FailedConsole Output

Skipping 5,818 KB.. Full Log
/maven-model-2.0.pom (2.4 kB at 301 kB/s)
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-error-diagnostics/2.0/maven-error-diagnostics-2.0.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-descriptor/2.0/maven-plugin-descriptor-2.0.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.2/plexus-utils-1.2.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus/1.0.5/plexus-1.0.5.pom
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Progress (1): 5.9 kB    
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.7/plexus-interpolation-1.7.pom
Progress (1): 2.9 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-archiver/1.0-alpha-12/plexus-archiver-1.0-alpha-12.pom
Progress (1): 1.6 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-io/1.0-alpha-4/plexus-io-1.0-alpha-4.pom
Progress (1): 1.2 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-io/1.0-alpha-4/plexus-io-1.0-alpha-4.pom (1.2 kB at 149 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/1.1/file-management-1.1.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/4/maven-shared-components-4.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-io/1.0/maven-shared-io-1.0.pom
Progress (1): 3.0 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0.2/maven-artifact-2.0.2.pom
Progress (1): 765 B
                   
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven/2.0.2/maven-2.0.2.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.1/plexus-utils-1.1.pom
Progress (1): 767 B
                   
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact-manager/2.0.2/maven-artifact-manager-2.0.2.pom
Progress (1): 1.4 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.0.2/maven-repository-metadata-2.0.2.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/1.0-alpha-6/wagon-provider-api-1.0-alpha-6.pom
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/1.0-alpha-6/wagon-provider-api-1.0-alpha-6.pom (588 B at 74 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon/1.0-alpha-6/wagon-1.0-alpha-6.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-io/1.1/maven-shared-io-1.1.pom
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Progress (1): 2.7 kB
                    
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Progress (1): 21 kB   
                   
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-filtering/1.0-beta-2/maven-filtering-1.0-beta-2.pom
Progress (1): 4.0 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-filtering/1.0-beta-2/maven-filtering-1.0-beta-2.pom (4.0 kB at 403 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-interpolation/1.6/plexus-interpolation-1.6.pom
Progress (1): 2.9 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-active-collections/1.0-beta-2/plexus-active-collections-1.0-beta-2.pom
Progress (1): 2.8 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-container-default/1.0-alpha-22/plexus-container-default-1.0-alpha-22.pom
Progress (1): 3.0 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-containers/1.0-alpha-22/plexus-containers-1.0-alpha-22.pom
Progress (1): 1.9 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-api/2.0.4/maven-plugin-api-2.0.4.pom
Progress (1): 643 B
                   
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.0.4/maven-project-2.0.4.pom
Progress (1): 1.8 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-settings/2.0.4/maven-settings-2.0.4.pom
Progress (1): 1.6 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model/2.0.4/maven-model-2.0.4.pom
Progress (1): 2.7 kB
                    
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Progress (1): 1.6 kB
                    
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Progress (1): 1.4 kB
                    
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.0.4/maven-repository-metadata-2.0.4.pom
Progress (1): 1.5 kB
                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-repository-metadata/2.0.4/maven-repository-metadata-2.0.4.pom (1.5 kB at 212 kB/s)
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Progress (1): 765 B
                   
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Progress (1): 3.4 kB
                    
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Progress (1): 1.8 kB
                    
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Progress (1): 1.7 kB
                    
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Progress (1): 1.9 kB
                    
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Progress (1): 948 B
                   
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Progress (1): 1.4 kB
                    
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Progress (1): 1.9 kB
                    
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Progress (1): 2.3 kB
                    
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Progress (1): 3.3 kB
                    
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Progress (1): 3.2 kB
                    
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Progress (1): 1.8 kB
                    
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Progress (4): 49 kB | 48 kB | 8.3 kB | 29/109 kB
                                                
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0.4/maven-profile-2.0.4.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/2.4/maven-archiver-2.4.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/2.0.1/plexus-utils-2.0.1.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-io/1.0-alpha-4/plexus-io-1.0-alpha-4.jar (48 kB at 645 kB/s)
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0.4/maven-artifact-2.0.4.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0.4/maven-profile-2.0.4.jar (30 kB at 369 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model/2.0.4/maven-model-2.0.4.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-repository-builder/1.0-alpha-2/maven-repository-builder-1.0-alpha-2.jar
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Progress (4): 98/222 kB | 80 kB | 29/80 kB | 4.1/23 kB
                                                      
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Progress (1): 222 kB
                    
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[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu/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 : /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu/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: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu/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 [ 24.009 s]
[INFO] mango_2.12: CLI .................................... SUCCESS [ 32.948 s]
[INFO] Mango_2.12: Assembly ............................... SUCCESS [ 25.026 s]
[INFO] mango_2.12: Distribution ........................... SUCCESS [ 53.413 s]
[INFO] mango_2.12 ......................................... SUCCESS [  0.958 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:16 min
[INFO] Finished at: 2020-08-17T17:30:59Z
[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/mangoTestMvnrWKq4nL
/tmp/mangoTestMvnrWKq4nL
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/._samples.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/._SUCCESS.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/_partitionedByStartPos
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/._references.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/_SUCCESS
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/_references.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/._header.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/_samples.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/referenceName=1
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/referenceName=1/positionBin=0/.part-00000-bbe87673-a09f-4bd4-a7b9-45d6a5833460.c000.snappy.parquet.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/referenceName=1/positionBin=0/part-00000-bbe87673-a09f-4bd4-a7b9-45d6a5833460.c000.snappy.parquet
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603.adam/_header
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655
/tmp/mangoTestMvnrWKq4nL/fake-7545366729987792246.txt
/tmp/mangoTestMvnrWKq4nL/invalidBuild.genome885413255393877366
/tmp/mangoTestMvnrWKq4nL/invalidBuild.genome885413255393877366/properties.txt
/tmp/mangoTestMvnrWKq4nL/genomes1236214336123964425
/tmp/mangoTestMvnrWKq4nL/genomes1236214336123964425/hg19.genome
/tmp/mangoTestMvnrWKq4nL/fake-1129261138326257035.sh
/tmp/mangoTestMvnrWKq4nL/invalidBuild.genome8736212362507180786
/tmp/mangoTestMvnrWKq4nL/invalidBuild.genome8736212362507180786/properties.txt
/tmp/mangoTestMvnrWKq4nL/TempSuite1500420916547195603
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/._SUCCESS.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/_processingSteps.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=2
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=2/positionBin=189/part-00000-bcfd10b8-9e5f-4f83-a518-fe35be206d2b.c000.snappy.parquet
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=2/positionBin=189/.part-00000-bcfd10b8-9e5f-4f83-a518-fe35be206d2b.c000.snappy.parquet.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/_partitionedByStartPos
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/._references.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/_SUCCESS
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/_references.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/_readGroups.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/._readGroups.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=1
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=1/positionBin=240/part-00000-bcfd10b8-9e5f-4f83-a518-fe35be206d2b.c000.snappy.parquet
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=1/positionBin=240/.part-00000-bcfd10b8-9e5f-4f83-a518-fe35be206d2b.c000.snappy.parquet.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=1/positionBin=26/part-00000-bcfd10b8-9e5f-4f83-a518-fe35be206d2b.c000.snappy.parquet
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870.adam/referenceName=1/positionBin=26/.part-00000-bcfd10b8-9e5f-4f83-a518-fe35be206d2b.c000.snappy.parquet.crc
/tmp/mangoTestMvnrWKq4nL/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/._SUCCESS.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/_processingSteps.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=2
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=2/positionBin=189/part-00000-ee35d369-26e7-4513-9342-c0ee7ab216af.c000.snappy.parquet
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=2/positionBin=189/.part-00000-ee35d369-26e7-4513-9342-c0ee7ab216af.c000.snappy.parquet.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/_partitionedByStartPos
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/._references.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/_SUCCESS
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/_references.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/_readGroups.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/._readGroups.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=1
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=1/positionBin=240/part-00000-ee35d369-26e7-4513-9342-c0ee7ab216af.c000.snappy.parquet
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=1/positionBin=240/.part-00000-ee35d369-26e7-4513-9342-c0ee7ab216af.c000.snappy.parquet.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=1/positionBin=26/part-00000-ee35d369-26e7-4513-9342-c0ee7ab216af.c000.snappy.parquet
/tmp/mangoTestMvnrWKq4nL/TempSuite5322444630435611655.adam/referenceName=1/positionBin=26/.part-00000-ee35d369-26e7-4513-9342-c0ee7ab216af.c000.snappy.parquet.crc
/tmp/mangoTestMvnrWKq4nL/fake-2131196026600062827.sh
/tmp/mangoTestMvnrWKq4nL/9011341591922459322
/tmp/mangoTestMvnrWKq4nL/9011341591922459322/anoGam1.genome
/tmp/mangoTestMvnrWKq4nL/genomes8008466455730304907
/tmp/mangoTestMvnrWKq4nL/genomes8008466455730304907/hg19.genome
/tmp/mangoTestMvnrWKq4nL/1491332380911911966
/tmp/mangoTestMvnrWKq4nL/TempSuite7203306040893080870
/tmp/mangoTestMvnrWKq4nL/8324899464684868928
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393
/tmp/mangoTestMvnrWKq4nL/465966388079386387
/tmp/mangoTestMvnrWKq4nL/465966388079386387/anoGam1.genome
/tmp/mangoTestMvnrWKq4nL/fake-7396476736056662031.txt
/tmp/mangoTestMvnrWKq4nL/mmbroken4129819237476192342.genome
/tmp/mangoTestMvnrWKq4nL/mmbroken7214776319967917082.genome
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/._samples.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/._SUCCESS.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/_partitionedByStartPos
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/._references.avro.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/_SUCCESS
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/_references.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/._header.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/_samples.avro
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/referenceName=1
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/referenceName=1/positionBin=0/.part-00000-35d2976d-0318-4b7f-8920-050ca2701473.c000.snappy.parquet.crc
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/referenceName=1/positionBin=0/part-00000-35d2976d-0318-4b7f-8920-050ca2701473.c000.snappy.parquet
/tmp/mangoTestMvnrWKq4nL/TempSuite1790796582077159393.adam/_header
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvnrWKq4nL

