Console Output
Skipping 5,772 KB..
Full Logrg/scalatra/scalatra-common_2.12/2.5.0/scalatra-common_2.12-2.5.0.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalatra-common_2.12/2.5.0/scalatra-common_2.12-2.5.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-parser-combinators_2.12/1.0.4/scala-parser-combinators_2.12-1.0.4.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-parser-combinators_2.12/1.0.4/scala-parser-combinators_2.12-1.0.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-core_2.12/1.9.1/scalate-core_2.12-1.9.1.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-core_2.12/1.9.1/scalate-core_2.12-1.9.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-compiler/2.12.8/scala-compiler-2.12.8.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scala-compiler/2.12.8/scala-compiler-2.12.8.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-util_2.12/1.9.1/scalate-util_2.12-1.9.1.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-util_2.12/1.9.1/scalate-util_2.12-1.9.1.jar
[INFO] Installing artifact /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core-spark3_2.12/0.0.6-SNAPSHOT/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark2_2.12/0.3.0/utils-io-spark2_2.12-0.3.0.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark2_2.12/0.3.0/utils-io-spark2_2.12-0.3.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-ga4gh/0.9.0/convert-ga4gh-0.9.0.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.9.0/convert-ga4gh-0.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.9.0/convert-htsjdk-0.9.0.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.9.0/convert-htsjdk-0.9.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/extensions/guice-assistedinject/4.2.2/guice-assistedinject-4.2.2.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/inject/extensions/guice-assistedinject/4.2.2/guice-assistedinject-4.2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.9.0/convert-0.9.0.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.9.0/convert-0.9.0.jar
[INFO] Installing artifact /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli-spark3_2.12/0.0.6-SNAPSHOT/mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO]
[INFO] ----------< org.bdgenomics.mango:mango-assembly-spark3_2.12 >-----------
[INFO] Building Mango_2.12: Assembly 0.0.6-SNAPSHOT [3/5]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-shade-plugin/3.2.0/maven-shade-plugin-3.2.0.pom
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[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO]
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly-spark3_2.12 ---
[INFO]
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO]
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO]
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO]
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/resources
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING] Expected all dependencies to require Scala version: 2.12.8
[WARNING] net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ mango-assembly-spark3_2.12 ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly-spark3_2.12 ---
[INFO] Test Source directory: /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/scala added.
[INFO]
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly-spark3_2.12 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/resources
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING] Expected all dependencies to require Scala version: 2.12.8
[WARNING] net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO]
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ mango-assembly-spark3_2.12 ---
[INFO] No sources to compile
[INFO]
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly-spark3_2.12 ---
[INFO] Tests are skipped.
[INFO]
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO]
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar
[INFO]
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly-spark3_2.12 ---
[INFO]
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly-spark3_2.12 >>>
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO]
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO]
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly-spark3_2.12 ---
[INFO]
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly-spark3_2.12 ---
[INFO] Request to add '/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO]
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly-spark3_2.12 ---
[INFO] Source directory: /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO]
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly-spark3_2.12 <<<
[INFO]
[INFO]
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly-spark3_2.12 ---
[WARNING] Expected all dependencies to require Scala version: 2.12.8
[WARNING] net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Expected all dependencies to require Scala version: 2.12.8
[WARNING] net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar
[INFO]
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ mango-assembly-spark3_2.12 ---
Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-shade-spark2_2.12/0.32.0/adam-shade-spark2_2.12-0.32.0.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/ow2/asm/asm-analysis/6.2.1/asm-analysis-6.2.1.jar
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[INFO] Including org.bdgenomics.mango:mango-cli-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.12:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.12.6 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.12.6 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.32.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.12:jar:2.5.0 in the shaded jar.
[INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar.
[INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.12:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.12:jar:1.0.6 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.12.8 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.12:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core-spark3_2.12:jar:0.0.6-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar.
[INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar.
[INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.9.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.9.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-assistedinject:jar:4.2.2 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.9.0 in the shaded jar.
[WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] adam-cli-spark2_2.12-0.32.0.jar, mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar define 3 overlapping classes:
[WARNING] - org.bdgenomics.adam.cli.CommandGroup
[WARNING] - org.bdgenomics.adam.cli.InitArgs
[WARNING] - org.bdgenomics.adam.cli.CommandGroup$
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes:
[WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING] - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar with /tmp/mangoTestbjdu6pk/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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[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /tmp/mangoTestbjdu6pk/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/mangoTestbjdu6pk/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/mangoTestbjdu6pk/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 [ 29.294 s]
[INFO] mango_2.12: CLI .................................... SUCCESS [ 47.656 s]
[INFO] Mango_2.12: Assembly ............................... SUCCESS [ 30.380 s]
[INFO] mango_2.12: Distribution ........................... SUCCESS [01:41 min]
[INFO] mango_2.12 ......................................... SUCCESS [ 1.919 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 03:31 min
[INFO] Finished at: 2020-08-19T12:32:05Z
[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 jar
+ grep -v -e sources -e javadoc
+ grep mango-assembly
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/mangoTestMvnIPSmVRC
/tmp/mangoTestMvnIPSmVRC
/tmp/mangoTestMvnIPSmVRC/1221805556916531119
/tmp/mangoTestMvnIPSmVRC/mmbroken3554889425551245441.genome
/tmp/mangoTestMvnIPSmVRC/1775143511026468529
/tmp/mangoTestMvnIPSmVRC/1775143511026468529/anoGam1.genome
/tmp/mangoTestMvnIPSmVRC/5339042930921767507
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/._references.avro.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/_readGroups.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/_processingSteps.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/_SUCCESS
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/_partitionedByStartPos
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=1
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=1/positionBin=26/part-00000-2f84fbdf-063d-45de-ad42-771cdc46f954.c000.snappy.parquet
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=1/positionBin=26/.part-00000-2f84fbdf-063d-45de-ad42-771cdc46f954.c000.snappy.parquet.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=1/positionBin=240/part-00000-2f84fbdf-063d-45de-ad42-771cdc46f954.c000.snappy.parquet
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=1/positionBin=240/.part-00000-2f84fbdf-063d-45de-ad42-771cdc46f954.c000.snappy.parquet.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/_references.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=2
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=2/positionBin=189/part-00000-2f84fbdf-063d-45de-ad42-771cdc46f954.c000.snappy.parquet
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/referenceName=2/positionBin=189/.part-00000-2f84fbdf-063d-45de-ad42-771cdc46f954.c000.snappy.parquet.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/._SUCCESS.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606.adam/._readGroups.avro.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1141014258703590606
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852
