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Full Log12/0.32.0/adam-shade-spark2_2.12-0.32.0.jar (13 kB at 893 kB/s)
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[INFO] Including org.bdgenomics.mango:mango-cli-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.12:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.6 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.12.6 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar.
[INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.12:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.12:jar:1.0.6 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.12.8 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.9.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.9.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-assistedinject:jar:4.2.2 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.9.0 in the shaded jar.
[WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes:
[WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING] - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar, adam-cli-spark2_2.12-0.32.0.jar define 3 overlapping classes:
[WARNING] - org.bdgenomics.adam.cli.CommandGroup
[WARNING] - org.bdgenomics.adam.cli.InitArgs
[WARNING] - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar with /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-shaded.jar
[INFO]
[INFO] --------< org.bdgenomics.mango:mango-distribution-spark3_2.12 >---------
[INFO] Building mango_2.12: Distribution 0.0.6-SNAPSHOT [4/5]
[INFO] --------------------------------[ pom ]---------------------------------
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[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution-spark3_2.12 >>>
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO]
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution-spark3_2.12 <<<
[INFO]
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution-spark3_2.12 ---
[INFO] No source files found
[INFO]
[INFO] --- maven-assembly-plugin:2.2-beta-5:single (default) @ mango-distribution-spark3_2.12 ---
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Progress (3): 109 kB | 53/80 kB | 41/222 kB
Progress (3): 109 kB | 53/80 kB | 45/222 kB
Progress (3): 109 kB | 57/80 kB | 45/222 kB
Progress (3): 109 kB | 57/80 kB | 49/222 kB
Progress (3): 109 kB | 61/80 kB | 49/222 kB
Progress (3): 109 kB | 66/80 kB | 49/222 kB
Progress (3): 109 kB | 70/80 kB | 49/222 kB
Progress (3): 109 kB | 70/80 kB | 53/222 kB
Progress (3): 109 kB | 74/80 kB | 53/222 kB
Progress (3): 109 kB | 74/80 kB | 57/222 kB
Progress (3): 109 kB | 78/80 kB | 57/222 kB
Progress (3): 109 kB | 78/80 kB | 61/222 kB
Progress (3): 109 kB | 80 kB | 61/222 kB
Progress (3): 109 kB | 80 kB | 66/222 kB
Progress (4): 109 kB | 80 kB | 66/222 kB | 4.1/23 kB
Progress (5): 109 kB | 80 kB | 66/222 kB | 4.1/23 kB | 4.1/80 kB
Progress (5): 109 kB | 80 kB | 66/222 kB | 8.2/23 kB | 4.1/80 kB
Progress (5): 109 kB | 80 kB | 66/222 kB | 8.2/23 kB | 8.2/80 kB
Progress (5): 109 kB | 80 kB | 66/222 kB | 12/23 kB | 8.2/80 kB
Progress (5): 109 kB | 80 kB | 66/222 kB | 12/23 kB | 12/80 kB
Progress (5): 109 kB | 80 kB | 66/222 kB | 16/23 kB | 12/80 kB
Progress (5): 109 kB | 80 kB | 66/222 kB | 16/23 kB | 16/80 kB
Progress (5): 109 kB | 80 kB | 70/222 kB | 16/23 kB | 16/80 kB
Progress (5): 109 kB | 80 kB | 70/222 kB | 20/23 kB | 16/80 kB
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project/2.0.4/maven-project-2.0.4.jar (109 kB at 1.4 MB/s)
Progress (4): 80 kB | 70/222 kB | 20/23 kB | 20/80 kB
Progress (4): 80 kB | 70/222 kB | 23 kB | 20/80 kB
Progress (4): 80 kB | 74/222 kB | 23 kB | 20/80 kB
Progress (4): 80 kB | 74/222 kB | 23 kB | 25/80 kB
Progress (4): 80 kB | 78/222 kB | 23 kB | 25/80 kB
Progress (4): 80 kB | 78/222 kB | 23 kB | 29/80 kB
Progress (4): 80 kB | 82/222 kB | 23 kB | 29/80 kB
Progress (4): 80 kB | 82/222 kB | 23 kB | 33/80 kB
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0.4/maven-artifact-2.0.4.jar (80 kB at 1.0 MB/s)
