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[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 ]---------------------------------
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[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 ---
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Progress (3): 109 kB | 49/222 kB | 33/80 kB
Progress (4): 109 kB | 49/222 kB | 33/80 kB | 4.1/80 kB
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 | 45/80 kB | 16/80 kB
Progress (4): 109 kB | 57/222 kB | 45/80 kB | 20/80 kB
Progress (4): 109 kB | 57/222 kB | 49/80 kB | 20/80 kB
Progress (4): 109 kB | 57/222 kB | 49/80 kB | 25/80 kB
Progress (4): 109 kB | 61/222 kB | 49/80 kB | 25/80 kB
Progress (5): 109 kB | 61/222 kB | 49/80 kB | 25/80 kB | 4.1/23 kB
Progress (5): 109 kB | 66/222 kB | 49/80 kB | 25/80 kB | 4.1/23 kB
Progress (5): 109 kB | 66/222 kB | 49/80 kB | 29/80 kB | 4.1/23 kB
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
Progress (4): 78/222 kB | 61/80 kB | 37/80 kB | 23 kB
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
Progress (4): 78/222 kB | 66/80 kB | 45/80 kB | 23 kB
Progress (4): 82/222 kB | 66/80 kB | 45/80 kB | 23 kB
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
Progress (4): 86/222 kB | 74/80 kB | 53/80 kB | 23 kB
Progress (4): 86/222 kB | 74/80 kB | 57/80 kB | 23 kB
Progress (4): 90/222 kB | 74/80 kB | 57/80 kB | 23 kB
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
Progress (3): 98/222 kB | 80 kB | 61/80 kB
Progress (3): 98/222 kB | 80 kB | 66/80 kB
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Progress (3): 123/222 kB | 80 kB | 80 kB
Progress (3): 127/222 kB | 80 kB | 80 kB
Progress (3): 131/222 kB | 80 kB | 80 kB
Progress (3): 135/222 kB | 80 kB | 80 kB
Progress (3): 139/222 kB | 80 kB | 80 kB
Progress (3): 143/222 kB | 80 kB | 80 kB
Progress (3): 147/222 kB | 80 kB | 80 kB
Progress (3): 152/222 kB | 80 kB | 80 kB
Progress (3): 156/222 kB | 80 kB | 80 kB
Progress (3): 160/222 kB | 80 kB | 80 kB
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)
Progress (1): 172/222 kB
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Progress (1): 221/222 kB
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)
Requirement already satisfied: traitlets>=4.2 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)) (4.3.3)
Requirement already satisfied: backcall 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)) (0.2.0)
Collecting prompt-toolkit<2.1.0,>=2.0.0
Downloading https://files.pythonhosted.org/packages/87/61/2dfea88583d5454e3a64f9308a686071d58d59a55db638268a6413e1eb6d/prompt_toolkit-2.0.10-py3-none-any.whl (340kB)
Requirement already satisfied: setuptools>=18.5 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)) (49.6.0.post20200814)
Requirement already satisfied: decorator 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)) (4.4.2)
Requirement already satisfied: pickleshare 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)) (0.7.5)
Collecting jupyter-console
Downloading https://files.pythonhosted.org/packages/0a/89/742fa5a80b552ffcb6a8922712697c6e6828aee7b91ee4ae2b79f00f8401/jupyter_console-6.1.0-py2.py3-none-any.whl
Requirement already satisfied: notebook in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (6.1.3)
Requirement already satisfied: ipykernel in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.3.4)
Requirement already satisfied: nbconvert in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.6.1)
Collecting qtconsole
Downloading https://files.pythonhosted.org/packages/41/27/82ed9d2c2e9a30c885f6782d674c8bfe3e3f903d06d837c2978f8b55be56/qtconsole-4.7.6-py2.py3-none-any.whl (118kB)
Collecting pyspark>=1.6.0
Downloading https://files.pythonhosted.org/packages/8e/b0/bf9020b56492281b9c9d8aae8f44ff51e1bc91b3ef5a884385cb4e389a40/pyspark-3.0.0.tar.gz (204.7MB)
Collecting modin[ray]==0.6.1
Downloading https://files.pythonhosted.org/packages/4f/62/dbea5f16c685aa1bab65787562f4990d5b78caa915c7d323b47013c454ad/modin-0.6.1-py3-none-any.whl (230kB)
Collecting widgetsnbextension~=3.0.0
Downloading https://files.pythonhosted.org/packages/8d/f2/c8bcccccbed39d51d3e237fb0c0f0c9bbc845d12afc41f5ca5f5728fffc7/widgetsnbextension-3.0.8-py2.py3-none-any.whl (2.2MB)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 7)) (5.0.7)
Collecting atomicwrites>=1.0
Downloading https://files.pythonhosted.org/packages/2c/a0/da5f49008ec6e9a658dbf5d7310a4debd397bce0b4db03cf8a410066bb87/atomicwrites-1.4.0-py2.py3-none-any.whl
Collecting py>=1.5.0
Downloading https://files.pythonhosted.org/packages/68/0f/41a43535b52a81e4f29e420a151032d26f08b62206840c48d14b70e53376/py-1.9.0-py2.py3-none-any.whl (99kB)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from pytest==3.9.1->-r requirements.txt (line 9)) (19.3.0)
Collecting pluggy>=0.7
Downloading https://files.pythonhosted.org/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl
Collecting more-itertools>=4.0.0
Downloading https://files.pythonhosted.org/packages/ef/9b/6c35ec5483710492e21252465160ee508170159f7e0e2d6cd769022f52f6/more_itertools-8.4.0-py3-none-any.whl (43kB)
Collecting pyyaml
Downloading https://files.pythonhosted.org/packages/64/c2/b80047c7ac2478f9501676c988a5411ed5572f35d1beff9cae07d321512c/PyYAML-5.3.1.tar.gz (269kB)
Collecting lxml
Downloading https://files.pythonhosted.org/packages/79/37/d420b7fdc9a550bd29b8cfeacff3b38502d9600b09d7dfae9a69e623b891/lxml-4.5.2-cp36-cp36m-manylinux1_x86_64.whl (5.5MB)
Collecting jupyter-latex-envs>=1.3.8
Downloading https://files.pythonhosted.org/packages/0e/15/55805de080d5542f76920364635e96e64d3b37f678befdfe3b16aa154205/jupyter_latex_envs-1.4.6.tar.gz (861kB)