/tmp/mangoTestMvnIPSmVRC/fake-3512801018155623019.txt
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/._references.avro.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/_readGroups.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/_processingSteps.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/_SUCCESS
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/_partitionedByStartPos
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=1
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=1/positionBin=26/part-00000-e483394d-242c-4f36-b78a-edbeaedff249.c000.snappy.parquet
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=1/positionBin=26/.part-00000-e483394d-242c-4f36-b78a-edbeaedff249.c000.snappy.parquet.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=1/positionBin=240/part-00000-e483394d-242c-4f36-b78a-edbeaedff249.c000.snappy.parquet
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=1/positionBin=240/.part-00000-e483394d-242c-4f36-b78a-edbeaedff249.c000.snappy.parquet.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/_references.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=2
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=2/positionBin=189/part-00000-e483394d-242c-4f36-b78a-edbeaedff249.c000.snappy.parquet
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/referenceName=2/positionBin=189/.part-00000-e483394d-242c-4f36-b78a-edbeaedff249.c000.snappy.parquet.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/._SUCCESS.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835.adam/._readGroups.avro.crc
/tmp/mangoTestMvnIPSmVRC/mmbroken8745151231051701150.genome
/tmp/mangoTestMvnIPSmVRC/4980701061802161530
/tmp/mangoTestMvnIPSmVRC/4980701061802161530/anoGam1.genome
/tmp/mangoTestMvnIPSmVRC/invalidBuild.genome4952146666127342843
/tmp/mangoTestMvnIPSmVRC/invalidBuild.genome4952146666127342843/properties.txt
/tmp/mangoTestMvnIPSmVRC/invalidBuild.genome8198242789934114953
/tmp/mangoTestMvnIPSmVRC/invalidBuild.genome8198242789934114953/properties.txt
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/._references.avro.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/_SUCCESS
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/_partitionedByStartPos
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/referenceName=1
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/referenceName=1/positionBin=0/.part-00000-859f1e76-cbb8-41a9-94b3-4a632bbd5cc2.c000.snappy.parquet.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/referenceName=1/positionBin=0/part-00000-859f1e76-cbb8-41a9-94b3-4a632bbd5cc2.c000.snappy.parquet
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/_references.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/_samples.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/._SUCCESS.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/._samples.avro.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/._header.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184.adam/_header
/tmp/mangoTestMvnIPSmVRC/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvnIPSmVRC/fake-5028187153568572035.sh
/tmp/mangoTestMvnIPSmVRC/fake-3944696173852564422.sh
/tmp/mangoTestMvnIPSmVRC/genomes2972000361085382300
/tmp/mangoTestMvnIPSmVRC/genomes2972000361085382300/hg19.genome
/tmp/mangoTestMvnIPSmVRC/fake-3526100286071724719.txt
/tmp/mangoTestMvnIPSmVRC/TempSuite3417088002956913184
