1           |   py36h8c4c3a4_1          26 KB  conda-forge
    mistune-0.8.4              |py36h8c4c3a4_1001          53 KB  conda-forge
    nbconvert-5.6.1            |   py36h9f0ad1d_1         487 KB  conda-forge
    nbformat-5.0.7             |             py_0          99 KB  conda-forge
    ncurses-6.2                |       he1b5a44_1         993 KB  conda-forge
    notebook-6.1.3             |   py36h9f0ad1d_0         6.2 MB  conda-forge
    openssl-1.1.1g             |       h516909a_1         2.1 MB  conda-forge
    packaging-20.4             |     pyh9f0ad1d_0          32 KB  conda-forge
    pandoc-2.10.1              |       h516909a_0        19.3 MB  conda-forge
    pandocfilters-1.4.2        |             py_1           9 KB  conda-forge
    parso-0.7.1                |     pyh9f0ad1d_0          70 KB  conda-forge
    pexpect-4.8.0              |   py36h9f0ad1d_1          79 KB  conda-forge
    pickleshare-0.7.5          |py36h9f0ad1d_1001          13 KB  conda-forge
    pip-19.3.1                 |           py36_0         1.9 MB  conda-forge
    prometheus_client-0.8.0    |     pyh9f0ad1d_0          44 KB  conda-forge
    prompt-toolkit-3.0.6       |             py_0         235 KB  conda-forge
    ptyprocess-0.6.0           |          py_1001          15 KB  conda-forge
    pycparser-2.20             |     pyh9f0ad1d_2          94 KB  conda-forge
    pygments-2.6.1             |             py_0         683 KB  conda-forge
    pyopenssl-19.1.0           |             py_1          47 KB  conda-forge
    pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  conda-forge
    pyrsistent-0.16.0          |   py36h8c4c3a4_0          89 KB  conda-forge
    pysocks-1.7.1              |   py36h9f0ad1d_1          27 KB  conda-forge
    python-3.6.11              |h4d41432_2_cpython        34.2 MB  conda-forge
    python-dateutil-2.8.1      |             py_0         220 KB  conda-forge
    python_abi-3.6             |          1_cp36m           4 KB  conda-forge
    pyzmq-19.0.2               |   py36h9947dbf_0         465 KB  conda-forge
    readline-8.0               |       he28a2e2_2         281 KB  conda-forge
    requests-2.24.0            |     pyh9f0ad1d_0          47 KB  conda-forge
    send2trash-1.5.0           |             py_0          12 KB  conda-forge
    setuptools-49.6.0          |   py36h9f0ad1d_0         935 KB  conda-forge
    six-1.15.0                 |     pyh9f0ad1d_0          14 KB  conda-forge
    sqlite-3.33.0              |       h4cf870e_0         1.4 MB  conda-forge
    terminado-0.8.3            |   py36h9f0ad1d_1          23 KB  conda-forge
    testpath-0.4.4             |             py_0          85 KB  conda-forge
    tk-8.6.10                  |       hed695b0_0         3.2 MB  conda-forge
    tornado-6.0.4              |   py36h8c4c3a4_1         639 KB  conda-forge
    traitlets-4.3.3            |   py36h9f0ad1d_1         133 KB  conda-forge
    urllib3-1.25.10            |             py_0          92 KB  conda-forge
    wcwidth-0.2.5              |     pyh9f0ad1d_1          33 KB  conda-forge
    webencodings-0.5.1         |             py_1          12 KB  conda-forge
    wheel-0.35.1               |     pyh9f0ad1d_0          29 KB  conda-forge
    xz-5.2.5                   |       h516909a_1         343 KB  conda-forge
    zeromq-4.3.2               |       he1b5a44_3         326 KB  conda-forge
    zipp-3.1.0                 |             py_0          10 KB  conda-forge
    zlib-1.2.11                |    h516909a_1007         106 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        98.7 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  argon2-cffi        conda-forge/linux-64::argon2-cffi-20.1.0-py36h8c4c3a4_1
  attrs              conda-forge/noarch::attrs-19.3.0-py_0
  backcall           conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
  backports          conda-forge/noarch::backports-1.0-py_2
  backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.1-py_0
  bleach             conda-forge/noarch::bleach-3.1.5-pyh9f0ad1d_0
  brotlipy           conda-forge/linux-64::brotlipy-0.7.0-py36h8c4c3a4_1000
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/linux-64::certifi-2020.6.20-py36h9f0ad1d_0
  cffi               conda-forge/linux-64::cffi-1.14.1-py36h0ff685e_0
  chardet            conda-forge/linux-64::chardet-3.0.4-py36h9f0ad1d_1006
