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Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm-commons/6.2/asm-commons-6.2.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm-util/6.2/asm-util-6.2.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-shade-spark2_2.11/0.32.0/adam-shade-spark2_2.11-0.32.0.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-shade-spark2_2.11/0.32.0/adam-shade-spark2_2.11-0.32.0.jar (13 kB at 1.2 MB/s)
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/3.0.1/maven-common-artifact-filters-3.0.1.jar (61 kB at 2.6 MB/s)
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Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm-tree/6.2.1/asm-tree-6.2.1.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm-commons/6.2.1/asm-commons-6.2.1.jar (79 kB at 1.8 MB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm/6.2.1/asm-6.2.1.jar (113 kB at 2.6 MB/s)
Progress (3): 128 kB | 152/164 kB | 50 kB
                                         
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-artifact-transfer/0.10.0/maven-artifact-transfer-0.10.0.jar (128 kB at 2.8 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-dependency-tree/2.2/maven-dependency-tree-2.2.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/jdom/jdom2/2.0.6/jdom2-2.0.6.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/vafer/jdependency/2.0/jdependency-2.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm-analysis/6.2.1/asm-analysis-6.2.1.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm-util/6.2/asm-util-6.2.jar
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[INFO] Including org.bdgenomics.mango:mango-cli-spark3_2.11:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11: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_2.11:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.32.0 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_2.11: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_2.11: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_2.11:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11: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_2.11:jar:2.5.0 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.11: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_2.11:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.6 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.11.12 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core-spark3_2.11:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.3.0 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.9.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.9.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-assistedinject:jar:4.2.2 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.9.0 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] mango-cli-spark3_2.11-0.0.6-SNAPSHOT.jar, adam-cli-spark2_2.11-0.32.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT.jar with /tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT-shaded.jar
[INFO] 
[INFO] --------< org.bdgenomics.mango:mango-distribution-spark3_2.11 >---------
[INFO] Building mango_2.11: Distribution 0.0.6-SNAPSHOT                   [4/5]
[INFO] --------------------------------[ pom ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-assembly-plugin/2.2-beta-5/maven-assembly-plugin-2.2-beta-5.pom
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution-spark3_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution-spark3_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution-spark3_2.11 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution-spark3_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.11 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution-spark3_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution-spark3_2.11 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.2-beta-5:single (default) @ mango-distribution-spark3_2.11 ---
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/1.1/maven-common-artifact-filters-1.1.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0/maven-profile-2.0.pom
Progress (1): 1.4 kB
                    