/tmp/mangoTestMvnIPSmVRC/TempSuite1439345241475865835
/tmp/mangoTestMvnIPSmVRC/genomes6706949309432013206
/tmp/mangoTestMvnIPSmVRC/genomes6706949309432013206/hg19.genome
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/._references.avro.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/_SUCCESS
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/_partitionedByStartPos
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/referenceName=1
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/referenceName=1/positionBin=0/.part-00000-6b107ddb-2ee1-4ef5-8c82-1f0eeedc7bb0.c000.snappy.parquet.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/referenceName=1/positionBin=0/part-00000-6b107ddb-2ee1-4ef5-8c82-1f0eeedc7bb0.c000.snappy.parquet
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/_references.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/_samples.avro
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/._SUCCESS.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/._samples.avro.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/._header.crc
/tmp/mangoTestMvnIPSmVRC/TempSuite4175942446383830852.adam/_header
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvnIPSmVRC
find . -name pom.xml \
-exec sed -i.bak \
-e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/mangoTestMvnIPSmVRC: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/mangoTestbjdu6pk/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 43136 0 0 38303 0 1:03:47 0:00:01 1:03:46 38303
2 139M 2 3124k 0 0 1477k 0 0:01:36 0:00:02 0:01:34 3116k
2 139M 2 4035k 0 0 1138k 0 0:02:05 0:00:03 0:02:02 1652k
2 139M 2 4101k 0 0 996k 0 0:02:23 0:00:04 0:02:19 1356k
3 139M 3 5664k 0 0 1107k 0 0:02:09 0:00:05 0:02:04 1410k
5 139M 5 7400k 0 0 1209k 0 0:01:58 0:00:06 0:01:52 1474k
7 139M 7 10.3M 0 0 1491k 0 0:01:35 0:00:07 0:01:28 1497k
10 139M 10 14.5M 0 0 1831k 0 0:01:18 0:00:08 0:01:10 2369k
11 139M 11 15.4M 0 0 1737k 0 0:01:22 0:00:09 0:01:13 2347k
11 139M 11 15.8M 0 0 1605k 0 0:01:29 0:00:10 0:01:19 2114k
13 139M 13 18.9M 0 0 1745k 0 0:01:22 0:00:11 0:01:11 2400k
16 139M 16 23.0M 0 0 1945k 0 0:01:13 0:00:12 0:01:01 2591k
18 139M 18 26.5M 0 0 2073k 0 0:01:09 0:00:13 0:00:56 2464k
21 139M 21 30.7M 0 0 2231k 0 0:01:04 0:00:14 0:00:50 3134k
25 139M 25 34.9M 0 0 2368k 0 0:01:00 0:00:15 0:00:45 3915k
27 139M 27 39.0M 0 0 2482k 0 0:00:57 0:00:16 0:00:41 4122k
30 139M 30 42.2M 0 0 2525k 0 0:00:56 0:00:17 0:00:39 3931k
32 139M 32 46.0M 0 0 2605k 0 0:00:54 0:00:18 0:00:36 3999k
35 139M 35 50.2M 0 0 2691k 0 0:00:53 0:00:19 0:00:34 3989k
38 139M 38 53.5M 0 0 2712k 0 0:00:52 0:00:20 0:00:32 3734k
38 139M 38 53.6M 0 0 2601k 0 0:00:55 0:00:21 0:00:34 2981k
39 139M 39 55.0M 0 0 2549k 0 0:00:56 0:00:22 0:00:34 2630k
41 139M 41 58.3M 0 0 2585k 0 0:00:55 0:00:23 0:00:32 2512k
43 139M 43 60.8M 0 0 2582k 0 0:00:55 0:00:24 0:00:31 2167k
46 139M 46 64.3M 0 0 2624k 0 0:00:54 0:00:25 0:00:29 2259k
48 139M 48 67.9M 0 0 2663k 0 0:00:53 0:00:26 0:00:27 2929k
50 139M 50 70.8M 0 0 2676k 0 0:00:53 0:00:27 0:00:26 3240k
53 139M 53 75.1M 0 0 2736k 0 0:00:52 0:00:28 0:00:24 3434k
56 139M 56 79.3M 0 0 2789k 0 0:00:51 0:00:29 0:00:22 3788k
59 139M 59 83.5M 0 0 2840k 0 0:00:50 0:00:30 0:00:20 3926k
62 139M 62 87.7M 0 0 2887k 0 0:00:49 0:00:31 0:00:18 4055k
65 139M 65 91.8M 0 0 2928k 0 0:00:48 0:00:32 0:00:16 4291k
68 139M 68 96.0M 0 0 2970k 0 0:00:48 0:00:33 0:00:15 4285k
71 139M 71 100M 0 0 3008k 0 0:00:47 0:00:34 0:00:13 4283k