  cryptography       conda-forge/linux-64::cryptography-3.0-py36h45558ae_0
  decorator          conda-forge/noarch::decorator-4.4.2-py_0
  defusedxml         conda-forge/noarch::defusedxml-0.6.0-py_0
  entrypoints        conda-forge/linux-64::entrypoints-0.3-py36h9f0ad1d_1001
  idna               conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
  importlib-metadata conda-forge/linux-64::importlib-metadata-1.7.0-py36h9f0ad1d_0
  importlib_metadata conda-forge/noarch::importlib_metadata-1.7.0-0
  ipykernel          conda-forge/linux-64::ipykernel-5.3.4-py36h95af2a2_0
  ipython            conda-forge/linux-64::ipython-7.16.1-py36h95af2a2_0
  ipython_genutils   conda-forge/noarch::ipython_genutils-0.2.0-py_1
  jedi               conda-forge/linux-64::jedi-0.17.2-py36h9f0ad1d_0
  jinja2             conda-forge/noarch::jinja2-2.11.2-pyh9f0ad1d_0
  json5              conda-forge/noarch::json5-0.9.4-pyh9f0ad1d_0
  jsonschema         conda-forge/linux-64::jsonschema-3.2.0-py36h9f0ad1d_1
  jupyter_client     conda-forge/noarch::jupyter_client-6.1.6-py_0
  jupyter_core       conda-forge/linux-64::jupyter_core-4.6.3-py36h9f0ad1d_1
  jupyterlab         conda-forge/noarch::jupyterlab-2.0.1-py_0
  jupyterlab_server  conda-forge/noarch::jupyterlab_server-1.2.0-py_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_15
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_15
  libsodium          conda-forge/linux-64::libsodium-1.0.18-h516909a_0
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_15
  markupsafe         conda-forge/linux-64::markupsafe-1.1.1-py36h8c4c3a4_1
  mistune            conda-forge/linux-64::mistune-0.8.4-py36h8c4c3a4_1001
  nbconvert          conda-forge/linux-64::nbconvert-5.6.1-py36h9f0ad1d_1
  nbformat           conda-forge/noarch::nbformat-5.0.7-py_0
  ncurses            conda-forge/linux-64::ncurses-6.2-he1b5a44_1
  notebook           conda-forge/linux-64::notebook-6.1.3-py36h9f0ad1d_0
  openssl            conda-forge/linux-64::openssl-1.1.1g-h516909a_1
  packaging          conda-forge/noarch::packaging-20.4-pyh9f0ad1d_0
  pandoc             conda-forge/linux-64::pandoc-2.10.1-h516909a_0
  pandocfilters      conda-forge/noarch::pandocfilters-1.4.2-py_1
  parso              conda-forge/noarch::parso-0.7.1-pyh9f0ad1d_0
  pexpect            conda-forge/linux-64::pexpect-4.8.0-py36h9f0ad1d_1
  pickleshare        conda-forge/linux-64::pickleshare-0.7.5-py36h9f0ad1d_1001
  pip                conda-forge/linux-64::pip-19.3.1-py36_0
  prometheus_client  conda-forge/noarch::prometheus_client-0.8.0-pyh9f0ad1d_0
  prompt-toolkit     conda-forge/noarch::prompt-toolkit-3.0.6-py_0
  ptyprocess         conda-forge/noarch::ptyprocess-0.6.0-py_1001
  pycparser          conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2
  pygments           conda-forge/noarch::pygments-2.6.1-py_0
  pyopenssl          conda-forge/noarch::pyopenssl-19.1.0-py_1
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  pyrsistent         conda-forge/linux-64::pyrsistent-0.16.0-py36h8c4c3a4_0
  pysocks            conda-forge/linux-64::pysocks-1.7.1-py36h9f0ad1d_1
  python             conda-forge/linux-64::python-3.6.11-h4d41432_2_cpython
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/linux-64::python_abi-3.6-1_cp36m
  pyzmq              conda-forge/linux-64::pyzmq-19.0.2-py36h9947dbf_0
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  requests           conda-forge/noarch::requests-2.24.0-pyh9f0ad1d_0
  send2trash         conda-forge/noarch::send2trash-1.5.0-py_0
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py36h9f0ad1d_0
  six                conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
  sqlite             conda-forge/linux-64::sqlite-3.33.0-h4cf870e_0
  terminado          conda-forge/linux-64::terminado-0.8.3-py36h9f0ad1d_1
  testpath           conda-forge/noarch::testpath-0.4.4-py_0
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  tornado            conda-forge/linux-64::tornado-6.0.4-py36h8c4c3a4_1
  traitlets          conda-forge/linux-64::traitlets-4.3.3-py36h9f0ad1d_1
  urllib3            conda-forge/noarch::urllib3-1.25.10-py_0
  wcwidth            conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_1
  webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zeromq             conda-forge/linux-64::zeromq-4.3.2-he1b5a44_3
  zipp               conda-forge/noarch::zipp-3.1.0-py_0
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1007


Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ conda install -y nodejs
+ '[' 3 -lt 1 ']'
+ local cmd=install
+ shift
+ case "$cmd" in
+ CONDA_INTERNAL_OLDPATH=/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/conda/bin/conda
+ SYSP=/opt/conda/bin
++ dirname /opt/conda/bin
+ SYSP=/opt/conda
+ '[' -n '' ']'
+ PATH=/opt/conda/bin:/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
+ /opt/conda/bin/conda install -y nodejs
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab

  added / updated specs:
    - nodejs


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2020.6.20          |           py36_0         156 KB
    ------------------------------------------------------------
                                           Total:         156 KB

The following NEW packages will be INSTALLED:

  nodejs             pkgs/main/linux-64::nodejs-10.13.0-he6710b0_0

The following packages will be UPDATED:

  ca-certificates    conda-forge::ca-certificates-2020.6.2~ --> pkgs/main::ca-certificates-2020.6.24-0

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            conda-forge::certifi-2020.6.20-py36h9~ --> pkgs/main::certifi-2020.6.20-py36_0
  openssl            conda-forge::openssl-1.1.1g-h516909a_1 --> pkgs/main::openssl-1.1.1g-h7b6447c_0



Downloading and Extracting Packages

certifi-2020.6.20    | 156 KB    |            |   0% 
certifi-2020.6.20    | 156 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ local t1=0
+ PATH=/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ '[' 0 = 0 ']'
+ __conda_reactivate
+ local ask_conda
+ CONDA_INTERNAL_OLDPATH=/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/conda/bin/conda
+ SYSP=/opt/conda/bin
++ dirname /opt/conda/bin
+ SYSP=/opt/conda
+ '[' -n '' ']'
+ PATH=/opt/conda/bin:/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
++ PS1='(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '
++ /opt/conda/bin/conda shell.posix reactivate
+ ask_conda='PS1='\''(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '\''
export PATH='\''/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '\'''
+ PATH=/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ eval 'PS1='\''(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '\''
export PATH='\''/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'\''
export CONDA_SHLVL='\''1'\''
export CONDA_PROMPT_MODIFIER='\''(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '\'''
PS1='(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '
++ PS1='(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '
export PATH='/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
++ export PATH=/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ PATH=/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
export CONDA_SHLVL='1'
++ export CONDA_SHLVL=1
++ CONDA_SHLVL=1
export CONDA_PROMPT_MODIFIER='(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '
++ export 'CONDA_PROMPT_MODIFIER=(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '
++ CONDA_PROMPT_MODIFIER='(mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab) '
+ __conda_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ pushd mango-python
/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded /home
+ make prepare
which pip
/home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin/pip
# ipython version required for python 2.7
pip install -r requirements.txt
Collecting cigar==0.1.3
  Downloading https://files.pythonhosted.org/packages/2d/5f/ffa58a8c64f811772b69a01eeab25c602b72d02a0c83006177c21abedaa3/cigar-0.1.3.tar.gz
Collecting matplotlib==2.0.2
  Downloading https://files.pythonhosted.org/packages/60/d4/6b6d8a7a6bc69a1602ab372f6fc6e88ef88a8a96398a1a25edbac636295b/matplotlib-2.0.2-cp36-cp36m-manylinux1_x86_64.whl (14.6MB)
Collecting ipython==7.8.0
  Downloading https://files.pythonhosted.org/packages/fb/44/f28a13852e562af719f9de1761680a84a93e8b4c50e22d00d68f60ee2e8b/ipython-7.8.0-py3-none-any.whl (775kB)
Collecting jupyter==1.0.0
  Downloading https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl
Collecting bdgenomics.adam==0.30.0