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/mangoTestMvnrWKq4nL: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/mangoTestWC0pww5/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     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0  139M    0  911k    0     0   514k      0  0:04:38  0:00:01  0:04:37  960k
  2  139M    2 3778k    0     0  1298k      0  0:01:50  0:00:02  0:01:48 1812k
  2  139M    2 4002k    0     0   999k      0  0:02:23  0:00:04  0:02:19 1257k
  2  139M    2 4004k    0     0   838k      0  0:02:50  0:00:04  0:02:46 1013k
  2  139M    2 4021k    0     0   637k      0  0:03:44  0:00:06  0:03:38  732k
  2  139M    2 4117k    0     0   604k      0  0:03:56  0:00:06  0:03:50  636k
  2  139M    2 4205k    0     0   539k      0  0:04:25  0:00:07  0:04:18 89426
  3  139M    3 4357k    0     0   496k      0  0:04:48  0:00:08  0:04:40 76178
  3  139M    3 4626k    0     0   473k      0  0:05:02  0:00:09  0:04:53  124k
  3  139M    3 5090k    0     0   472k      0  0:05:03  0:00:10  0:04:53  239k
  4  139M    4 5916k    0     0   502k      0  0:04:44  0:00:11  0:04:33  362k
  4  139M    4 7041k    0     0   551k      0  0:04:19  0:00:12  0:04:07  570k
  5  139M    5 8368k    0     0   607k      0  0:03:55  0:00:13  0:03:42  801k
  6  139M    6 9971k    0     0   674k      0  0:03:32  0:00:14  0:03:18 1069k
  7  139M    7 11.0M    0     0   714k      0  0:03:20  0:00:15  0:03:05 1235k
  8  139M    8 12.2M    0     0   747k      0  0:03:11  0:00:16  0:02:55 1322k
  9  139M    9 13.5M    0     0   781k      0  0:03:03  0:00:17  0:02:46 1369k
 10  139M   10 15.2M    0     0   831k      0  0:02:52  0:00:18  0:02:34 1448k
 12  139M   12 17.0M    0     0   882k      0  0:02:42  0:00:19  0:02:23 1494k
 13  139M   13 18.8M    0     0   931k      0  0:02:33  0:00:20  0:02:13 1615k
 14  139M   14 20.7M    0     0   978k      0  0:02:26  0:00:21  0:02:05 1752k
 16  139M   16 22.5M    0     0  1014k      0  0:02:21  0:00:22  0:01:59 1843k
 17  139M   17 24.3M    0     0  1048k      0  0:02:16  0:00:23  0:01:53 1866k
 18  139M   18 26.1M    0     0  1079k      0  0:02:12  0:00:24  0:01:48 1858k
 19  139M   19 27.8M    0     0  1106k      0  0:02:09  0:00:25  0:01:44 1836k
 21  139M   21 29.5M    0     0  1131k      0  0:02:06  0:00:26  0:01:40 1798k
 22  139M   22 31.2M    0     0  1153k      0  0:02:04  0:00:27  0:01:37 1783k
 23  139M   23 33.0M    0     0  1175k      0  0:02:01  0:00:28  0:01:33 1776k
 24  139M   24 34.8M    0     0  1199k      0  0:01:59  0:00:29  0:01:30 1791k
 26  139M   26 36.4M    0     0  1213k      0  0:01:57  0:00:30  0:01:27 1763k
 27  139M   27 38.2M    0     0  1233k      0  0:01:56  0:00:31  0:01:25 1779k
 28  139M   28 40.0M    0     0  1251k      0  0:01:54  0:00:32  0:01:22 1797k
 29  139M   29 41.8M    0     0  1269k      0  0:01:52  0:00:33  0:01:19 1810k
 31  139M   31 43.6M    0     0  1285k      0  0:01:51  0:00:34  0:01:17 1798k
 32  139M   32 45.4M    0     0  1301k      0  0:01:49  0:00:35  0:01:14 1844k
 33  139M   33 47.3M    0     0  1317k      0  0:01:48  0:00:36  0:01:12 1850k
 35  139M   35 49.1M    0     0  1332k      0  0:01:47  0:00:37  0:01:10 1864k
 36  139M   36 50.9M    0     0  1345k      0  0:01:46  0:00:38  0:01:08 1861k
 37  139M   37 52.7M    0     0  1357k      0  0:01:45  0:00:39  0:01:06 1857k
 38  139M   38 54.5M    0     0  1369k      0  0:01:44  0:00:40  0:01:04 1851k
 40  139M   40 56.2M    0     0  1379k      0  0:01:43  0:00:41  0:01:02 1838k
 41  139M   41 58.1M    0     0  1391k      0  0:01:42  0:00:42  0:01:00 1832k
 42  139M   42 59.8M    0     0  1400k      0  0:01:42  0:00:43  0:00:59 1829k
 44  139M   44 61.6M    0     0  1410k      0  0:01:41  0:00:44  0:00:57 1829k
 45  139M   45 63.4M    0     0  1419k      0  0:01:40  0:00:45  0:00:55 1826k
 46  139M   46 65.2M    0     0  1427k      0  0:01:40  0:00:46  0:00:54 1829k
 47  139M   47 66.9M    0     0  1434k      0  0:01:39  0:00:47  0:00:52 1810k
 49  139M   49 68.7M    0     0  1442k      0  0:01:39  0:00:48  0:00:51 1805k
 50  139M   50 70.4M    0     0  1448k      0  0:01:38  0:00:49  0:00:49 1793k
 51  139M   51 72.1M    0     0  1454k      0  0:01:38  0:00:50  0:00:48 1782k
 52  139M   52 73.9M    0     0  1461k      0  0:01:37  0:00:51  0:00:46 1780k
 54  139M   54 75.7M    0     0  1469k      0  0:01:37  0:00:52  0:00:45 1800k
 55  139M   55 77.5M    0     0  1475k      0  0:01:37  0:00:53  0:00:44 1802k
 56  139M   56 79.2M    0     0  1481k      0  0:01:36  0:00:54  0:00:42 1812k
 57  139M   57 81.0M    0     0  1488k      0  0:01:36  0:00:55  0:00:41 1826k
 59  139M   59 82.8M    0     0  1494k      0  0:01:35  0:00:56  0:00:39 1827k
 60  139M   60 84.3M    0     0  1495k      0  0:01:35  0:00:57  0:00:38 1770k
 61  139M   61 85.6M    0     0  1492k      0  0:01:35  0:00:58  0:00:37 1675k
 62  139M   62 86.9M    0     0  1490k      0  0:01:36  0:00:59  0:00:37 1583k
 63  139M   63 88.3M    0     0  1488k      0  0:01:36  0:01:00  0:00:36 1490k
 64  139M   64 89.6M    0     0  1486k      0  0:01:36  0:01:01  0:00:35 1395k
 65  139M   65 90.9M    0     0  1483k      0  0:01:36  0:01:02  0:00:34 1347k
 65  139M   65 92.2M    0     0  1481k      0  0:01:36  0:01:03  0:00:33 1349k
 66  139M   66 93.5M    0     0  1479k      0  0:01:36  0:01:04  0:00:32 1351k
 67  139M   67 94.9M    0     0  1478k      0  0:01:36  0:01:05  0:00:31 1356k
 68  139M   68 96.3M    0     0  1477k      0  0:01:36  0:01:06  0:00:30 1364k
 69  139M   69 97.6M    0     0  1476k      0  0:01:36  0:01:07  0:00:29 1377k
 70  139M   70 99.0M    0     0  1475k      0  0:01:37  0:01:08  0:00:29 1393k
 71  139M   71  100M    0     0  1473k      0  0:01:37  0:01:09  0:00:28 1397k
 72  139M   72  101M    0     0  1471k      0  0:01:37  0:01:10  0:00:27 1380k
 73  139M   73  102M    0     0  1468k      0  0:01:37  0:01:11  0:00:26 1349k
 74  139M   74  104M    0     0  1465k      0  0:01:37  0:01:12  0:00:25 1316k
 75  139M   75  105M    0     0  1461k      0  0:01:37  0:01:13  0:00:24 1278k
 76  139M   76  106M    0     0  1459k      0  0:01:38  0:01:14  0:00:24 1265k
 77  139M   77  107M    0     0  1456k      0  0:01:38  0:01:15  0:00:23 1248k
 77  139M   77  109M    0     0  1454k      0  0:01:38  0:01:16  0:00:22 1253k
 78  139M   78  110M    0     0  1453k      0  0:01:38  0:01:17  0:00:21 1279k