Progress (3): 86/222 kB | 23 kB | 33/80 kB
Progress (3): 86/222 kB | 23 kB | 37/80 kB
Progress (3): 90/222 kB | 23 kB | 37/80 kB
Progress (3): 90/222 kB | 23 kB | 41/80 kB
Progress (3): 94/222 kB | 23 kB | 41/80 kB
Progress (3): 94/222 kB | 23 kB | 45/80 kB
Progress (3): 98/222 kB | 23 kB | 45/80 kB
Progress (3): 98/222 kB | 23 kB | 49/80 kB
Progress (3): 98/222 kB | 23 kB | 53/80 kB
Progress (3): 98/222 kB | 23 kB | 57/80 kB
Progress (3): 102/222 kB | 23 kB | 57/80 kB
Progress (3): 102/222 kB | 23 kB | 61/80 kB
Progress (3): 106/222 kB | 23 kB | 61/80 kB
Progress (3): 106/222 kB | 23 kB | 66/80 kB
Progress (3): 111/222 kB | 23 kB | 66/80 kB
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-repository-builder/1.0-alpha-2/maven-repository-builder-1.0-alpha-2.jar (23 kB at 279 kB/s)
Progress (2): 111/222 kB | 70/80 kB
Progress (2): 115/222 kB | 70/80 kB
Progress (2): 115/222 kB | 74/80 kB
Progress (2): 115/222 kB | 78/80 kB
Progress (2): 115/222 kB | 80 kB
Progress (2): 119/222 kB | 80 kB
Progress (2): 123/222 kB | 80 kB
Progress (2): 127/222 kB | 80 kB
Progress (2): 131/222 kB | 80 kB
Progress (2): 135/222 kB | 80 kB
Progress (2): 139/222 kB | 80 kB
Progress (2): 143/222 kB | 80 kB
Progress (2): 147/222 kB | 80 kB
Progress (2): 152/222 kB | 80 kB
Progress (2): 156/222 kB | 80 kB
Progress (2): 160/222 kB | 80 kB
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model/2.0.4/maven-model-2.0.4.jar (80 kB at 922 kB/s)
Progress (1): 164/222 kB
Progress (1): 168/222 kB
Progress (1): 172/222 kB
Progress (1): 176/222 kB
Progress (1): 180/222 kB
Progress (1): 184/222 kB
Progress (1): 188/222 kB
Progress (1): 193/222 kB
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Progress (1): 201/222 kB
Progress (1): 205/222 kB
Progress (1): 209/222 kB
Progress (1): 213/222 kB
Progress (1): 217/222 kB
Progress (1): 221/222 kB
Progress (1): 222 kB
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/2.0.1/plexus-utils-2.0.1.jar (222 kB at 2.3 MB/s)
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building tar : /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.bz2
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: mango-distribution-spark3_2.12-0.0.6-SNAPSHOT/repo/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar longer than 100 characters.
[INFO] Building zip: /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.zip
[INFO]
[INFO] -----------< org.bdgenomics.mango:mango-parent-spark3_2.12 >------------
[INFO] Building mango_2.12 0.0.6-SNAPSHOT [5/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent-spark3_2.12 ---
[INFO] Modified 0 of 41 .scala files
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent-spark3_2.12 >>>
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO]
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent-spark3_2.12 <<<
[INFO]
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent-spark3_2.12 ---
[INFO] No source files found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango_2.12 0.0.6-SNAPSHOT:
[INFO]
[INFO] mango_2.12: CORE ................................... SUCCESS [ 30.624 s]
[INFO] mango_2.12: CLI .................................... SUCCESS [ 49.839 s]
[INFO] Mango_2.12: Assembly ............................... SUCCESS [ 30.437 s]
[INFO] mango_2.12: Distribution ........................... SUCCESS [01:41 min]
[INFO] mango_2.12 ......................................... SUCCESS [ 1.725 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:33 min
[INFO] Finished at: 2020-08-19T12:52:39Z
[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
+ tar tzf mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
+ grep mango-assembly
+ 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/mangoTestMvnwpco1T3
/tmp/mangoTestMvnwpco1T3
/tmp/mangoTestMvnwpco1T3/mmbroken214917521318082643.genome
/tmp/mangoTestMvnwpco1T3/fake-98997763702733220.sh
/tmp/mangoTestMvnwpco1T3/fake-4260642322305958798.txt
/tmp/mangoTestMvnwpco1T3/5935850737273087280
/tmp/mangoTestMvnwpco1T3/297315911163882494