74 139M 74 104M 0 0 3045k 0 0:00:47 0:00:35 0:00:12 4277k
77 139M 77 108M 0 0 3079k 0 0:00:46 0:00:36 0:00:10 4272k
80 139M 80 112M 0 0 3110k 0 0:00:46 0:00:37 0:00:09 4279k
83 139M 83 116M 0 0 3129k 0 0:00:45 0:00:38 0:00:07 4187k
86 139M 86 120M 0 0 3159k 0 0:00:45 0:00:39 0:00:06 4189k
89 139M 89 124M 0 0 3188k 0 0:00:44 0:00:40 0:00:04 4191k
92 139M 92 129M 0 0 3214k 0 0:00:44 0:00:41 0:00:03 4193k
95 139M 95 133M 0 0 3240k 0 0:00:44 0:00:42 0:00:02 4205k
97 139M 97 136M 0 0 3247k 0 0:00:44 0:00:43 0:00:01 4142k
99 139M 99 139M 0 0 3234k 0 0:00:44 0:00:44 --:--:-- 3816k
100 139M 100 139M 0 0 3231k 0 0:00:44 0:00:44 --:--:-- 3648k
+ tar xzf /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12.tgz --directory /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded
+ export SPARK_HOME=/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.6-bin-without-hadoop-scala-2.12
+ SPARK_HOME=/tmp/mangoTestbjdu6pk/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/mangoTestbjdu6pk/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 237k 0 0 273k 0 0:12:59 --:--:-- 0:12:59 273k
0 208M 0 1395k 0 0 748k 0 0:04:45 0:00:01 0:04:44 1161k
1 208M 1 3855k 0 0 1347k 0 0:02:38 0:00:02 0:02:36 1813k
3 208M 3 6688k 0 0 1733k 0 0:02:03 0:00:03 0:02:00 2156k
4 208M 4 9677k 0 0 1991k 0 0:01:47 0:00:04 0:01:43 2363k
5 208M 5 12.5M 0 0 2186k 0 0:01:37 0:00:05 0:01:32 2518k
7 208M 7 15.5M 0 0 2315k 0 0:01:32 0:00:06 0:01:26 2899k
9 208M 9 18.8M 0 0 2460k 0 0:01:26 0:00:07 0:01:19 3098k
11 208M 11 23.0M 0 0 2665k 0 0:01:20 0:00:08 0:01:12 3385k
13 208M 13 27.2M 0 0 2831k 0 0:01:15 0:00:09 0:01:06 3647k
15 208M 15 31.4M 0 0 2963k 0 0:01:12 0:00:10 0:01:02 3874k
17 208M 17 35.6M 0 0 3076k 0 0:01:09 0:00:11 0:00:58 4119k
19 208M 19 39.8M 0 0 3171k 0 0:01:07 0:00:12 0:00:55 4287k
21 208M 21 43.9M 0 0 3250k 0 0:01:05 0:00:13 0:00:52 4286k
23 208M 23 48.1M 0 0 3321k 0 0:01:04 0:00:14 0:00:50 4288k
25 208M 25 52.3M 0 0 3382k 0 0:01:03 0:00:15 0:00:48 4291k
27 208M 27 56.5M 0 0 3436k 0 0:01:02 0:00:16 0:00:46 4289k
28 208M 28 59.3M 0 0 3400k 0 0:01:02 0:00:17 0:00:45 3987k
28 208M 28 59.5M 0 0 3182k 0 0:01:07 0:00:19 0:00:48 3004k
28 208M 28 59.5M 0 0 3063k 0 0:01:09 0:00:19 0:00:50 2301k
28 208M 28 59.5M 0 0 2899k 0 0:01:13 0:00:21 0:00:52 1415k
28 208M 28 59.5M 0 0 2754k 0 0:01:17 0:00:22 0:00:55 573k
28 208M 28 59.5M 0 0 2666k 0 0:01:20 0:00:22 0:00:58 33424
28 208M 28 59.5M 0 0 2544k 0 0:01:23 0:00:23 0:01:00 3917
28 208M 28 59.5M 0 0 2434k 0 0:01:27 0:00:25 0:01:02 3937
28 208M 28 59.5M 0 0 2332k 0 0:01:31 0:00:26 0:01:05 3960
28 208M 28 59.5M 0 0 2269k 0 0:01:34 0:00:26 0:01:08 3974
28 208M 28 59.5M 0 0 2180k 0 0:01:37 0:00:27 0:01:10 3974
28 208M 28 59.5M 0 0 2098k 0 0:01:41 0:00:29 0:01:12 3974
28 208M 28 59.5M 0 0 2022k 0 0:01:45 0:00:30 0:01:15 3967
28 208M 28 59.5M 0 0 1974k 0 0:01:48 0:00:30 0:01:18 3969
28 208M 28 59.5M 0 0 1906k 0 0:01:52 0:00:31 0:01:21 3954
28 208M 28 59.5M 0 0 1843k 0 0:01:55 0:00:33 0:01:22 3955
28 208M 28 59.5M 0 0 1784k 0 0:01:59 0:00:34 0:01:25 3955
28 208M 28 59.5M 0 0 1747k 0 0:02:02 0:00:34 0:01:28 3960
28 208M 28 59.5M 0 0 1694k 0 0:02:06 0:00:36 0:01:30 3958
28 208M 28 59.6M 0 0 1655k 0 0:02:08 0:00:36 0:01:32 23030
28 208M 28 59.7M 0 0 1613k 0 0:02:12 0:00:37 0:01:35 40430
28 208M 28 59.9M 0 0 1579k 0 0:02:15 0:00:38 0:01:37 86484
28 208M 28 60.3M 0 0 1550k 0 0:02:17 0:00:39 0:01:38 161k
29 208M 29 61.0M 0 0 1530k 0 0:02:19 0:00:40 0:01:39 316k
29 208M 29 62.3M 0 0 1525k 0 0:02:20 0:00:41 0:01:39 554k