 79  139M   79  111M    0     0  1451k      0  0:01:38  0:01:18  0:00:20 1295k
 80  139M   80  112M    0     0  1449k      0  0:01:38  0:01:19  0:00:19 1296k
 81  139M   81  114M    0     0  1448k      0  0:01:38  0:01:20  0:00:18 1315k
 82  139M   82  115M    0     0  1445k      0  0:01:39  0:01:21  0:00:18 1310k
 83  139M   83  116M    0     0  1442k      0  0:01:39  0:01:22  0:00:17 1279k
 84  139M   84  117M    0     0  1440k      0  0:01:39  0:01:23  0:00:16 1267k
 85  139M   85  119M    0     0  1437k      0  0:01:39  0:01:24  0:00:15 1246k
 86  139M   86  120M    0     0  1435k      0  0:01:39  0:01:25  0:00:14 1236k
 86  139M   86  121M    0     0  1433k      0  0:01:39  0:01:26  0:00:13 1238k
 87  139M   87  122M    0     0  1430k      0  0:01:40  0:01:27  0:00:13 1233k
 88  139M   88  123M    0     0  1425k      0  0:01:40  0:01:28  0:00:12 1176k
 89  139M   89  124M    0     0  1419k      0  0:01:40  0:01:29  0:00:11 1120k
 89  139M   89  125M    0     0  1414k      0  0:01:41  0:01:30  0:00:11 1055k
 90  139M   90  126M    0     0  1409k      0  0:01:41  0:01:31  0:00:10  990k
 90  139M   90  127M    0     0  1404k      0  0:01:41  0:01:32  0:00:09  936k
 91  139M   91  128M    0     0  1399k      0  0:01:42  0:01:33  0:00:09  931k
 92  139M   92  129M    0     0  1393k      0  0:01:42  0:01:34  0:00:08  928k
 92  139M   92  129M    0     0  1388k      0  0:01:43  0:01:35  0:00:08  919k
 93  139M   93  130M    0     0  1383k      0  0:01:43  0:01:36  0:00:07  914k
 94  139M   94  131M    0     0  1378k      0  0:01:43  0:01:37  0:00:06  899k
 94  139M   94  132M    0     0  1373k      0  0:01:44  0:01:38  0:00:06  891k
 95  139M   95  133M    0     0  1368k      0  0:01:44  0:01:39  0:00:05  894k
 96  139M   96  134M    0     0  1364k      0  0:01:44  0:01:40  0:00:04  898k
 97  139M   97  136M    0     0  1368k      0  0:01:44  0:01:41  0:00:03 1081k
 98  139M   98  137M    0     0  1373k      0  0:01:44  0:01:42  0:00:02 1283k
 99  139M   99  139M    0     0  1377k      0  0:01:43  0:01:43 --:--:-- 1468k
100  139M  100  139M    0     0  1378k      0  0:01:43  0:01:43 --:--:-- 1611k
+ tar xzf /tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12.tgz --directory /tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded
+ export SPARK_HOME=/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12
+ SPARK_HOME=/tmp/mangoTestWC0pww5/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/mangoTestWC0pww5/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  152k    0     0   122k      0  0:29:04  0:00:01  0:29:03  122k
  0  208M    0 1015k    0     0   452k      0  0:07:52  0:00:02  0:07:50  862k
  0  208M    0 1929k    0     0   594k      0  0:05:59  0:00:03  0:05:56  888k
  1  208M    1 2861k    0     0   674k      0  0:05:16  0:00:04  0:05:12  903k
  1  208M    1 3783k    0     0   721k      0  0:04:56  0:00:05  0:04:51  907k
  2  208M    2 4701k    0     0   752k      0  0:04:43  0:00:06  0:04:37  909k
  2  208M    2 5709k    0     0   788k      0  0:04:30  0:00:07  0:04:23  938k
  3  208M    3 6965k    0     0   844k      0  0:04:12  0:00:08  0:04:04 1007k
  3  208M    3 8150k    0     0   881k      0  0:04:02  0:00:09  0:03:53 1057k
  4  208M    4 9359k    0     0   913k      0  0:03:53  0:00:10  0:03:43 1114k
  4  208M    4 10.1M    0     0   926k      0  0:03:50  0:00:11  0:03:39 1144k
  5  208M    5 11.2M    0     0   936k      0  0:03:48  0:00:12  0:03:36 1151k
  5  208M    5 12.4M    0     0   961k      0  0:03:42  0:00:13  0:03:29 1153k
  6  208M    6 13.7M    0     0   987k      0  0:03:36  0:00:14  0:03:22 1182k
  7  208M    7 15.0M    0     0  1007k      0  0:03:31  0:00:15  0:03:16 1201k
  7  208M    7 16.2M    0     0  1025k      0  0:03:28  0:00:16  0:03:12 1248k
  8  208M    8 17.6M    0     0  1046k      0  0:03:24  0:00:17  0:03:07 1315k
  9  208M    9 19.0M    0     0  1071k      0  0:03:19  0:00:18  0:03:01 1362k
  9  208M    9 20.4M    0     0  1086k      0  0:03:16  0:00:19  0:02:57 1367k
 10  208M   10 21.7M    0     0  1098k      0  0:03:14  0:00:20  0:02:54 1373k
 11  208M   11 23.0M    0     0  1108k      0  0:03:12  0:00:21  0:02:51 1378k
 11  208M   11 24.3M    0     0  1118k      0  0:03:10  0:00:22  0:02:48 1366k
 12  208M   12 25.5M    0     0  1125k      0  0:03:09  0:00:23  0:02:46 1321k
 12  208M   12 26.8M    0     0  1132k      0  0:03:08  0:00:24  0:02:44 1311k
 13  208M   13 28.0M    0     0  1139k      0  0:03:07  0:00:25  0:02:42 1308k
 14  208M   14 29.3M    0     0  1146k      0  0:03:06  0:00:26  0:02:40 1306k
 14  208M   14 30.6M    0     0  1152k      0  0:03:05  0:00:27  0:02:38 1305k
 15  208M   15 31.9M    0     0  1157k      0  0:03:04  0:00:28  0:02:36 1310k
 15  208M   15 33.1M    0     0  1161k      0  0:03:03  0:00:29  0:02:34 1302k
 16  208M   16 34.4M    0     0  1165k      0  0:03:03  0:00:30  0:02:33 1298k
 17  208M   17 35.6M    0     0  1168k      0  0:03:02  0:00:31  0:02:31 1284k
 17  208M   17 36.8M    0     0  1170k      0  0:03:02  0:00:32  0:02:30 1266k
 18  208M   18 38.2M    0     0  1178k      0  0:03:01  0:00:33  0:02:28 1298k
 18  208M   18 39.5M    0     0  1183k      0  0:03:00  0:00:34  0:02:26 1313k
 19  208M   19 40.8M    0     0  1187k      0  0:02:59  0:00:35  0:02:24 1318k
 20  208M   20 42.1M    0     0  1190k      0  0:02:59  0:00:36  0:02:23 1329k
 20  208M   20 43.5M    0     0  1195k      0  0:02:58  0:00:37  0:02:21 1357k
 21  208M   21 44.7M    0     0  1199k      0  0:02:58  0:00:38  0:02:20 1334k
 22  208M   22 46.0M    0     0  1202k      0  0:02:57  0:00:39  0:02:18 1328k
 22  208M   22 47.3M    0     0  1205k      0  0:02:57  0:00:40  0:02:17 1328k
 23  208M   23 48.6M    0     0  1207k      0  0:02:56  0:00:41  0:02:15 1328k
 23  208M   23 49.9M    0     0  1209k      0  0:02:56  0:00:42  0:02:14 1317k
 24  208M   24 51.2M    0     0  1213k      0  0:02:56  0:00:43  0:02:13 1320k
 25  208M   25 52.4M    0     0  1214k      0  0:02:55  0:00:44  0:02:11 1315k
 25  208M   25 53.5M    0     0  1211k      0  0:02:56  0:00:45  0:02:11 1260k
 26  208M   26 54.4M    0     0  1206k      0  0:02:57  0:00:46  0:02:11 1195k
 26  208M   26 55.6M    0     0  1205k      0  0:02:57  0:00:47  0:02:10 1171k
 27  208M   27 56.4M    0     0  1198k      0  0:02:58  0:00:48  0:02:10 1071k
 27  208M   27 57.2M    0     0  1189k      0  0:02:59  0:00:49  0:02:10  965k