/tmp/mangoTestMvnwpco1T3/297315911163882494/anoGam1.genome
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692
/tmp/mangoTestMvnwpco1T3/2125215195123885896
/tmp/mangoTestMvnwpco1T3/fake-1961649410847967809.sh
/tmp/mangoTestMvnwpco1T3/genomes3126182681163901858
/tmp/mangoTestMvnwpco1T3/genomes3126182681163901858/hg19.genome
/tmp/mangoTestMvnwpco1T3/genomes7671698873329890333
/tmp/mangoTestMvnwpco1T3/genomes7671698873329890333/hg19.genome
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/._references.avro.crc
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/_SUCCESS
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/_partitionedByStartPos
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/referenceName=1
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/referenceName=1/positionBin=0/.part-00000-d8c796fe-d9e3-460b-bd5f-64d71f68fd57.c000.snappy.parquet.crc
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/referenceName=1/positionBin=0/part-00000-d8c796fe-d9e3-460b-bd5f-64d71f68fd57.c000.snappy.parquet
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/_references.avro
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/_samples.avro
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/._SUCCESS.crc
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/._samples.avro.crc
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/._header.crc
/tmp/mangoTestMvnwpco1T3/TempSuite6914624683452109692.adam/_header
/tmp/mangoTestMvnwpco1T3/invalidBuild.genome4400350117468351241
/tmp/mangoTestMvnwpco1T3/invalidBuild.genome4400350117468351241/properties.txt
/tmp/mangoTestMvnwpco1T3/invalidBuild.genome1517392712111235856
/tmp/mangoTestMvnwpco1T3/invalidBuild.genome1517392712111235856/properties.txt
/tmp/mangoTestMvnwpco1T3/mmbroken2405128817230789653.genome
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488
/tmp/mangoTestMvnwpco1T3/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/._references.avro.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/_SUCCESS
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/_partitionedByStartPos
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/referenceName=1
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/referenceName=1/positionBin=0/part-00000-124f6955-d8e0-4659-8026-db10ab926373.c000.snappy.parquet
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/referenceName=1/positionBin=0/.part-00000-124f6955-d8e0-4659-8026-db10ab926373.c000.snappy.parquet.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/_references.avro
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/_samples.avro
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/._SUCCESS.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/._samples.avro.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/._header.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7750649200178188310.adam/_header
/tmp/mangoTestMvnwpco1T3/1549232700856071859
/tmp/mangoTestMvnwpco1T3/1549232700856071859/anoGam1.genome
/tmp/mangoTestMvnwpco1T3/fake-8445889066738133911.txt
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/._references.avro.crc
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/_readGroups.avro
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/_processingSteps.avro
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/_SUCCESS
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/_partitionedByStartPos
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=1
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=1/positionBin=26/.part-00000-c02daa99-d3e0-41aa-bb74-504399c9f4e6.c000.snappy.parquet.crc
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=1/positionBin=26/part-00000-c02daa99-d3e0-41aa-bb74-504399c9f4e6.c000.snappy.parquet
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=1/positionBin=240/.part-00000-c02daa99-d3e0-41aa-bb74-504399c9f4e6.c000.snappy.parquet.crc
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=1/positionBin=240/part-00000-c02daa99-d3e0-41aa-bb74-504399c9f4e6.c000.snappy.parquet