Collecting jupyter-nbextensions-configurator>=0.4.0
Downloading https://files.pythonhosted.org/packages/51/a3/d72d5f2dc10c5ccf5a6f4c79f636bf071a5ce462dedd07af2f70384db6cb/jupyter_nbextensions_configurator-0.4.1.tar.gz (479kB)
Requirement already satisfied: tornado in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from jupyter_contrib_nbextensions->-r requirements.txt (line 10)) (6.0.4)
Requirement already satisfied: jupyter-core in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from jupyter_contrib_nbextensions->-r requirements.txt (line 10)) (4.6.3)
Collecting jupyter-contrib-core>=0.3.3
Downloading https://files.pythonhosted.org/packages/e6/8f/04a752a8b66a66e7092c035e5d87d2502ac7ec07f9fb6059059b6c0dc272/jupyter_contrib_core-0.3.3-py2.py3-none-any.whl
Collecting jupyter-highlight-selected-word>=0.1.1
Downloading https://files.pythonhosted.org/packages/50/d7/19ab7cfd60bf268d2abbacc52d4295a40f52d74dfc0d938e4761ee5e598b/jupyter_highlight_selected_word-0.2.0-py2.py3-none-any.whl
Requirement already satisfied: ipython-genutils in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from jupyter_contrib_nbextensions->-r requirements.txt (line 10)) (0.2.0)
Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython==7.8.0->-r requirements.txt (line 3)) (0.6.0)
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Requirement already satisfied: wcwidth in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from prompt-toolkit<2.1.0,>=2.0.0->ipython==7.8.0->-r requirements.txt (line 3)) (0.2.5)
Requirement already satisfied: jupyter-client in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from jupyter-console->jupyter==1.0.0->-r requirements.txt (line 4)) (6.1.6)
Requirement already satisfied: prometheus-client in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.0)
Requirement already satisfied: terminado>=0.8.3 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.3)
Requirement already satisfied: argon2-cffi in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (20.1.0)
Requirement already satisfied: Send2Trash in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.5.0)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (19.0.2)
Requirement already satisfied: jinja2 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (2.11.2)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.3)
Requirement already satisfied: defusedxml in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.6.0)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.4.2)
Requirement already satisfied: bleach in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.1.5)
Requirement already satisfied: testpath in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.4.4)
Requirement already satisfied: mistune<2,>=0.8.1 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.4)
Collecting qtpy
Downloading https://files.pythonhosted.org/packages/cd/fd/9972948f02e967b691cc0ca1f26124826a3b88cb38f412a8b7935b8c3c72/QtPy-1.9.0-py2.py3-none-any.whl (54kB)
Collecting py4j==0.10.9
Downloading https://files.pythonhosted.org/packages/9e/b6/6a4fb90cd235dc8e265a6a2067f2a2c99f0d91787f06aca4bcf7c23f3f80/py4j-0.10.9-py2.py3-none-any.whl (198kB)
Collecting pandas==0.25.1
Downloading https://files.pythonhosted.org/packages/73/9b/52e228545d14f14bb2a1622e225f38463c8726645165e1cb7dde95bfe6d4/pandas-0.25.1-cp36-cp36m-manylinux1_x86_64.whl (10.5MB)
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)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (3.2.0)
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from pluggy>=0.7->pytest==3.9.1->-r requirements.txt (line 9)) (1.7.0)
Requirement already satisfied: cffi>=1.0.0 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.14.1)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from jinja2->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.1.1)
Requirement already satisfied: webencodings in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5.1)
Requirement already satisfied: packaging in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (20.4)
Collecting filelock
Downloading https://files.pythonhosted.org/packages/93/83/71a2ee6158bb9f39a90c0dea1637f81d5eef866e188e1971a1b1ab01a35a/filelock-3.0.12-py3-none-any.whl
Collecting colorama
Downloading https://files.pythonhosted.org/packages/c9/dc/45cdef1b4d119eb96316b3117e6d5708a08029992b2fee2c143c7a0a5cc5/colorama-0.4.3-py2.py3-none-any.whl
Collecting redis
Downloading https://files.pythonhosted.org/packages/a7/7c/24fb0511df653cf1a5d938d8f5d19802a88cef255706fdda242ff97e91b7/redis-3.5.3-py2.py3-none-any.whl (72kB)
Collecting funcsigs
Downloading https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting click
Downloading https://files.pythonhosted.org/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82kB)
Collecting protobuf>=3.8.0
Downloading https://files.pythonhosted.org/packages/30/79/510974552cebff2ba04038544799450defe75e96ea5f1675dbf72cc8744f/protobuf-3.13.0-cp36-cp36m-manylinux1_x86_64.whl (1.3MB)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (0.16.0)
Requirement already satisfied: zipp>=0.5 in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pluggy>=0.7->pytest==3.9.1->-r requirements.txt (line 9)) (3.1.0)
Requirement already satisfied: pycparser in /home/jenkins/.conda/envs/mango-build-c74e685a-12ad-4f29-aa12-2e90e79ae5ab/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (2.20)
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
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