 27  208M   27 58.0M    0     0  1182k      0  0:03:00  0:00:50  0:02:10  924k
 28  208M   28 58.8M    0     0  1175k      0  0:03:01  0:00:51  0:02:10  892k
 28  208M   28 59.6M    0     0  1168k      0  0:03:02  0:00:52  0:02:10  812k
 28  208M   28 60.3M    0     0  1159k      0  0:03:04  0:00:53  0:02:11  787k
 29  208M   29 61.0M    0     0  1151k      0  0:03:05  0:00:54  0:02:11  780k
 29  208M   29 61.7M    0     0  1144k      0  0:03:06  0:00:55  0:02:11  758k
 29  208M   29 62.4M    0     0  1137k      0  0:03:07  0:00:56  0:02:11  744k
 30  208M   30 63.3M    0     0  1132k      0  0:03:08  0:00:57  0:02:11  764k
 30  208M   30 64.1M    0     0  1128k      0  0:03:09  0:00:58  0:02:11  794k
 31  208M   31 65.0M    0     0  1123k      0  0:03:10  0:00:59  0:02:11  814k
 31  208M   31 65.8M    0     0  1118k      0  0:03:10  0:01:00  0:02:10  833k
 31  208M   31 66.6M    0     0  1113k      0  0:03:11  0:01:01  0:02:10  850k
 32  208M   32 67.7M    0     0  1114k      0  0:03:11  0:01:02  0:02:09  905k
 33  208M   33 69.2M    0     0  1120k      0  0:03:10  0:01:03  0:02:07 1029k
 33  208M   33 70.6M    0     0  1125k      0  0:03:09  0:01:04  0:02:05 1151k
 34  208M   34 72.0M    0     0  1131k      0  0:03:08  0:01:05  0:02:03 1283k
 35  208M   35 73.4M    0     0  1135k      0  0:03:08  0:01:06  0:02:02 1401k
 35  208M   35 74.8M    0     0  1139k      0  0:03:07  0:01:07  0:02:00 1454k
 36  208M   36 76.2M    0     0  1143k      0  0:03:06  0:01:08  0:01:58 1436k
 37  208M   37 77.5M    0     0  1147k      0  0:03:06  0:01:09  0:01:57 1428k
 37  208M   37 78.8M    0     0  1149k      0  0:03:05  0:01:10  0:01:55 1393k
 38  208M   38 80.2M    0     0  1153k      0  0:03:05  0:01:11  0:01:54 1391k
 39  208M   39 81.6M    0     0  1157k      0  0:03:04  0:01:12  0:01:52 1389k
 39  208M   39 83.0M    0     0  1160k      0  0:03:04  0:01:13  0:01:51 1389k
 40  208M   40 84.4M    0     0  1164k      0  0:03:03  0:01:14  0:01:49 1394k
 40  208M   40 85.3M    0     0  1160k      0  0:03:03  0:01:15  0:01:48 1314k
 41  208M   41 86.1M    0     0  1154k      0  0:03:05  0:01:16  0:01:49 1167k
 41  208M   41 86.7M    0     0  1149k      0  0:03:05  0:01:17  0:01:48 1034k
 41  208M   41 87.4M    0     0  1144k      0  0:03:06  0:01:18  0:01:48  907k
 42  208M   42 88.5M    0     0  1144k      0  0:03:06  0:01:19  0:01:47  850k
 43  208M   43 89.9M    0     0  1147k      0  0:03:06  0:01:20  0:01:46  950k
 43  208M   43 91.4M    0     0  1152k      0  0:03:05  0:01:21  0:01:44 1120k
 44  208M   44 92.9M    0     0  1157k      0  0:03:04  0:01:22  0:01:42 1296k
 45  208M   45 94.5M    0     0  1162k      0  0:03:03  0:01:23  0:01:40 1449k
 46  208M   46 96.0M    0     0  1167k      0  0:03:02  0:01:24  0:01:38 1531k
 46  208M   46 97.5M    0     0  1171k      0  0:03:02  0:01:25  0:01:37 1553k
 47  208M   47 99.0M    0     0  1176k      0  0:03:01  0:01:26  0:01:35 1564k
 48  208M   48  100M    0     0  1180k      0  0:03:00  0:01:27  0:01:33 1556k
 48  208M   48  102M    0     0  1185k      0  0:03:00  0:01:28  0:01:32 1558k
 49  208M   49  103M    0     0  1188k      0  0:02:59  0:01:29  0:01:30 1552k
 50  208M   50  105M    0     0  1192k      0  0:02:59  0:01:30  0:01:29 1540k
 50  208M   50  106M    0     0  1193k      0  0:02:58  0:01:31  0:01:27 1493k
 51  208M   51  107M    0     0  1193k      0  0:02:59  0:01:32  0:01:27 1408k
 52  208M   52  108M    0     0  1191k      0  0:02:59  0:01:33  0:01:26 1307k
 52  208M   52  109M    0     0  1189k      0  0:02:59  0:01:34  0:01:25 1193k
 52  208M   52  110M    0     0  1186k      0  0:02:59  0:01:35  0:01:24 1092k
 53  208M   53  111M    0     0  1184k      0  0:03:00  0:01:36  0:01:24 1019k
 53  208M   53  112M    0     0  1182k      0  0:03:00  0:01:37  0:01:23  985k
 54  208M   54  113M    0     0  1180k      0  0:03:00  0:01:38  0:01:22  966k
 54  208M   54  114M    0     0  1177k      0  0:03:01  0:01:39  0:01:22  957k
 55  208M   55  115M    0     0  1175k      0  0:03:01  0:01:40  0:01:21  959k
 55  208M   55  116M    0     0  1175k      0  0:03:01  0:01:41  0:01:20 1008k
 56  208M   56  117M    0     0  1177k      0  0:03:01  0:01:42  0:01:19 1077k
 56  208M   56  118M    0     0  1178k      0  0:03:01  0:01:43  0:01:18 1155k
 57  208M   57  120M    0     0  1180k      0  0:03:00  0:01:44  0:01:16 1231k
 58  208M   58  121M    0     0  1181k      0  0:03:00  0:01:45  0:01:15 1305k
 58  208M   58  122M    0     0  1180k      0  0:03:00  0:01:46  0:01:14 1271k
 59  208M   59  123M    0     0  1178k      0  0:03:01  0:01:47  0:01:14 1200k
 59  208M   59  124M    0     0  1175k      0  0:03:01  0:01:48  0:01:13 1097k
 59  208M   59  125M    0     0  1173k      0  0:03:02  0:01:49  0:01:13 1026k
 60  208M   60  126M    0     0  1173k      0  0:03:02  0:01:50  0:01:12  994k
 61  208M   61  127M    0     0  1173k      0  0:03:02  0:01:51  0:01:11 1014k
 61  208M   61  128M    0     0  1173k      0  0:03:01  0:01:52  0:01:09 1070k
 62  208M   62  129M    0     0  1173k      0  0:03:01  0:01:53  0:01:08 1144k
 62  208M   62  130M    0     0  1173k      0  0:03:01  0:01:54  0:01:07 1187k
 63  208M   63  132M    0     0  1174k      0  0:03:01  0:01:55  0:01:06 1192k
 63  208M   63  133M    0     0  1173k      0  0:03:01  0:01:56  0:01:05 1184k
 64  208M   64  134M    0     0  1173k      0  0:03:02  0:01:57  0:01:05 1166k
 64  208M   64  135M    0     0  1172k      0  0:03:02  0:01:58  0:01:04 1138k
 65  208M   65  136M    0     0  1171k      0  0:03:02  0:01:59  0:01:03 1122k
 65  208M   65  137M    0     0  1171k      0  0:03:02  0:02:00  0:01:02 1118k
 66  208M   66  138M    0     0  1171k      0  0:03:02  0:02:01  0:01:01 1118k
 67  208M   67  139M    0     0  1171k      0  0:03:02  0:02:02  0:01:00 1120k
 67  208M   67  140M    0     0  1170k      0  0:03:02  0:02:03  0:00:59 1133k
 68  208M   68  142M    0     0  1171k      0  0:03:02  0:02:04  0:00:58 1162k
 68  208M   68  143M    0     0  1171k      0  0:03:02  0:02:05  0:00:57 1168k
 69  208M   69  144M    0     0  1172k      0  0:03:02  0:02:06  0:00:56 1189k
 69  208M   69  145M    0     0  1172k      0  0:03:02  0:02:07  0:00:55 1214k
 70  208M   70  146M    0     0  1173k      0  0:03:02  0:02:08  0:00:54 1239k
 71  208M   71  148M    0     0  1173k      0  0:03:01  0:02:09  0:00:52 1242k