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/_references.avro
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=2
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=2/positionBin=189/.part-00000-c02daa99-d3e0-41aa-bb74-504399c9f4e6.c000.snappy.parquet.crc
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/referenceName=2/positionBin=189/part-00000-c02daa99-d3e0-41aa-bb74-504399c9f4e6.c000.snappy.parquet
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/._SUCCESS.crc
/tmp/mangoTestMvnwpco1T3/TempSuite853820302818547091.adam/._readGroups.avro.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/._references.avro.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/_readGroups.avro
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/_processingSteps.avro
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/_SUCCESS
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/_partitionedByStartPos
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=1
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=1/positionBin=26/.part-00000-0f29aa7a-8c45-4b10-9245-ae1a8fefdba4.c000.snappy.parquet.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=1/positionBin=26/part-00000-0f29aa7a-8c45-4b10-9245-ae1a8fefdba4.c000.snappy.parquet
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=1/positionBin=240/.part-00000-0f29aa7a-8c45-4b10-9245-ae1a8fefdba4.c000.snappy.parquet.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=1/positionBin=240/part-00000-0f29aa7a-8c45-4b10-9245-ae1a8fefdba4.c000.snappy.parquet
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/_references.avro
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=2
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=2/positionBin=189/.part-00000-0f29aa7a-8c45-4b10-9245-ae1a8fefdba4.c000.snappy.parquet.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/referenceName=2/positionBin=189/part-00000-0f29aa7a-8c45-4b10-9245-ae1a8fefdba4.c000.snappy.parquet
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/._SUCCESS.crc
/tmp/mangoTestMvnwpco1T3/TempSuite7754278434092167488.adam/._readGroups.avro.crc
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvnwpco1T3
find . -name pom.xml \
-exec sed -i.bak \
-e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/mangoTestMvnwpco1T3: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/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12.tgz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 139M 0 416k 0 0 454k 0 0:05:15 --:--:-- 0:05:15 454k
24 139M 24 33.7M 0 0 17.8M 0 0:00:07 0:00:01 0:00:06 34.3M
52 139M 52 73.0M 0 0 25.3M 0 0:00:05 0:00:02 0:00:03 36.8M
81 139M 81 113M 0 0 29.2M 0 0:00:04 0:00:03 0:00:01 38.1M
100 139M 100 139M 0 0 30.7M 0 0:00:04 0:00:04 --:--:-- 38.4M
+ tar xzf /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12.tgz --directory /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded
+ export SPARK_HOME=/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12
+ SPARK_HOME=/tmp/mangoTestNXTtGjI/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/mangoTestNXTtGjI/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 208M 0 8437 0 0 17794 0 3:24:51 --:--:-- 3:24:51 17794
0 208M 0 455k 0 0 293k 0 0:12:08 0:00:01 0:12:07 414k
0 208M 0 877k 0 0 353k 0 0:10:03 0:00:02 0:10:01 433k
0 208M 0 1343k 0 0 384k 0 0:09:14 0:00:03 0:09:11 442k
0 208M 0 1853k 0 0 413k 0 0:08:36 0:00:04 0:08:32 460k
1 208M 1 2396k 0 0 439k 0 0:08:06 0:00:05 0:08:01 479k
1 208M 1 2969k 0 0 462k 0 0:07:42 0:00:06 0:07:36 515k
1 208M 1 3679k 0 0 497k 0 0:07:09 0:00:07 0:07:02 569k
2 208M 2 4598k 0 0 541k 0 0:06:34 0:00:08 0:06:26 651k
2 208M 2 5713k 0 0 607k 0 0:05:51 0:00:09 0:05:42 784k
2 208M 2 6347k 0 0 610k 0 0:05:50 0:00:10 0:05:40 797k
2 208M 2 6398k 0 0 560k 0 0:06:21 0:00:11 0:06:10 685k
3 208M 3 6531k 0 0 526k 0 0:06:45 0:00:12 0:06:33 570k
3 208M 3 7434k 0 0 553k 0 0:06:25 0:00:13 0:06:12 574k
4 208M 4 8816k 0 0 599k 0 0:05:56 0:00:14 0:05:42 585k
4 208M 4 8932k 0 0 577k 0 0:06:09 0:00:15 0:05:54 510k