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Progress (1): 1.3 kB
                    
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[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.11-0.0.6-SNAPSHOT-bin.tar.gz
[WARNING] Entry: mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building tar : /tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.11-0.0.6-SNAPSHOT-bin.tar.bz2
[WARNING] Entry: mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building zip: /tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.11-0.0.6-SNAPSHOT-bin.zip
[INFO] 
[INFO] -----------< org.bdgenomics.mango:mango-parent-spark3_2.11 >------------
[INFO] Building mango_2.11 0.0.6-SNAPSHOT                                 [5/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent-spark3_2.11 ---
[INFO] Modified 0 of 41 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent-spark3_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.11 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent-spark3_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent-spark3_2.11 ---
[INFO] No source files found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.11 0.0.6-SNAPSHOT:
[INFO] 
[INFO] mango_2.11: CORE ................................... SUCCESS [ 27.283 s]
[INFO] mango_2.11: CLI .................................... SUCCESS [ 30.322 s]
[INFO] Mango_2.11: Assembly ............................... SUCCESS [ 26.151 s]
[INFO] mango_2.11: Distribution ........................... SUCCESS [01:01 min]
[INFO] mango_2.11 ......................................... SUCCESS [  0.850 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:26 min
[INFO] Finished at: 2020-08-19T12:52:34Z
[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_2.11-0.0.6-SNAPSHOT-bin.tar.gz
+ grep jar
+ grep -v -e sources -e javadoc
mango-distribution-spark3_2.11-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.11-0.0.6-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvn7fQY326
/tmp/mangoTestMvn7fQY326
/tmp/mangoTestMvn7fQY326/8664246577965724469
/tmp/mangoTestMvn7fQY326/8664246577965724469/anoGam1.genome
/tmp/mangoTestMvn7fQY326/fake-8619880347879455359.txt
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229
/tmp/mangoTestMvn7fQY326/mmbroken3221103562799644038.genome
/tmp/mangoTestMvn7fQY326/invalidBuild.genome7330220458767595894
/tmp/mangoTestMvn7fQY326/invalidBuild.genome7330220458767595894/properties.txt
/tmp/mangoTestMvn7fQY326/7660839816960890220
/tmp/mangoTestMvn7fQY326/7660839816960890220/anoGam1.genome
/tmp/mangoTestMvn7fQY326/fake-9190064751623922314.sh
/tmp/mangoTestMvn7fQY326/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387
/tmp/mangoTestMvn7fQY326/genomes7031469916209981562
/tmp/mangoTestMvn7fQY326/genomes7031469916209981562/hg19.genome
/tmp/mangoTestMvn7fQY326/genomes400714393032947225
/tmp/mangoTestMvn7fQY326/genomes400714393032947225/hg19.genome
/tmp/mangoTestMvn7fQY326/mmbroken3716594044694839530.genome
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/_readGroups.avro
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=1
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=1/positionBin=240/part-00000-fb59c877-15ab-4809-9084-5d9c3dacfc78.c000.snappy.parquet
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=1/positionBin=240/.part-00000-fb59c877-15ab-4809-9084-5d9c3dacfc78.c000.snappy.parquet.crc
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=1/positionBin=26/part-00000-fb59c877-15ab-4809-9084-5d9c3dacfc78.c000.snappy.parquet
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=1/positionBin=26/.part-00000-fb59c877-15ab-4809-9084-5d9c3dacfc78.c000.snappy.parquet.crc
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/._references.avro.crc
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/_partitionedByStartPos
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/_processingSteps.avro
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=2
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=2/positionBin=189/part-00000-fb59c877-15ab-4809-9084-5d9c3dacfc78.c000.snappy.parquet
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/referenceName=2/positionBin=189/.part-00000-fb59c877-15ab-4809-9084-5d9c3dacfc78.c000.snappy.parquet.crc
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/._SUCCESS.crc
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/_references.avro
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/_SUCCESS
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn7fQY326/TempSuite466307939216452667.adam/._readGroups.avro.crc
/tmp/mangoTestMvn7fQY326/invalidBuild.genome6616425703895270531
/tmp/mangoTestMvn7fQY326/invalidBuild.genome6616425703895270531/properties.txt
/tmp/mangoTestMvn7fQY326/1803659773137685889
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/_processingSteps.avro
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/_SUCCESS
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/_readGroups.avro
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/._references.avro.crc
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/._SUCCESS.crc
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=2
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=2/positionBin=189/part-00000-03a5aa66-de8c-4827-a3a7-3d876971432d.c000.snappy.parquet
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=2/positionBin=189/.part-00000-03a5aa66-de8c-4827-a3a7-3d876971432d.c000.snappy.parquet.crc
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/._readGroups.avro.crc
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=1
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=1/positionBin=26/part-00000-03a5aa66-de8c-4827-a3a7-3d876971432d.c000.snappy.parquet
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=1/positionBin=26/.part-00000-03a5aa66-de8c-4827-a3a7-3d876971432d.c000.snappy.parquet.crc
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=1/positionBin=240/.part-00000-03a5aa66-de8c-4827-a3a7-3d876971432d.c000.snappy.parquet.crc
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/referenceName=1/positionBin=240/part-00000-03a5aa66-de8c-4827-a3a7-3d876971432d.c000.snappy.parquet
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/_partitionedByStartPos
/tmp/mangoTestMvn7fQY326/TempSuite5997428359066834387.adam/_references.avro
/tmp/mangoTestMvn7fQY326/4248780627635347826
/tmp/mangoTestMvn7fQY326/fake-4219098432681808482.sh
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/_header
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/._references.avro.crc
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/._samples.avro.crc
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/._SUCCESS.crc
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/_partitionedByStartPos
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/_samples.avro
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/_references.avro
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/referenceName=1
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/referenceName=1/positionBin=0/.part-00000-181d8e21-de10-4fc1-8585-3350479d592d.c000.snappy.parquet.crc
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/referenceName=1/positionBin=0/part-00000-181d8e21-de10-4fc1-8585-3350479d592d.c000.snappy.parquet
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/._header.crc
/tmp/mangoTestMvn7fQY326/TempSuite9027706436510995229.adam/_SUCCESS
/tmp/mangoTestMvn7fQY326/fake-5382914851591493509.txt
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/._SUCCESS.crc
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/_references.avro
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/_header
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/referenceName=1
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/referenceName=1/positionBin=0/part-00000-7df21556-c96f-4e7d-87f1-b134aefad8eb.c000.snappy.parquet
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/referenceName=1/positionBin=0/.part-00000-7df21556-c96f-4e7d-87f1-b134aefad8eb.c000.snappy.parquet.crc
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/._header.crc
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/_partitionedByStartPos
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/_samples.avro
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/._samples.avro.crc
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/_SUCCESS
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/._references.avro.crc
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn7fQY326/TempSuite3220846571711766302
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvn7fQY326