 71  208M   71  149M    0     0  1175k      0  0:03:01  0:02:10  0:00:51 1262k
 72  208M   72  150M    0     0  1173k      0  0:03:02  0:02:11  0:00:51 1201k
 72  208M   72  151M    0     0  1171k      0  0:03:02  0:02:12  0:00:50 1138k
 72  208M   72  152M    0     0  1169k      0  0:03:02  0:02:13  0:00:49 1072k
 73  208M   73  153M    0     0  1167k      0  0:03:02  0:02:14  0:00:48 1008k
 73  208M   73  154M    0     0  1166k      0  0:03:03  0:02:15  0:00:48  931k
 74  208M   74  154M    0     0  1164k      0  0:03:03  0:02:16  0:00:47  925k
 74  208M   74  155M    0     0  1162k      0  0:03:03  0:02:17  0:00:46  922k
 75  208M   75  156M    0     0  1160k      0  0:03:04  0:02:18  0:00:46  919k
 75  208M   75  157M    0     0  1158k      0  0:03:04  0:02:19  0:00:45  914k
 75  208M   75  158M    0     0  1156k      0  0:03:04  0:02:20  0:00:44  902k
 76  208M   76  159M    0     0  1154k      0  0:03:04  0:02:21  0:00:43  897k
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 77  208M   77  161M    0     0  1151k      0  0:03:05  0:02:23  0:00:42  885k
 77  208M   77  161M    0     0  1149k      0  0:03:05  0:02:24  0:00:41  883k
 78  208M   78  162M    0     0  1147k      0  0:03:06  0:02:25  0:00:41  881k
 78  208M   78  163M    0     0  1145k      0  0:03:06  0:02:26  0:00:40  881k
 78  208M   78  164M    0     0  1143k      0  0:03:06  0:02:27  0:00:39  881k
 79  208M   79  165M    0     0  1141k      0  0:03:07  0:02:28  0:00:39  879k
 79  208M   79  166M    0     0  1139k      0  0:03:07  0:02:29  0:00:38  873k
 80  208M   80  166M    0     0  1137k      0  0:03:07  0:02:30  0:00:37  864k
 80  208M   80  167M    0     0  1135k      0  0:03:08  0:02:31  0:00:37  856k
 80  208M   80  168M    0     0  1133k      0  0:03:08  0:02:32  0:00:36  847k
 81  208M   81  169M    0     0  1132k      0  0:03:08  0:02:33  0:00:35  840k
 81  208M   81  170M    0     0  1129k      0  0:03:09  0:02:34  0:00:35  832k
 81  208M   81  171M    0     0  1128k      0  0:03:09  0:02:35  0:00:34  836k
 82  208M   82  171M    0     0  1126k      0  0:03:09  0:02:36  0:00:33  839k
 82  208M   82  172M    0     0  1124k      0  0:03:09  0:02:37  0:00:32  840k
 83  208M   83  173M    0     0  1123k      0  0:03:10  0:02:38  0:00:32  851k
 83  208M   83  174M    0     0  1122k      0  0:03:10  0:02:39  0:00:31  883k
 84  208M   84  175M    0     0  1121k      0  0:03:10  0:02:40  0:00:30  909k
 84  208M   84  176M    0     0  1120k      0  0:03:10  0:02:41  0:00:29  931k
 85  208M   85  177M    0     0  1119k      0  0:03:10  0:02:42  0:00:28  958k
 85  208M   85  178M    0     0  1118k      0  0:03:10  0:02:43  0:00:27  967k
 85  208M   85  179M    0     0  1116k      0  0:03:11  0:02:44  0:00:27  946k
 86  208M   86  179M    0     0  1115k      0  0:03:11  0:02:45  0:00:26  921k
 86  208M   86  180M    0     0  1113k      0  0:03:11  0:02:46  0:00:25  899k
 87  208M   87  181M    0     0  1112k      0  0:03:11  0:02:47  0:00:24  895k
 87  208M   87  183M    0     0  1116k      0  0:03:11  0:02:48  0:00:23 1042k
 88  208M   88  185M    0     0  1119k      0  0:03:10  0:02:49  0:00:21 1203k
 89  208M   89  186M    0     0  1123k      0  0:03:10  0:02:50  0:00:20 1378k
 90  208M   90  188M    0     0  1126k      0  0:03:09  0:02:51  0:00:18 1541k
 91  208M   91  189M    0     0  1129k      0  0:03:09  0:02:52  0:00:17 1676k
 91  208M   91  191M    0     0  1132k      0  0:03:08  0:02:53  0:00:15 1671k
 92  208M   92  193M    0     0  1134k      0  0:03:08  0:02:54  0:00:14 1657k
 93  208M   93  194M    0     0  1137k      0  0:03:07  0:02:55  0:00:12 1641k
 94  208M   94  196M    0     0  1141k      0  0:03:07  0:02:56  0:00:11 1654k
 94  208M   94  196M    0     0  1131k      0  0:03:08  0:02:58  0:00:10 1196k
 94  208M   94  196M    0     0  1130k      0  0:03:08  0:02:58  0:00:10 1068k
 94  208M   94  197M    0     0  1127k      0  0:03:09  0:02:59  0:00:10  864k
 95  208M   95  198M    0     0  1126k      0  0:03:09  0:03:00  0:00:09  739k
 95  208M   95  199M    0     0  1126k      0  0:03:09  0:03:01  0:00:08  597k
 96  208M   96  200M    0     0  1126k      0  0:03:09  0:03:02  0:00:07  899k
 96  208M   96  201M    0     0  1125k      0  0:03:09  0:03:03  0:00:06  948k
 97  208M   97  202M    0     0  1124k      0  0:03:09  0:03:04  0:00:05 1035k
 97  208M   97  202M    0     0  1120k      0  0:03:10  0:03:05  0:00:05  918k
 97  208M   97  203M    0     0  1117k      0  0:03:11  0:03:06  0:00:05  807k
 97  208M   97  203M    0     0  1114k      0  0:03:11  0:03:07  0:00:04  679k
 97  208M   97  204M    0     0  1109k      0  0:03:12  0:03:08  0:00:04  556k
 98  208M   98  204M    0     0  1106k      0  0:03:12  0:03:09  0:00:03  448k
 98  208M   98  205M    0     0  1104k      0  0:03:13  0:03:10  0:00:03  492k
 98  208M   98  206M    0     0  1103k      0  0:03:13  0:03:11  0:00:02  594k
 99  208M   99  206M    0     0  1100k      0  0:03:14  0:03:12  0:00:02  587k
 99  208M   99  207M    0     0  1098k      0  0:03:14  0:03:13  0:00:01  655k
 99  208M   99  208M    0     0  1099k      0  0:03:14  0:03:14 --:--:--  811k
100  208M  100  208M    0     0  1099k      0  0:03:14  0:03:14 --:--:--  838k
+ tar xzf /tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7.tar.gz --directory /tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded
+ grep avro
+ find /tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7 -name '*.jar'
+ xargs rm
++ /tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/bin/hadoop classpath
+ export 'SPARK_DIST_CLASSPATH=/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/etc/hadoop:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/lib/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/lib/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/lib/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/lib/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/*:/contrib/capacity-scheduler/*.jar'
+ SPARK_DIST_CLASSPATH='/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/etc/hadoop:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/lib/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/lib/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/lib/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/lib/*:/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/*:/contrib/capacity-scheduler/*.jar'