4 208M 4 9090k 0 0 553k 0 0:06:25 0:00:16 0:06:09 539k
4 208M 4 9878k 0 0 564k 0 0:06:18 0:00:17 0:06:01 658k
5 208M 5 10.4M 0 0 580k 0 0:06:08 0:00:18 0:05:50 650k
5 208M 5 11.2M 0 0 594k 0 0:05:59 0:00:19 0:05:40 577k
5 208M 5 12.1M 0 0 607k 0 0:05:51 0:00:20 0:05:31 703k
6 208M 6 12.9M 0 0 620k 0 0:05:44 0:00:21 0:05:23 839k
6 208M 6 13.8M 0 0 632k 0 0:05:37 0:00:22 0:05:15 871k
7 208M 7 14.8M 0 0 646k 0 0:05:30 0:00:23 0:05:07 894k
7 208M 7 15.8M 0 0 665k 0 0:05:20 0:00:24 0:04:56 945k
8 208M 8 16.8M 0 0 677k 0 0:05:15 0:00:25 0:04:50 963k
8 208M 8 17.8M 0 0 692k 0 0:05:08 0:00:26 0:04:42 1001k
9 208M 9 18.9M 0 0 708k 0 0:05:01 0:00:27 0:04:34 1049k
9 208M 9 20.1M 0 0 724k 0 0:04:54 0:00:28 0:04:26 1090k
10 208M 10 21.0M 0 0 727k 0 0:04:53 0:00:29 0:04:24 1018k
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10 208M 10 22.0M 0 0 696k 0 0:05:06 0:00:32 0:04:34 632k
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+ tar xzf /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7.tar.gz --directory /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded
+ find /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7 -name '*.jar'
+ grep avro
+ xargs rm
++ /tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/bin/hadoop classpath
+ export 'SPARK_DIST_CLASSPATH=/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/etc/hadoop:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/lib/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/lib/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/lib/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/lib/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/*:/contrib/capacity-scheduler/*.jar'
+ SPARK_DIST_CLASSPATH='/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/etc/hadoop:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/lib/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/lib/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/lib/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/lib/*:/tmp/mangoTestNXTtGjI/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/*:/contrib/capacity-scheduler/*.jar'
# create a conda environment for python build, if necessary
pythons=( 3.6 )
+ pythons=(3.6)
for python in ${pythons[*]}
do
conda create -y -q -c conda-forge -n mango-build-${PYTHON_UUID} python=${python} pip=19.3.1 jupyterlab=2.0.1
conda activate mango-build-${PYTHON_UUID}
# install npm and node in the venv for mango-pileup
conda install -y nodejs
# prepare mango python
pushd mango-python
make prepare
popd
# we can run the python build, now that we have a spark executable
# requires SPARK_HOME to be set
mvn -U \
-P python,distribution \
package \
-DskipTests \
-Dhadoop.version=${HADOOP_VERSION} \
-Dspark.version=${SPARK_VERSION}
# clean mango python
pushd mango-python
make clean
popd
# prepare mango viz
pushd mango-pileup
make prepare
popd
# run the widgets tests (mango-pileup)
mvn -P widgets test
# clean mango viz
pushd mango-pileup
make clean
popd
# make sure that the distribution package contains an egg
# if no assembly jar is found, this will exit with code 1 and fail the build
tar tzf mango-distribution/target/mango-distribution*-bin.tar.gz | \
grep bdgenomics.mango | \
grep egg
# test mango notebook, output to temporary log file
MANGO_NOTEBOOK_LOGS=${MANGO_TMP_DIR}/mango-notebook.log
# notebook args --ip=0.0.0.0 --no-browser --allow-root required for docker
bash -xv ${PROJECT_ROOT}/bin/mango-notebook -- --ip=0.0.0.0 --no-browser --allow-root &> ${MANGO_NOTEBOOK_LOGS} &
# sleep for 2 seconds to let mango-notebook start up
sleep 2
# if mango-notebook fails, then trying to kill the process will fail
if kill $! ; then
echo "Mango Notebook Succeeded"
else
echo "Mango Notebook failed with logs:"
cat ${MANGO_NOTEBOOK_LOGS}
exit 1
fi
# deactivate and remove the conda env
set +e +x
source deactivate
conda remove -y --name mango-build-${PYTHON_UUID} --all
set -e -x
done
+ for python in ${pythons[*]}
+ conda create -y -q -c conda-forge -n mango-build-07c30dd7-8d52-4b82-805b-3e285cb24a57 python=3.6 pip=19.3.1 jupyterlab=2.0.1