31 208M 31 64.7M 0 0 1547k 0 0:02:18 0:00:42 0:01:36 1040k
32 208M 32 68.7M 0 0 1604k 0 0:02:13 0:00:43 0:01:30 1795k
34 208M 34 72.9M 0 0 1664k 0 0:02:08 0:00:44 0:01:24 2571k
36 208M 36 77.0M 0 0 1721k 0 0:02:04 0:00:45 0:01:19 3282k
38 208M 38 81.2M 0 0 1776k 0 0:02:00 0:00:46 0:01:14 3879k
40 208M 40 84.6M 0 0 1811k 0 0:01:57 0:00:47 0:01:10 4079k
41 208M 41 85.5M 0 0 1791k 0 0:01:59 0:00:48 0:01:11 3418k
41 208M 41 85.6M 0 0 1743k 0 0:02:02 0:00:50 0:01:12 2391k
41 208M 41 85.6M 0 0 1711k 0 0:02:04 0:00:51 0:01:13 1632k
41 208M 41 85.6M 0 0 1682k 0 0:02:06 0:00:52 0:01:14 846k
41 208M 41 85.6M 0 0 1654k 0 0:02:09 0:00:53 0:01:16 193k
41 208M 41 85.6M 0 0 1627k 0 0:02:11 0:00:53 0:01:18 18792
41 208M 41 85.7M 0 0 1600k 0 0:02:13 0:00:54 0:01:19 27852
41 208M 41 85.8M 0 0 1574k 0 0:02:15 0:00:55 0:01:20 50319
41 208M 41 86.1M 0 0 1550k 0 0:02:17 0:00:56 0:01:21 99249
41 208M 41 86.4M 0 0 1530k 0 0:02:19 0:00:57 0:01:22 175k
41 208M 41 87.1M 0 0 1515k 0 0:02:20 0:00:58 0:01:22 300k
42 208M 42 88.0M 0 0 1505k 0 0:02:21 0:00:59 0:01:22 459k
43 208M 43 89.9M 0 0 1513k 0 0:02:21 0:01:00 0:01:21 837k
44 208M 44 93.4M 0 0 1547k 0 0:02:18 0:01:01 0:01:17 1511k
46 208M 46 97.6M 0 0 1591k 0 0:02:14 0:01:02 0:01:12 2289k
48 208M 48 101M 0 0 1633k 0 0:02:10 0:01:03 0:01:07 3019k
50 208M 50 106M 0 0 1674k 0 0:02:07 0:01:04 0:01:03 3698k
52 208M 52 110M 0 0 1711k 0 0:02:04 0:01:05 0:00:59 4121k
54 208M 54 114M 0 0 1750k 0 0:02:02 0:01:06 0:00:56 4258k
56 208M 56 117M 0 0 1773k 0 0:02:00 0:01:07 0:00:53 4064k
58 208M 58 121M 0 0 1809k 0 0:01:58 0:01:08 0:00:50 4064k
58 208M 58 122M 0 0 1791k 0 0:01:59 0:01:10 0:00:49 3198k
58 208M 58 123M 0 0 1777k 0 0:02:00 0:01:10 0:00:50 2643k
60 208M 60 125M 0 0 1788k 0 0:01:59 0:01:11 0:00:48 2304k
62 208M 62 129M 0 0 1823k 0 0:01:57 0:01:12 0:00:45 2496k
64 208M 64 133M 0 0 1856k 0 0:01:55 0:01:13 0:00:42 2499k
66 208M 66 138M 0 0 1888k 0 0:01:53 0:01:14 0:00:39 3376k
67 208M 67 139M 0 0 1887k 0 0:01:53 0:01:15 0:00:38 3445k
67 208M 67 140M 0 0 1857k 0 0:01:54 0:01:17 0:00:37 2789k
67 208M 67 140M 0 0 1840k 0 0:01:56 0:01:17 0:00:39 2085k
67 208M 67 140M 0 0 1814k 0 0:01:57 0:01:19 0:00:38 1213k
67 208M 67 140M 0 0 1788k 0 0:01:59 0:01:20 0:00:39 383k
67 208M 67 140M 0 0 1772k 0 0:02:00 0:01:20 0:00:40 34455
67 208M 67 140M 0 0 1748k 0 0:02:02 0:01:22 0:00:40 3869
67 208M 67 140M 0 0 1724k 0 0:02:03 0:01:23 0:00:40 3870
67 208M 67 140M 0 0 1709k 0 0:02:04 0:01:23 0:00:41 3870
67 208M 67 140M 0 0 1686k 0 0:02:06 0:01:25 0:00:41 3869
67 208M 67 140M 0 0 1664k 0 0:02:08 0:01:26 0:00:42 3870
67 208M 67 140M 0 0 1650k 0 0:02:09 0:01:26 0:00:43 3870
67 208M 67 140M 0 0 1629k 0 0:02:11 0:01:28 0:00:43 3869
67 208M 67 140M 0 0 1609k 0 0:02:12 0:01:29 0:00:43 3870
67 208M 67 140M 0 0 1595k 0 0:02:13 0:01:29 0:00:44 5952
67 208M 67 140M 0 0 1580k 0 0:02:15 0:01:30 0:00:45 35444
67 208M 67 140M 0 0 1565k 0 0:02:16 0:01:31 0:00:45 63096
67 208M 67 140M 0 0 1551k 0 0:02:17 0:01:32 0:00:45 125k
67 208M 67 141M 0 0 1541k 0 0:02:18 0:01:33 0:00:45 258k
68 208M 68 142M 0 0 1535k 0 0:02:19 0:01:34 0:00:45 441k
69 208M 69 144M 0 0 1541k 0 0:02:18 0:01:35 0:00:43 831k
70 208M 70 147M 0 0 1563k 0 0:02:16 0:01:36 0:00:40 1530k
72 208M 72 151M 0 0 1590k 0 0:02:14 0:01:37 0:00:37 2307k
74 208M 74 156M 0 0 1617k 0 0:02:12 0:01:38 0:00:34 3044k
76 208M 76 160M 0 0 1644k 0 0:02:09 0:01:39 0:00:30 3709k
78 208M 78 164M 0 0 1670k 0 0:02:07 0:01:40 0:00:27 4136k