# run integration tests
# set the TMPDIR envar, which is used by python to choose where to make temp directories
export TMPDIR=${MANGO_TMP_DIR}
+ export TMPDIR=/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded

pushd $PROJECT_ROOT
+ pushd /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu/scripts/..
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu /home

# Copy the jar into our temp space for testing
cp -r . $MANGO_TMP_DIR
+ cp -r . /tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd

pushd $MANGO_TMP_DIR
+ pushd /tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu /home
/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu /home

# 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

    which python
    python -h

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

    # prepare mango python
    pushd mango-python
    make prepare

    python -h
	make develop
    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

    # copy python targets back
    cp -r mango-python/target ${PROJECT_ROOT}/mango-python/

    # 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: /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7

  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-3.32.3              |       h4cf870e_1         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-3.32.3-h4cf870e_1
  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
+ which python
/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/bin/python
+ python -h
usage: python [option] ... [-c cmd | -m mod | file | -] [arg] ...
Options and arguments (and corresponding environment variables):
-b     : issue warnings about str(bytes_instance), str(bytearray_instance)
         and comparing bytes/bytearray with str. (-bb: issue errors)
-B     : don't write .pyc files on import; also PYTHONDONTWRITEBYTECODE=x
-c cmd : program passed in as string (terminates option list)
-d     : debug output from parser; also PYTHONDEBUG=x
-E     : ignore PYTHON* environment variables (such as PYTHONPATH)
-h     : print this help message and exit (also --help)
-i     : inspect interactively after running script; forces a prompt even
         if stdin does not appear to be a terminal; also PYTHONINSPECT=x
-I     : isolate Python from the user's environment (implies -E and -s)
-m mod : run library module as a script (terminates option list)
-O     : remove assert and __debug__-dependent statements; add .opt-1 before
         .pyc extension; also PYTHONOPTIMIZE=x
-OO    : do -O changes and also discard docstrings; add .opt-2 before
         .pyc extension
-q     : don't print version and copyright messages on interactive startup
-s     : don't add user site directory to sys.path; also PYTHONNOUSERSITE
-S     : don't imply 'import site' on initialization
-u     : force the binary I/O layers of stdout and stderr to be unbuffered;
         stdin is always buffered; text I/O layer will be line-buffered;
         also PYTHONUNBUFFERED=x
-v     : verbose (trace import statements); also PYTHONVERBOSE=x
         can be supplied multiple times to increase verbosity
-V     : print the Python version number and exit (also --version)
         when given twice, print more information about the build
-W arg : warning control; arg is action:message:category:module:lineno
         also PYTHONWARNINGS=arg
-x     : skip first line of source, allowing use of non-Unix forms of #!cmd
-X opt : set implementation-specific option
file   : program read from script file
-      : program read from stdin (default; interactive mode if a tty)
arg ...: arguments passed to program in sys.argv[1:]

Other environment variables:
PYTHONSTARTUP: file executed on interactive startup (no default)
PYTHONPATH   : ':'-separated list of directories prefixed to the
               default module search path.  The result is sys.path.
PYTHONHOME   : alternate <prefix> directory (or <prefix>:<exec_prefix>).
               The default module search path uses <prefix>/lib/pythonX.X.
PYTHONCASEOK : ignore case in 'import' statements (Windows).
PYTHONIOENCODING: Encoding[:errors] used for stdin/stdout/stderr.
PYTHONFAULTHANDLER: dump the Python traceback on fatal errors.
PYTHONHASHSEED: if this variable is set to 'random', a random value is used
   to seed the hashes of str, bytes and datetime objects.  It can also be
   set to an integer in the range [0,4294967295] to get hash values with a
   predictable seed.
PYTHONMALLOC: set the Python memory allocators and/or install debug hooks
   on Python memory allocators. Use PYTHONMALLOC=debug to install debug
   hooks.
+ conda install -y nodejs
+ '[' 3 -lt 1 ']'
+ local cmd=install
+ shift
+ case "$cmd" in
+ CONDA_INTERNAL_OLDPATH=/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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:/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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: /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7