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/jenkins/.conda/envs/mango-build-07c30dd7-8d52-4b82-805b-3e285cb24a57
added / updated specs:
- jupyterlab=2.0.1
- pip=19.3.1
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
_openmp_mutex-4.5 | 1_gnu 22 KB conda-forge
argon2-cffi-20.1.0 | py36h8c4c3a4_1 47 KB conda-forge
attrs-19.3.0 | py_0 35 KB conda-forge
backcall-0.2.0 | pyh9f0ad1d_0 13 KB conda-forge
backports-1.0 | py_2 4 KB conda-forge
backports.functools_lru_cache-1.6.1| py_0 8 KB conda-forge
bleach-3.1.5 | pyh9f0ad1d_0 112 KB conda-forge
brotlipy-0.7.0 |py36h8c4c3a4_1000 346 KB conda-forge
ca-certificates-2020.6.20 | hecda079_0 145 KB conda-forge
certifi-2020.6.20 | py36h9f0ad1d_0 151 KB conda-forge
cffi-1.14.1 | py36h0ff685e_0 223 KB conda-forge
chardet-3.0.4 |py36h9f0ad1d_1006 188 KB conda-forge
cryptography-3.0 | py36h45558ae_0 640 KB conda-forge
decorator-4.4.2 | py_0 11 KB conda-forge
defusedxml-0.6.0 | py_0 22 KB conda-forge
entrypoints-0.3 |py36h9f0ad1d_1001 12 KB conda-forge
idna-2.10 | pyh9f0ad1d_0 52 KB conda-forge
importlib-metadata-1.7.0 | py36h9f0ad1d_0 44 KB conda-forge
importlib_metadata-1.7.0 | 0 3 KB conda-forge
ipykernel-5.3.4 | py36h95af2a2_0 165 KB conda-forge
ipython-7.16.1 | py36h95af2a2_0 1.1 MB conda-forge
ipython_genutils-0.2.0 | py_1 21 KB conda-forge
jedi-0.17.2 | py36h9f0ad1d_0 950 KB conda-forge
jinja2-2.11.2 | pyh9f0ad1d_0 93 KB conda-forge
json5-0.9.4 | pyh9f0ad1d_0 20 KB conda-forge
jsonschema-3.2.0 | py36h9f0ad1d_1 89 KB conda-forge
jupyter_client-6.1.6 | py_0 75 KB conda-forge
jupyter_core-4.6.3 | py36h9f0ad1d_1 71 KB conda-forge
jupyterlab-2.0.1 | py_0 5.7 MB conda-forge
jupyterlab_server-1.2.0 | py_0 25 KB conda-forge
ld_impl_linux-64-2.34 | hc38a660_9 612 KB conda-forge
libffi-3.2.1 | he1b5a44_1007 47 KB conda-forge
libgcc-ng-9.3.0 | h24d8f2e_15 7.8 MB conda-forge
libgomp-9.3.0 | h24d8f2e_15 378 KB conda-forge
libsodium-1.0.18 | h516909a_0 339 KB conda-forge
libstdcxx-ng-9.3.0 | hdf63c60_15 4.0 MB conda-forge
markupsafe-1.1.1 | py36h8c4c3a4_1 26 KB conda-forge
mistune-0.8.4 |py36h8c4c3a4_1001 53 KB conda-forge
nbconvert-5.6.1 | py36h9f0ad1d_1 487 KB conda-forge
nbformat-5.0.7 | py_0 99 KB conda-forge
ncurses-6.2 | he1b5a44_1 993 KB conda-forge
notebook-6.1.3 | py36h9f0ad1d_0 6.2 MB conda-forge
openssl-1.1.1g | h516909a_1 2.1 MB conda-forge
packaging-20.4 | pyh9f0ad1d_0 32 KB conda-forge
pandoc-2.10.1 | h516909a_0 19.3 MB conda-forge
pandocfilters-1.4.2 | py_1 9 KB conda-forge
parso-0.7.1 | pyh9f0ad1d_0 70 KB conda-forge
pexpect-4.8.0 | py36h9f0ad1d_1 79 KB conda-forge
pickleshare-0.7.5 |py36h9f0ad1d_1001 13 KB conda-forge
pip-19.3.1 | py36_0 1.9 MB conda-forge
prometheus_client-0.8.0 | pyh9f0ad1d_0 44 KB conda-forge
prompt-toolkit-3.0.6 | py_0 235 KB conda-forge
ptyprocess-0.6.0 | py_1001 15 KB conda-forge
pycparser-2.20 | pyh9f0ad1d_2 94 KB conda-forge
pygments-2.6.1 | py_0 683 KB conda-forge
pyopenssl-19.1.0 | py_1 47 KB conda-forge
pyparsing-2.4.7 | pyh9f0ad1d_0 60 KB conda-forge
pyrsistent-0.16.0 | py36h8c4c3a4_0 89 KB conda-forge
pysocks-1.7.1 | py36h9f0ad1d_1 27 KB conda-forge
python-3.6.11 |h4d41432_2_cpython 34.2 MB conda-forge
python-dateutil-2.8.1 | py_0 220 KB conda-forge
python_abi-3.6 | 1_cp36m 4 KB conda-forge
pyzmq-19.0.2 | py36h9947dbf_0 465 KB conda-forge
readline-8.0 | he28a2e2_2 281 KB conda-forge
requests-2.24.0 | pyh9f0ad1d_0 47 KB conda-forge
send2trash-1.5.0 | py_0 12 KB conda-forge
setuptools-49.6.0 | py36h9f0ad1d_0 935 KB conda-forge
six-1.15.0 | pyh9f0ad1d_0 14 KB conda-forge
sqlite-3.33.0 | h4cf870e_0 1.4 MB conda-forge
terminado-0.8.3 | py36h9f0ad1d_1 23 KB conda-forge
testpath-0.4.4 | py_0 85 KB conda-forge
tk-8.6.10 | hed695b0_0 3.2 MB conda-forge
tornado-6.0.4 | py36h8c4c3a4_1 639 KB conda-forge
traitlets-4.3.3 | py36h9f0ad1d_1 133 KB conda-forge
urllib3-1.25.10 | py_0 92 KB conda-forge
wcwidth-0.2.5 | pyh9f0ad1d_1 33 KB conda-forge
webencodings-0.5.1 | py_1 12 KB conda-forge
wheel-0.35.1 | pyh9f0ad1d_0 29 KB conda-forge