  Downloading https://files.pythonhosted.org/packages/8d/4b/b5b92dedae5ddd4e6f425f40a61332a3f646ac4616f840262ebb9441d396/bdgenomics.adam-0.30.0.tar.gz (39.5MB)
Collecting bdgenomics.mango.pileup==0.0.6a0
  Downloading https://files.pythonhosted.org/packages/48/8f/06f3e694caf8ba67dadbfca5c7f050343e7e3363ba348d94a224aa964cfb/bdgenomics.mango.pileup-0.0.6a0.tar.gz (892kB)
Collecting ipywidgets==7.0.0
  Downloading https://files.pythonhosted.org/packages/14/ea/793f6588d5be295d103fb868e26ba8671686b70bd855a21d02302f8dcd37/ipywidgets-7.0.0-py2.py3-none-any.whl (64kB)
Collecting psutil
  Downloading https://files.pythonhosted.org/packages/aa/3e/d18f2c04cf2b528e18515999b0c8e698c136db78f62df34eee89cee205f1/psutil-5.7.2.tar.gz (460kB)
Collecting pytest==3.9.1
  Downloading https://files.pythonhosted.org/packages/bf/14/a16e1ac03aeb9776d98374bb76495a6623d56dff0f7b815ed5a1e04d893e/pytest-3.9.1-py2.py3-none-any.whl (213kB)
Collecting jupyter_contrib_nbextensions
  Downloading https://files.pythonhosted.org/packages/33/f0/6e2c00afda860f655fbf0f795f7310bdbf12122846344dfdc803fc7455d5/jupyter_contrib_nbextensions-0.5.1-py2.py3-none-any.whl (20.9MB)
Collecting pytz
  Downloading https://files.pythonhosted.org/packages/4f/a4/879454d49688e2fad93e59d7d4efda580b783c745fd2ec2a3adf87b0808d/pytz-2020.1-py2.py3-none-any.whl (510kB)
Collecting cycler>=0.10
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Requirement already satisfied: six>=1.10 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.15.0)
Requirement already satisfied: python-dateutil in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.8.1)
Collecting numpy>=1.7.1
  Downloading https://files.pythonhosted.org/packages/b1/9a/7d474ba0860a41f771c9523d8c4ea56b084840b5ca4092d96bdee8a3b684/numpy-1.19.1-cp36-cp36m-manylinux2010_x86_64.whl (14.5MB)
Requirement already satisfied: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.4.7)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (4.8.0)
Requirement already satisfied: jedi>=0.10 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.17.2)
Requirement already satisfied: pygments in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (2.6.1)
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Collecting qtconsole
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Collecting pyspark>=1.6.0
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Collecting modin[ray]==0.6.1
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Collecting py>=1.5.0
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Collecting pyyaml
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Collecting jupyter-latex-envs>=1.3.8
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Collecting jupyter-nbextensions-configurator>=0.4.0
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Collecting qtpy
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Collecting py4j==0.10.9
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Collecting pandas==0.25.1
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Collecting ray==0.7.3; extra == "ray"
  Downloading https://files.pythonhosted.org/packages/a7/21/de080b8458de41fd8ac20dd96547418c0ed94eab4359e5885f4041d61337/ray-0.7.3-cp36-cp36m-manylinux1_x86_64.whl (48.5MB)
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Collecting filelock
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Collecting funcsigs
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Collecting click
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Building wheels for collected packages: cigar, bdgenomics.adam, bdgenomics.mango.pileup, psutil, pyspark, pyyaml, jupyter-latex-envs, jupyter-nbextensions-configurator
  Building wheel for cigar (setup.py): started
  Building wheel for cigar (setup.py): finished with status 'done'
  Created wheel for cigar: filename=cigar-0.1.3-cp36-none-any.whl size=4024 sha256=128b143b0a0553e136068168594a698c398f47ced0c66e2d43a802b290346c0b
  Stored in directory: /home/jenkins/.cache/pip/wheels/eb/c0/e6/f0f525ada263f7f72f4b3efcc7f5b3c12a372f07f55a2d687d
  Building wheel for bdgenomics.adam (setup.py): started
  Building wheel for bdgenomics.adam (setup.py): finished with status 'done'