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/mangoTestMvn7fQY326: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
+ '[' 2.11 == 2.12 ']'
+ curl -v -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz' -o /tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7.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*   Trying 40.79.78.1...
* TCP_NODELAY set
* Connected to www.apache.org (40.79.78.1) port 443 (#0)
* ALPN, offering h2
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
*   CAfile: /etc/ssl/certs/ca-certificates.crt
  CApath: /etc/ssl/certs
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [113 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [4639 bytes data]
* TLSv1.2 (IN), TLS handshake, Server key exchange (12):
{ [333 bytes data]
* TLSv1.2 (IN), TLS handshake, Server finished (14):
{ [4 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client key exchange (16):
} [70 bytes data]
* TLSv1.2 (OUT), TLS change cipher, Client hello (1):
} [1 bytes data]
* TLSv1.2 (OUT), TLS handshake, Finished (20):
} [16 bytes data]
* TLSv1.2 (IN), TLS change cipher, Client hello (1):
{ [1 bytes data]
* TLSv1.2 (IN), TLS handshake, Finished (20):
{ [16 bytes data]
* SSL connection using TLSv1.2 / ECDHE-RSA-AES256-GCM-SHA384
* ALPN, server accepted to use http/1.1
* Server certificate:
*  subject: OU=Domain Control Validated; OU=PositiveSSL Wildcard; CN=*.apache.org
*  start date: Jul  1 00:00:00 2019 GMT
*  expire date: Jun 30 23:59:59 2021 GMT
*  subjectAltName: host "www.apache.org" matched cert's "*.apache.org"
*  issuer: C=GB; ST=Greater Manchester; L=Salford; O=Sectigo Limited; CN=Sectigo RSA Domain Validation Secure Server CA
*  SSL certificate verify ok.
} [5 bytes data]
> GET /dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz HTTP/1.1
> Host: www.apache.org
> User-Agent: curl/7.52.1
> Accept: */*
> 
{ [5 bytes data]
< HTTP/1.1 302 Found
< Date: Wed, 19 Aug 2020 12:52:36 GMT
< Server: Apache/2.4.18 (Ubuntu)
< Location: http://mirror.cc.columbia.edu/pub/software/apache/spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz
< Cache-Control: max-age=3600
< Expires: Wed, 19 Aug 2020 13:52:36 GMT
< Content-Length: 0
< 

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0* Curl_http_done: called premature == 0

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
* Connection #0 to host www.apache.org left intact
* Issue another request to this URL: 'http://mirror.cc.columbia.edu/pub/software/apache/spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz'
*   Trying 128.59.59.71...
* TCP_NODELAY set
* Connected to mirror.cc.columbia.edu (128.59.59.71) port 80 (#1)
> GET /pub/software/apache/spark/spark-2.4.6/spark-2.4.6-bin-hadoop2.7.tgz HTTP/1.1
> Host: mirror.cc.columbia.edu
> User-Agent: curl/7.52.1
> Accept: */*
> 
< HTTP/1.1 200 OK
< Date: Wed, 19 Aug 2020 12:52:07 GMT
< Server: Apache/2.2.22 (Fedora)
< Last-Modified: Sat, 30 May 2020 00:54:32 GMT
< ETag: "fce1580-de6945b-5a6d301334200"
< Accept-Ranges: bytes
< Content-Length: 233215067
< Content-Type: application/x-gzip
< 
{ [6984 bytes data]

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  9  222M    9 20.5M    0     0   549k      0  0:06:54  0:00:38  0:06:16  739k
  9  222M    9 21.7M    0     0   565k      0  0:06:42  0:00:39  0:06:03  837k
  9  222M    9 21.8M    0     0   554k      0  0:06:50  0:00:40  0:06:10  724k
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  9  222M    9 22.0M    0     0   534k      0  0:07:06  0:00:42  0:06:24  479k
 10  222M   10 22.2M    0     0   526k      0  0:07:12  0:00:43  0:06:29  355k
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 10  222M   10 23.1M    0     0   523k      0  0:07:15  0:00:45  0:06:30  271k
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* Connection #1 to host mirror.cc.columbia.edu left intact
+ tar xzf /tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7.tgz --directory /tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded
+ export SPARK_HOME=/tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7
+ SPARK_HOME=/tmp/mangoTestqS7M4mk/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-hadoop2.7



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

    # 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[*]}
+ conda create -y -q -c conda-forge -n mango-build-00015a5f-a73b-4367-bb5d-b059923c1c10 python=3.6 pip=19.3.1 jupyterlab=2.0.1
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-00015a5f-a73b-4367-bb5d-b059923c1c10

  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 activate mango-build-00015a5f-a73b-4367-bb5d-b059923c1c10

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.


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-00015a5f-a73b-4367-bb5d-b059923c1c10


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-2020.6.20-hecda079_0
  certifi-2020.6.20-py36h9f0ad1d_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
  notebook-6.1.3-py36h9f0ad1d_0
  openssl-1.1.1g-h516909a_1
  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-00015a5f-a73b-4367-bb5d-b059923c1c10:

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