xz-5.2.5 | h516909a_1 343 KB conda-forge
zeromq-4.3.2 | he1b5a44_3 326 KB conda-forge
zipp-3.1.0 | py_0 10 KB conda-forge
zlib-1.2.11 | h516909a_1007 106 KB conda-forge
------------------------------------------------------------
Total: 98.7 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
argon2-cffi conda-forge/linux-64::argon2-cffi-20.1.0-py36h8c4c3a4_1
attrs conda-forge/noarch::attrs-19.3.0-py_0
backcall conda-forge/noarch::backcall-0.2.0-pyh9f0ad1d_0
backports conda-forge/noarch::backports-1.0-py_2
backports.functoo~ conda-forge/noarch::backports.functools_lru_cache-1.6.1-py_0
bleach conda-forge/noarch::bleach-3.1.5-pyh9f0ad1d_0
brotlipy conda-forge/linux-64::brotlipy-0.7.0-py36h8c4c3a4_1000
ca-certificates conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
certifi conda-forge/linux-64::certifi-2020.6.20-py36h9f0ad1d_0
cffi conda-forge/linux-64::cffi-1.14.1-py36h0ff685e_0
chardet conda-forge/linux-64::chardet-3.0.4-py36h9f0ad1d_1006
cryptography conda-forge/linux-64::cryptography-3.0-py36h45558ae_0
decorator conda-forge/noarch::decorator-4.4.2-py_0
defusedxml conda-forge/noarch::defusedxml-0.6.0-py_0
entrypoints conda-forge/linux-64::entrypoints-0.3-py36h9f0ad1d_1001
idna conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
importlib-metadata conda-forge/linux-64::importlib-metadata-1.7.0-py36h9f0ad1d_0
importlib_metadata conda-forge/noarch::importlib_metadata-1.7.0-0
ipykernel conda-forge/linux-64::ipykernel-5.3.4-py36h95af2a2_0
ipython conda-forge/linux-64::ipython-7.16.1-py36h95af2a2_0
ipython_genutils conda-forge/noarch::ipython_genutils-0.2.0-py_1
jedi conda-forge/linux-64::jedi-0.17.2-py36h9f0ad1d_0
jinja2 conda-forge/noarch::jinja2-2.11.2-pyh9f0ad1d_0
json5 conda-forge/noarch::json5-0.9.4-pyh9f0ad1d_0
jsonschema conda-forge/linux-64::jsonschema-3.2.0-py36h9f0ad1d_1
jupyter_client conda-forge/noarch::jupyter_client-6.1.6-py_0
jupyter_core conda-forge/linux-64::jupyter_core-4.6.3-py36h9f0ad1d_1
jupyterlab conda-forge/noarch::jupyterlab-2.0.1-py_0
jupyterlab_server conda-forge/noarch::jupyterlab_server-1.2.0-py_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-hc38a660_9
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc-ng conda-forge/linux-64::libgcc-ng-9.3.0-h24d8f2e_15
libgomp conda-forge/linux-64::libgomp-9.3.0-h24d8f2e_15
libsodium conda-forge/linux-64::libsodium-1.0.18-h516909a_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.3.0-hdf63c60_15
markupsafe conda-forge/linux-64::markupsafe-1.1.1-py36h8c4c3a4_1
mistune conda-forge/linux-64::mistune-0.8.4-py36h8c4c3a4_1001
nbconvert conda-forge/linux-64::nbconvert-5.6.1-py36h9f0ad1d_1
nbformat conda-forge/noarch::nbformat-5.0.7-py_0
ncurses conda-forge/linux-64::ncurses-6.2-he1b5a44_1
notebook conda-forge/linux-64::notebook-6.1.3-py36h9f0ad1d_0
openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_1
packaging conda-forge/noarch::packaging-20.4-pyh9f0ad1d_0
pandoc conda-forge/linux-64::pandoc-2.10.1-h516909a_0
pandocfilters conda-forge/noarch::pandocfilters-1.4.2-py_1
parso conda-forge/noarch::parso-0.7.1-pyh9f0ad1d_0
pexpect conda-forge/linux-64::pexpect-4.8.0-py36h9f0ad1d_1
pickleshare conda-forge/linux-64::pickleshare-0.7.5-py36h9f0ad1d_1001
pip conda-forge/linux-64::pip-19.3.1-py36_0
prometheus_client conda-forge/noarch::prometheus_client-0.8.0-pyh9f0ad1d_0
prompt-toolkit conda-forge/noarch::prompt-toolkit-3.0.6-py_0
ptyprocess conda-forge/noarch::ptyprocess-0.6.0-py_1001
pycparser conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2
pygments conda-forge/noarch::pygments-2.6.1-py_0
pyopenssl conda-forge/noarch::pyopenssl-19.1.0-py_1
pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
pyrsistent conda-forge/linux-64::pyrsistent-0.16.0-py36h8c4c3a4_0
pysocks conda-forge/linux-64::pysocks-1.7.1-py36h9f0ad1d_1
python conda-forge/linux-64::python-3.6.11-h4d41432_2_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/linux-64::python_abi-3.6-1_cp36m
pyzmq conda-forge/linux-64::pyzmq-19.0.2-py36h9947dbf_0
readline conda-forge/linux-64::readline-8.0-he28a2e2_2