  Created wheel for bdgenomics.adam: filename=bdgenomics.adam-0.30.0-cp36-none-any.whl size=39575669 sha256=c83650d95b12feb3345e809afe98639a6e53563ef08caa1e256e162a82da63c5
  Stored in directory: /home/jenkins/.cache/pip/wheels/06/70/62/114cc2bb8d85bfc915d4571adb8f94cc558fdeef2bc09d61ee
  Building wheel for bdgenomics.mango.pileup (setup.py): started
  Building wheel for bdgenomics.mango.pileup (setup.py): finished with status 'done'
  Created wheel for bdgenomics.mango.pileup: filename=bdgenomics.mango.pileup-0.0.6a0-cp36-none-any.whl size=1798435 sha256=4789b71090e1bc1b3ed3e514ba93c0b16a0638e06ab987313461a81d143cec54
  Stored in directory: /home/jenkins/.cache/pip/wheels/ec/df/8e/7e6efc45fd34e2850763a5ec5ac7f27052424d26105f12f971
  Building wheel for psutil (setup.py): started
  Building wheel for psutil (setup.py): finished with status 'done'
  Created wheel for psutil: filename=psutil-5.7.2-cp36-cp36m-linux_x86_64.whl size=279911 sha256=038a940d00a1e1f69b681e76e8fe83520980984bcbe92947e62f71d405f73f69
  Stored in directory: /home/jenkins/.cache/pip/wheels/39/a0/f5/c4fa280463e29aea07797acb5312358fefb067c1f4f98e11b1
  Building wheel for pyspark (setup.py): started
  Building wheel for pyspark (setup.py): finished with status 'done'
  Created wheel for pyspark: filename=pyspark-3.0.0-py2.py3-none-any.whl size=205044184 sha256=f69702cdc37c7a735364475f5a83abe113ecc1617f958ec61e95a70f1c51f545
  Stored in directory: /home/jenkins/.cache/pip/wheels/57/27/4d/ddacf7143f8d5b76c45c61ee2e43d9f8492fc5a8e78ebd7d37
  Building wheel for pyyaml (setup.py): started
  Building wheel for pyyaml (setup.py): finished with status 'done'
  Created wheel for pyyaml: filename=PyYAML-5.3.1-cp36-cp36m-linux_x86_64.whl size=44619 sha256=4e70e17194a1acdf5e99889ca7468d8e122e8cb8fe2b428c68f00e3bdf98fb6a
  Stored in directory: /home/jenkins/.cache/pip/wheels/a7/c1/ea/cf5bd31012e735dc1dfea3131a2d5eae7978b251083d6247bd
  Building wheel for jupyter-latex-envs (setup.py): started
  Building wheel for jupyter-latex-envs (setup.py): finished with status 'done'
  Created wheel for jupyter-latex-envs: filename=jupyter_latex_envs-1.4.6-py2.py3-none-any.whl size=963395 sha256=976b501f92fc48145824d219a8a1a677fdbc2c62b70b9fe5fa9e6b73087e4cea
  Stored in directory: /home/jenkins/.cache/pip/wheels/0d/71/2a/164491997299b9f2479a251e254323fe35d946779e18f27956
  Building wheel for jupyter-nbextensions-configurator (setup.py): started
  Building wheel for jupyter-nbextensions-configurator (setup.py): finished with status 'done'
  Created wheel for jupyter-nbextensions-configurator: filename=jupyter_nbextensions_configurator-0.4.1-py2.py3-none-any.whl size=465825 sha256=5775d5aaaeb623746071d0dcfcf279cd7f01435aeb777bc645f493754c583f6f
  Stored in directory: /home/jenkins/.cache/pip/wheels/15/df/fe/2a74fe34709e7fdc5ae153a768675d9fda93cc7d5133ed1fb0
Successfully built cigar bdgenomics.adam bdgenomics.mango.pileup psutil pyspark pyyaml jupyter-latex-envs jupyter-nbextensions-configurator
ERROR: bdgenomics-mango-pileup 0.0.6a0 has requirement pytest==2.8.3, but you'll have pytest 3.9.1 which is incompatible.
ERROR: bdgenomics-mango-pileup 0.0.6a0 has requirement six==1.11.0, but you'll have six 1.15.0 which is incompatible.
Installing collected packages: cigar, pytz, cycler, numpy, matplotlib, prompt-toolkit, ipython, widgetsnbextension, ipywidgets, jupyter-console, qtpy, qtconsole, jupyter, py4j, pyspark, bdgenomics.adam, pandas, pyyaml, filelock, colorama, redis, funcsigs, click, atomicwrites, py, pluggy, more-itertools, pytest, protobuf, ray, modin, bdgenomics.mango.pileup, psutil, lxml, jupyter-latex-envs, jupyter-contrib-core, jupyter-nbextensions-configurator, jupyter-highlight-selected-word, jupyter-contrib-nbextensions
  Found existing installation: prompt-toolkit 3.0.6
    Uninstalling prompt-toolkit-3.0.6:
      Successfully uninstalled prompt-toolkit-3.0.6
  Found existing installation: ipython 7.16.1
    Uninstalling ipython-7.16.1:
      Successfully uninstalled ipython-7.16.1