80 208M 80 168M 0 0 1695k 0 0:02:05 0:01:41 0:00:24 4263k
82 208M 82 172M 0 0 1721k 0 0:02:04 0:01:42 0:00:22 4284k
84 208M 84 177M 0 0 1745k 0 0:02:02 0:01:43 0:00:19 4282k
86 208M 86 181M 0 0 1770k 0 0:02:00 0:01:44 0:00:16 4280k
88 208M 88 185M 0 0 1793k 0 0:01:59 0:01:45 0:00:14 4287k
90 208M 90 189M 0 0 1817k 0 0:01:57 0:01:46 0:00:11 4286k
92 208M 92 193M 0 0 1838k 0 0:01:56 0:01:47 0:00:09 4261k
93 208M 93 194M 0 0 1822k 0 0:01:57 0:01:49 0:00:08 3318k
93 208M 93 194M 0 0 1809k 0 0:01:58 0:01:49 0:00:09 2633k
93 208M 93 194M 0 0 1795k 0 0:01:58 0:01:50 0:00:08 1828k
93 208M 93 194M 0 0 1780k 0 0:01:59 0:01:51 0:00:08 990k
93 208M 93 194M 0 0 1767k 0 0:02:00 0:01:52 0:00:08 221k
93 208M 93 195M 0 0 1756k 0 0:02:01 0:01:53 0:00:08 226k
94 208M 94 196M 0 0 1749k 0 0:02:02 0:01:54 0:00:08 412k
94 208M 94 197M 0 0 1742k 0 0:02:02 0:01:55 0:00:07 560k
95 208M 95 198M 0 0 1741k 0 0:02:02 0:01:56 0:00:06 875k
96 208M 96 200M 0 0 1743k 0 0:02:02 0:01:57 0:00:05 1216k
97 208M 97 202M 0 0 1742k 0 0:02:02 0:01:59 0:00:03 1437k
97 208M 97 202M 0 0 1731k 0 0:02:03 0:01:59 0:00:04 1326k
97 208M 97 203M 0 0 1719k 0 0:02:04 0:02:00 0:00:04 1209k
97 208M 97 203M 0 0 1709k 0 0:02:04 0:02:01 0:00:03 969k
97 208M 97 203M 0 0 1699k 0 0:02:05 0:02:02 0:00:03 651k
97 208M 97 204M 0 0 1689k 0 0:02:06 0:02:03 0:00:03 343k
98 208M 98 204M 0 0 1680k 0 0:02:07 0:02:04 0:00:03 429k
98 208M 98 205M 0 0 1675k 0 0:02:07 0:02:05 0:00:02 582k
99 208M 99 206M 0 0 1669k 0 0:02:07 0:02:06 0:00:01 688k
100 208M 100 208M 0 0 1671k 0 0:02:07 0:02:07 --:--:-- 975k
+ tar xzf /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7.tar.gz --directory /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded
+ grep avro
+ find /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7 -name '*.jar'
+ xargs rm
++ /tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/bin/hadoop classpath
+ export 'SPARK_DIST_CLASSPATH=/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/etc/hadoop:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/lib/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/lib/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/lib/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/lib/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/*:/contrib/capacity-scheduler/*.jar'
+ SPARK_DIST_CLASSPATH='/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/etc/hadoop:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/lib/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/common/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/lib/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/hdfs/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/lib/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/yarn/*:/tmp/mangoTestbjdu6pk/deleteMePleaseThisIsNoLongerNeeded/hadoop-2.7.7/share/hadoop/mapreduce/lib/*:/tmp/mangoTestbjdu6pk/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-a757f1d0-c1df-47c7-997d-2aff9d66b75f 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-a757f1d0-c1df-47c7-997d-2aff9d66b75f
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-a757f1d0-c1df-47c7-997d-2aff9d66b75f
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-a757f1d0-c1df-47c7-997d-2aff9d66b75f
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-a757f1d0-c1df-47c7-997d-2aff9d66b75f:
Build step 'Execute shell' marked build as failure
Finished: FAILURE
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