  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=/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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=/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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:/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '
++ /opt/conda/bin/conda shell.posix reactivate
+ ask_conda='PS1='\''(mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '\''
export PATH='\''/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '\'''
+ PATH=/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '\''
export PATH='\''/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '\'''
PS1='(mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '
++ PS1='(mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '
export PATH='/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/bin:/opt/conda/condabin:/docker-java-home/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ PATH=/opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '
++ export 'CONDA_PROMPT_MODIFIER=(mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '
++ CONDA_PROMPT_MODIFIER='(mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7) '
+ __conda_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ pushd mango-python
/tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestWC0pww5/deleteMePleaseThisIsNoLongerNeeded /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu /home
+ make prepare
pip install pytest==3.9.1
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 more-itertools>=4.0.0
  Downloading https://files.pythonhosted.org/packages/ef/9b/6c35ec5483710492e21252465160ee508170159f7e0e2d6cd769022f52f6/more_itertools-8.4.0-py3-none-any.whl (43kB)
Requirement already satisfied: attrs>=17.4.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from pytest==3.9.1) (19.3.0)
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: six>=1.10.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from pytest==3.9.1) (1.15.0)
Collecting atomicwrites>=1.0
  Downloading https://files.pythonhosted.org/packages/2c/a0/da5f49008ec6e9a658dbf5d7310a4debd397bce0b4db03cf8a410066bb87/atomicwrites-1.4.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from pytest==3.9.1) (49.6.0.post20200814)
Collecting pluggy>=0.7
  Downloading https://files.pythonhosted.org/packages/a0/28/85c7aa31b80d150b772fbe4a229487bc6644da9ccb7e427dd8cc60cb8a62/pluggy-0.13.1-py2.py3-none-any.whl
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from pluggy>=0.7->pytest==3.9.1) (1.7.0)
Requirement already satisfied: zipp>=0.5 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pluggy>=0.7->pytest==3.9.1) (3.1.0)
Installing collected packages: more-itertools, py, atomicwrites, pluggy, pytest
Successfully installed atomicwrites-1.4.0 more-itertools-8.4.0 pluggy-0.13.1 py-1.9.0 pytest-3.9.1
# ipython version required for python 2.7
pip install jupyter_contrib_nbextensions
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)
Requirement already satisfied: jupyter-core in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (4.6.3)
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-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: notebook>=4.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (6.1.3)
Collecting lxml
  Downloading https://files.pythonhosted.org/packages/79/37/d420b7fdc9a550bd29b8cfeacff3b38502d9600b09d7dfae9a69e623b891/lxml-4.5.2-cp36-cp36m-manylinux1_x86_64.whl (5.5MB)
Requirement already satisfied: ipython-genutils in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (0.2.0)
Requirement already satisfied: traitlets>=4.1 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (4.3.3)
Collecting pyyaml
  Downloading https://files.pythonhosted.org/packages/64/c2/b80047c7ac2478f9501676c988a5411ed5572f35d1beff9cae07d321512c/PyYAML-5.3.1.tar.gz (269kB)
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)
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
Requirement already satisfied: tornado in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (6.0.4)
Requirement already satisfied: nbconvert>=4.2 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter_contrib_nbextensions) (5.6.1)
Requirement already satisfied: ipython in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (7.16.1)
Requirement already satisfied: terminado>=0.8.3 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (0.8.3)
Requirement already satisfied: prometheus-client in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (0.8.0)
Requirement already satisfied: ipykernel in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (5.3.4)
Requirement already satisfied: jinja2 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (2.11.2)
Requirement already satisfied: Send2Trash in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (1.5.0)
Requirement already satisfied: nbformat in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (5.0.7)
Requirement already satisfied: pyzmq>=17 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (19.0.2)
Requirement already satisfied: argon2-cffi in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (20.1.0)
Requirement already satisfied: jupyter-client>=5.3.4 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook>=4.0->jupyter_contrib_nbextensions) (6.1.6)
Requirement already satisfied: six in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from traitlets>=4.1->jupyter_contrib_nbextensions) (1.15.0)
Requirement already satisfied: decorator in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from traitlets>=4.1->jupyter_contrib_nbextensions) (4.4.2)
Requirement already satisfied: setuptools in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter-contrib-core>=0.3.3->jupyter_contrib_nbextensions) (49.6.0.post20200814)
Requirement already satisfied: pandocfilters>=1.4.1 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (1.4.2)
Requirement already satisfied: bleach in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (3.1.5)
Requirement already satisfied: defusedxml in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (0.6.0)
Requirement already satisfied: testpath in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (0.4.4)
Requirement already satisfied: entrypoints>=0.2.2 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (0.3)
Requirement already satisfied: pygments in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (2.6.1)
Requirement already satisfied: mistune<2,>=0.8.1 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert>=4.2->jupyter_contrib_nbextensions) (0.8.4)
Requirement already satisfied: backcall in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (0.2.0)
Requirement already satisfied: pickleshare in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (0.7.5)
Requirement already satisfied: pexpect; sys_platform != "win32" in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (4.8.0)
Requirement already satisfied: jedi>=0.10 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (0.17.2)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (3.0.6)
Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jinja2->notebook>=4.0->jupyter_contrib_nbextensions) (1.1.1)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbformat->notebook>=4.0->jupyter_contrib_nbextensions) (3.2.0)
Requirement already satisfied: cffi>=1.0.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from argon2-cffi->notebook>=4.0->jupyter_contrib_nbextensions) (1.14.1)
Requirement already satisfied: python-dateutil>=2.1 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter-client>=5.3.4->notebook>=4.0->jupyter_contrib_nbextensions) (2.8.1)
Requirement already satisfied: webencodings in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from bleach->nbconvert>=4.2->jupyter_contrib_nbextensions) (0.5.1)
Requirement already satisfied: packaging in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from bleach->nbconvert>=4.2->jupyter_contrib_nbextensions) (20.4)
Requirement already satisfied: ptyprocess>=0.5 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (0.6.0)
Requirement already satisfied: parso<0.8.0,>=0.7.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jedi>=0.10->ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (0.7.1)
Requirement already satisfied: wcwidth in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (0.2.5)
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Requirement already satisfied: importlib-metadata; python_version < "3.8" in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions) (1.7.0)
Requirement already satisfied: attrs>=17.4.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions) (19.3.0)
Requirement already satisfied: pycparser in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook>=4.0->jupyter_contrib_nbextensions) (2.20)
Requirement already satisfied: pyparsing>=2.0.2 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from packaging->bleach->nbconvert>=4.2->jupyter_contrib_nbextensions) (2.4.7)
Requirement already satisfied: zipp>=0.5 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions) (3.1.0)
Building wheels for collected packages: jupyter-latex-envs, pyyaml, jupyter-nbextensions-configurator
  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=2b0bbd0def5bdc532f70bdf672bcbb705412ac6b41560c2c86191b67f7ba4075
  Stored in directory: /root/.cache/pip/wheels/0d/71/2a/164491997299b9f2479a251e254323fe35d946779e18f27956
  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=c5c36542345d18d6991c2823e6e97fdaeccfc2744711ad9e81bf2cb7c23a6102
  Stored in directory: /root/.cache/pip/wheels/a7/c1/ea/cf5bd31012e735dc1dfea3131a2d5eae7978b251083d6247bd
  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=dc5167f3a61f5dd30142788a8b070df012e16cb9c108063ebcfba1d0efd0e3ae
  Stored in directory: /root/.cache/pip/wheels/15/df/fe/2a74fe34709e7fdc5ae153a768675d9fda93cc7d5133ed1fb0
Successfully built jupyter-latex-envs pyyaml jupyter-nbextensions-configurator
Installing collected packages: jupyter-latex-envs, jupyter-highlight-selected-word, lxml, pyyaml, jupyter-contrib-core, jupyter-nbextensions-configurator, jupyter-contrib-nbextensions
Successfully installed 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 pyyaml-5.3.1