Successfully installed atomicwrites-1.4.0 bdgenomics.adam-0.30.0 bdgenomics.mango.pileup-0.0.6a0 cigar-0.1.3 click-7.1.2 colorama-0.4.3 cycler-0.10.0 filelock-3.0.12 funcsigs-1.0.2 ipython-7.8.0 ipywidgets-7.0.0 jupyter-1.0.0 jupyter-console-6.1.0 jupyter-contrib-core-0.3.3 jupyter-contrib-nbextensions-0.5.1 jupyter-highlight-selected-word-0.2.0 jupyter-latex-envs-1.4.6 jupyter-nbextensions-configurator-0.4.1 lxml-4.5.2 matplotlib-2.0.2 modin-0.6.1 more-itertools-8.4.0 numpy-1.19.1 pandas-0.25.1 pluggy-0.13.1 prompt-toolkit-2.0.10 protobuf-3.13.0 psutil-5.7.2 py-1.9.0 py4j-0.10.9 pyspark-3.0.0 pytest-3.9.1 pytz-2020.1 pyyaml-5.3.1 qtconsole-4.7.6 qtpy-1.9.0 ray-0.7.3 redis-3.5.3 widgetsnbextension-3.0.8
+ popd
+ mvn -U -P python,distribution package -DskipTests -Dhadoop.version=2.7.5 -Dspark.version=2.4.6
/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded /home
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-core-spark3_2.12:jar:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-core-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/pom.xml, line 11, column 15
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-parent-spark3_${scala.version.prefix}:0.0.6-SNAPSHOT, /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/pom.xml, line 13, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-python-spark3_2.12:jar:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-python-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-python/pom.xml, line 11, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli-spark3_2.12:jar:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-cli-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-cli/pom.xml, line 11, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-assembly-spark3_2.12:jar:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-assembly-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/pom.xml, line 11, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-distribution-spark3_2.12:pom:0.0.6-SNAPSHOT
[WARNING] 'artifactId' contains an expression but should be a constant. @ org.bdgenomics.mango:mango-distribution-spark3_${scala.version.prefix}:[unknown-version], /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/pom.xml, line 11, 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/mangoTestui3gp92/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: CORE                                                   [jar]
[INFO] Mango_2.12: Python APIs                                            [jar]
[INFO] mango_2.12: CLI                                                    [jar]
[INFO] Mango_2.12: Assembly                                               [jar]
[INFO] mango_2.12: Distribution                                           [pom]
[INFO] mango_2.12                                                         [pom]
[INFO] 
[INFO] ------------< org.bdgenomics.mango:mango-core-spark3_2.12 >-------------
[INFO] Building mango_2.12: CORE 0.0.6-SNAPSHOT                           [1/6]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core-spark3_2.12 ---
[INFO] Modified 0 of 32 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-core-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-core-spark3_2.12 ---
[INFO] Test Source directory: /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-core-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 24 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-core-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-core-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ mango-core-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-core-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-core-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core-spark3_2.12 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-core-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-core-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.12.8
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
model contains 41 documentable templates
/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:55: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                  ^
/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:55: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                                    ^