requests conda-forge/noarch::requests-2.24.0-pyh9f0ad1d_0
send2trash conda-forge/noarch::send2trash-1.5.0-py_0
setuptools conda-forge/linux-64::setuptools-49.6.0-py36h9f0ad1d_0
six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
sqlite conda-forge/linux-64::sqlite-3.33.0-h4cf870e_0
terminado conda-forge/linux-64::terminado-0.8.3-py36h9f0ad1d_1
testpath conda-forge/noarch::testpath-0.4.4-py_0
tk conda-forge/linux-64::tk-8.6.10-hed695b0_0
tornado conda-forge/linux-64::tornado-6.0.4-py36h8c4c3a4_1
traitlets conda-forge/linux-64::traitlets-4.3.3-py36h9f0ad1d_1
urllib3 conda-forge/noarch::urllib3-1.25.10-py_0
wcwidth conda-forge/noarch::wcwidth-0.2.5-pyh9f0ad1d_1
webencodings conda-forge/noarch::webencodings-0.5.1-py_1
wheel conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
xz conda-forge/linux-64::xz-5.2.5-h516909a_1
zeromq conda-forge/linux-64::zeromq-4.3.2-he1b5a44_3
zipp conda-forge/noarch::zipp-3.1.0-py_0
zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1007
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
+ conda activate mango-build-07c30dd7-8d52-4b82-805b-3e285cb24a57
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
clean_up
+ clean_up
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
## Package Plan ##
environment location: /home/jenkins/.conda/envs/mango-build-07c30dd7-8d52-4b82-805b-3e285cb24a57
The following packages will be REMOVED:
_libgcc_mutex-0.1-conda_forge
_openmp_mutex-4.5-1_gnu
argon2-cffi-20.1.0-py36h8c4c3a4_1
attrs-19.3.0-py_0
backcall-0.2.0-pyh9f0ad1d_0
backports-1.0-py_2
backports.functools_lru_cache-1.6.1-py_0
bleach-3.1.5-pyh9f0ad1d_0
brotlipy-0.7.0-py36h8c4c3a4_1000
ca-certificates-2020.6.20-hecda079_0
certifi-2020.6.20-py36h9f0ad1d_0
cffi-1.14.1-py36h0ff685e_0
chardet-3.0.4-py36h9f0ad1d_1006
cryptography-3.0-py36h45558ae_0
decorator-4.4.2-py_0
defusedxml-0.6.0-py_0
entrypoints-0.3-py36h9f0ad1d_1001
idna-2.10-pyh9f0ad1d_0
importlib-metadata-1.7.0-py36h9f0ad1d_0
importlib_metadata-1.7.0-0
ipykernel-5.3.4-py36h95af2a2_0
ipython-7.16.1-py36h95af2a2_0
ipython_genutils-0.2.0-py_1
jedi-0.17.2-py36h9f0ad1d_0
jinja2-2.11.2-pyh9f0ad1d_0
json5-0.9.4-pyh9f0ad1d_0
jsonschema-3.2.0-py36h9f0ad1d_1
jupyter_client-6.1.6-py_0
jupyter_core-4.6.3-py36h9f0ad1d_1
jupyterlab-2.0.1-py_0
jupyterlab_server-1.2.0-py_0
ld_impl_linux-64-2.34-hc38a660_9
libffi-3.2.1-he1b5a44_1007
libgcc-ng-9.3.0-h24d8f2e_15
libgomp-9.3.0-h24d8f2e_15
libsodium-1.0.18-h516909a_0
libstdcxx-ng-9.3.0-hdf63c60_15
markupsafe-1.1.1-py36h8c4c3a4_1
mistune-0.8.4-py36h8c4c3a4_1001
nbconvert-5.6.1-py36h9f0ad1d_1
nbformat-5.0.7-py_0
ncurses-6.2-he1b5a44_1
notebook-6.1.3-py36h9f0ad1d_0
openssl-1.1.1g-h516909a_1
packaging-20.4-pyh9f0ad1d_0
pandoc-2.10.1-h516909a_0
pandocfilters-1.4.2-py_1
parso-0.7.1-pyh9f0ad1d_0
pexpect-4.8.0-py36h9f0ad1d_1
pickleshare-0.7.5-py36h9f0ad1d_1001
pip-19.3.1-py36_0
prometheus_client-0.8.0-pyh9f0ad1d_0
prompt-toolkit-3.0.6-py_0
ptyprocess-0.6.0-py_1001
pycparser-2.20-pyh9f0ad1d_2
pygments-2.6.1-py_0
pyopenssl-19.1.0-py_1
pyparsing-2.4.7-pyh9f0ad1d_0
pyrsistent-0.16.0-py36h8c4c3a4_0
pysocks-1.7.1-py36h9f0ad1d_1
python-3.6.11-h4d41432_2_cpython
python-dateutil-2.8.1-py_0
python_abi-3.6-1_cp36m
pyzmq-19.0.2-py36h9947dbf_0
readline-8.0-he28a2e2_2
requests-2.24.0-pyh9f0ad1d_0
send2trash-1.5.0-py_0
setuptools-49.6.0-py36h9f0ad1d_0
six-1.15.0-pyh9f0ad1d_0
sqlite-3.33.0-h4cf870e_0
terminado-0.8.3-py36h9f0ad1d_1
testpath-0.4.4-py_0
tk-8.6.10-hed695b0_0
tornado-6.0.4-py36h8c4c3a4_1
traitlets-4.3.3-py36h9f0ad1d_1
urllib3-1.25.10-py_0
wcwidth-0.2.5-pyh9f0ad1d_1
webencodings-0.5.1-py_1
wheel-0.35.1-pyh9f0ad1d_0
xz-5.2.5-h516909a_1
zeromq-4.3.2-he1b5a44_3
zipp-3.1.0-py_0
zlib-1.2.11-h516909a_1007
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Remove all packages in environment /home/jenkins/.conda/envs/mango-build-07c30dd7-8d52-4b82-805b-3e285cb24a57:
Build step 'Execute shell' marked build as failure
Finished: FAILURE
![[Jenkins]](/jenkins/static/7165055c/images/jenkins-header-logo-v2.svg){kind=logo}