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)
Requirement already satisfied: python-dateutil in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.4.7)
Collecting cycler>=0.10
  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Collecting pytz
  Downloading https://files.pythonhosted.org/packages/4f/a4/879454d49688e2fad93e59d7d4efda580b783c745fd2ec2a3adf87b0808d/pytz-2020.1-py2.py3-none-any.whl (510kB)
Requirement already satisfied: six>=1.10 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.15.0)
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: traitlets>=4.2 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (4.3.3)
Requirement already satisfied: pygments in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (2.6.1)
Requirement already satisfied: pexpect; sys_platform != "win32" in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (4.8.0)
Requirement already satisfied: setuptools>=18.5 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (49.6.0.post20200814)
Requirement already satisfied: decorator in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (4.4.2)
Requirement already satisfied: backcall in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.2.0)
Requirement already satisfied: jedi>=0.10 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.17.2)
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: pickleshare in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipython==7.8.0->-r requirements.txt (line 3)) (0.7.5)
Collecting qtconsole
  Downloading https://files.pythonhosted.org/packages/41/27/82ed9d2c2e9a30c885f6782d674c8bfe3e3f903d06d837c2978f8b55be56/qtconsole-4.7.6-py2.py3-none-any.whl (118kB)
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: ipykernel in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.3.4)
Requirement already satisfied: nbconvert in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.6.1)
Requirement already satisfied: notebook in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (6.1.3)
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 pytest==2.8.3
  Downloading https://files.pythonhosted.org/packages/b0/7b/7aa01fa919ca0d038cdf8744ba9fd0416b04ec1878a68bfd77f39534e408/pytest-2.8.3-py2.py3-none-any.whl (149kB)
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)
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Requirement already satisfied: ipython-genutils in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from traitlets>=4.2->ipython==7.8.0->-r requirements.txt (line 3)) (0.2.0)
Requirement already satisfied: ptyprocess>=0.5 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from pexpect; sys_platform != "win32"->ipython==7.8.0->-r requirements.txt (line 3)) (0.6.0)
Requirement already satisfied: parso<0.8.0,>=0.7.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jedi>=0.10->ipython==7.8.0->-r requirements.txt (line 3)) (0.7.1)
Requirement already satisfied: wcwidth in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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>=4.1 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (6.1.6)
Collecting qtpy
  Downloading https://files.pythonhosted.org/packages/cd/fd/9972948f02e967b691cc0ca1f26124826a3b88cb38f412a8b7935b8c3c72/QtPy-1.9.0-py2.py3-none-any.whl (54kB)
Requirement already satisfied: jupyter-core in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (4.6.3)
Requirement already satisfied: pyzmq>=17.1 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (19.0.2)
Requirement already satisfied: tornado>=4.2 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ipykernel->jupyter==1.0.0->-r requirements.txt (line 4)) (6.0.4)
Requirement already satisfied: jinja2>=2.4 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (2.11.2)
Requirement already satisfied: mistune<2,>=0.8.1 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.4)
Requirement already satisfied: testpath in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.4.4)
Requirement already satisfied: entrypoints>=0.2.2 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.3)
Requirement already satisfied: defusedxml in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.6.0)
Requirement already satisfied: bleach in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.1.5)
Requirement already satisfied: pandocfilters>=1.4.1 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.4.2)
Requirement already satisfied: argon2-cffi in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (20.1.0)
Requirement already satisfied: terminado>=0.8.3 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.3)
Requirement already satisfied: prometheus-client in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.0)
Requirement already satisfied: Send2Trash in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.5.0)
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: py>=1.4.29 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from pytest==2.8.3->bdgenomics.mango.pileup==0.0.6a0->-r requirements.txt (line 6)) (1.9.0)
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Requirement already satisfied: MarkupSafe>=0.23 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from jinja2>=2.4->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.1.1)
Requirement already satisfied: packaging in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (20.4)
Requirement already satisfied: webencodings in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5.1)
Requirement already satisfied: cffi>=1.0.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from argon2-cffi->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.14.1)
Collecting filelock
  Downloading https://files.pythonhosted.org/packages/93/83/71a2ee6158bb9f39a90c0dea1637f81d5eef866e188e1971a1b1ab01a35a/filelock-3.0.12-py3-none-any.whl
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)
Collecting click
  Downloading https://files.pythonhosted.org/packages/d2/3d/fa76db83bf75c4f8d338c2fd15c8d33fdd7ad23a9b5e57eb6c5de26b430e/click-7.1.2-py2.py3-none-any.whl (82kB)
Collecting funcsigs
  Downloading https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Requirement already satisfied: pyyaml in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from ray==0.7.3; extra == "ray"->modin[ray]==0.6.1->bdgenomics.mango.pileup==0.0.6a0->-r requirements.txt (line 6)) (5.3.1)
Collecting redis
  Downloading https://files.pythonhosted.org/packages/a7/7c/24fb0511df653cf1a5d938d8f5d19802a88cef255706fdda242ff97e91b7/redis-3.5.3-py2.py3-none-any.whl (72kB)
Collecting colorama
  Downloading https://files.pythonhosted.org/packages/c9/dc/45cdef1b4d119eb96316b3117e6d5708a08029992b2fee2c143c7a0a5cc5/colorama-0.4.3-py2.py3-none-any.whl
Requirement already satisfied: importlib-metadata; python_version < "3.8" in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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)) (1.7.0)
Requirement already satisfied: pyrsistent>=0.14.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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: attrs>=17.4.0 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/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)) (19.3.0)
Requirement already satisfied: pycparser in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from cffi>=1.0.0->argon2-cffi->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (2.20)
Requirement already satisfied: zipp>=0.5 in /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/lib/python3.6/site-packages (from importlib-metadata; python_version < "3.8"->jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (3.1.0)
Building wheels for collected packages: cigar, bdgenomics.adam, bdgenomics.mango.pileup, psutil, pyspark
  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=550ed68a42ad824a8119bd3043b588bf5b61eb31a584be1677d1191649e5d914
  Stored in directory: /root/.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=af6e657095259686ded3bcdac5603b7a81a5fbbd3f9e291d9ec4b0719bca5d21
  Stored in directory: /root/.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=698a5c188d05d0b19745fa1b25b4ee0018a52af57d12afea2b1de5b5b72a8d27
  Stored in directory: /root/.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=279849 sha256=e5afb159a048183a2d39885e7bfaa7b8fc0d05b909b063bc02f0d7ae6ae7b881
  Stored in directory: /root/.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=f2d4fa3f41e15892a28163fd5dfbb620e5dff91d611df47b70bfddc55d6f4751
  Stored in directory: /root/.cache/pip/wheels/57/27/4d/ddacf7143f8d5b76c45c61ee2e43d9f8492fc5a8e78ebd7d37
Successfully built cigar bdgenomics.adam bdgenomics.mango.pileup psutil pyspark
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, cycler, pytz, numpy, matplotlib, prompt-toolkit, ipython, widgetsnbextension, ipywidgets, qtpy, qtconsole, jupyter-console, jupyter, py4j, pyspark, bdgenomics.adam, pandas, filelock, protobuf, click, pytest, funcsigs, redis, colorama, ray, modin, bdgenomics.mango.pileup, psutil
  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
  Found existing installation: pytest 3.9.1
    Uninstalling pytest-3.9.1:
      Successfully uninstalled pytest-3.9.1
Successfully installed 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 matplotlib-2.0.2 modin-0.6.1 numpy-1.19.1 pandas-0.25.1 prompt-toolkit-2.0.10 protobuf-3.13.0 psutil-5.7.2 py4j-0.10.9 pyspark-3.0.0 pytest-2.8.3 pytz-2020.1 qtconsole-4.7.6 qtpy-1.9.0 ray-0.7.3 redis-3.5.3 widgetsnbextension-3.0.8
+ python -h
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.12/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test: line 233: /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7/bin/python: Invalid argument
clean_up
+ clean_up
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.

## Package Plan ##

  environment location: /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7


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-3.32.3-h4cf870e_1
  terminado-0.8.3-py36h9f0ad1d_1
  testpath-0.4.4-py_0
  tk-8.6.10-hed695b0_0
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  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 /opt/conda/envs/mango-build-d42b78e3-1921-4fb4-b34d-680ff9cc3db7:

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