/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:56: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz
                                                                                   ^
/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:57: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - refSeq.txt file: downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                 ^
/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/RefSeq.scala:29: warning: Variable GENOME undefined in comment for object RefSeqFile in object RefSeqFile
 * Processes refSeq file, downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                     ^
/tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/io/HttpDownloadUtility.scala:34: warning: Could not find any member to link for "IOException".
  /**
  ^
6 warnings found
[INFO] Building jar: /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -----------< org.bdgenomics.mango:mango-python-spark3_2.12 >------------
[INFO] Building Mango_2.12: Python APIs 0.0.6-SNAPSHOT                    [2/6]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-python-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-python-spark3_2.12 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-python-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-python-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestui3gp92/deleteMePleaseThisIsNoLongerNeeded/mango-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-python-spark3_2.12 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (dev-python) @ mango-python-spark3_2.12 ---
bash: /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin/python: Invalid argument
pip install -e .
bash: /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin/pip: /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/bin/python: bad interpreter: Invalid argument
Makefile:69: recipe for target 'develop' failed
make: *** [develop] Error 126
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 2 (Exit value: 2)
    at org.apache.commons.exec.DefaultExecutor.executeInternal (DefaultExecutor.java:404)
    at org.apache.commons.exec.DefaultExecutor.execute (DefaultExecutor.java:166)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:804)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:751)
    at org.codehaus.mojo.exec.ExecMojo.execute (ExecMojo.java:313)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:192)
    at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke (Method.java:498)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:289)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:229)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:415)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:356)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.12 0.0.6-SNAPSHOT:
[INFO] 
[INFO] mango_2.12: CORE ................................... SUCCESS [ 17.210 s]
[INFO] Mango_2.12: Python APIs ............................ FAILURE [  0.175 s]
[INFO] mango_2.12: CLI .................................... SKIPPED
[INFO] Mango_2.12: Assembly ............................... SKIPPED
[INFO] mango_2.12: Distribution ........................... SKIPPED
[INFO] mango_2.12 ......................................... SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  17.620 s
[INFO] Finished at: 2020-08-19T02:30:26Z
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:exec (dev-python) on project mango-python-spark3_2.12: Command execution failed.: Process exited with an error: 2 (Exit value: 2) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :mango-python-spark3_2.12
clean_up
+ clean_up
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.

## Package Plan ##

  environment location: /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab


The following packages will be REMOVED:

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


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

Remove all packages in environment /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab:

Build step 'Execute shell' marked build as failure
Finished: FAILURE