Console Output

Skipping 6,114 KB.. Full Log
[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/mangoTestftHpKkB/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/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTestftHpKkB/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-spark3_2.12/0.3.0/utils-io-spark3_2.12-0.3.0.jar to /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark3_2.12/0.3.0/utils-io-spark3_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/mangoTestftHpKkB/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/mangoTestftHpKkB/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/mangoTestftHpKkB/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/0.11.0/convert-ga4gh-0.11.0.jar to /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.11.0/convert-ga4gh-0.11.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.11.0/convert-htsjdk-0.11.0.jar to /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.11.0/convert-htsjdk-0.11.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/extensions/guice-assistedinject/5.0.1/guice-assistedinject-5.0.1.jar to /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/google/inject/extensions/guice-assistedinject/5.0.1/guice-assistedinject-5.0.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.11.0/convert-0.11.0.jar to /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.11.0/convert-0.11.0.jar
[INFO] Installing artifact /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar to /tmp/mangoTestftHpKkB/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/3.2.4/maven-shade-plugin-3.2.4.pom
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:4.0.3: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/mangoTestftHpKkB/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/mangoTestftHpKkB/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/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:compile (scala-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Using incremental compilation using Mixed compile order
[INFO] Compiler bridge file: /home/jenkins/.sbt/1.0/zinc/org.scala-sbt/org.scala-sbt-compiler-bridge_2.12-1.4.4-bin_2.12.10__52.0-1.4.4_20201220T223045.jar
[INFO] compiling 1 Scala source to /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/scala-2.12.10/classes ...
[INFO] done compiling
[INFO] compile in 3.8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1:compile (default-compile) @ mango-assembly-spark3_2.12 ---
[INFO] Changes detected - recompiling the module!
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly-spark3_2.12 ---
[INFO] Test Source directory: /tmp/mangoTestftHpKkB/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/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[WARNING]  net.liftweb:lift-json_2.12:3.3.0 requires scala version: 2.12.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.1: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:3.2.0:jar (default-jar) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar-no-fork (attach-sources) @ mango-assembly-spark3_2.12 ---
[INFO] Building jar: /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.2.0:jar (attach-javadocs) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] >>> scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-assembly-spark3_2.12 ---
[INFO] 
[INFO] --- git-commit-id-plugin:4.0.3: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/mangoTestftHpKkB/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/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) @ mango-assembly-spark3_2.12 ---
[WARNING]  Expected all dependencies to require Scala version: 2.12.10
[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: 2.12.10
[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/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.4:shade (default) @ mango-assembly-spark3_2.12 ---
Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-shade-spark3_2.12/0.35.0/adam-shade-spark3_2.12-0.35.0.pom
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Downloaded from central: https://repo.maven.apache.org/maven2/com/google/guava/guava/28.2-android/guava-28.2-android.jar (2.6 MB at 10 MB/s)
[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-spark3_2.12:jar:0.35.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.35.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.12:jar:5.0.0 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:5.0.1 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:2.12.13 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:3.0.2 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark3_2.12:jar:0.35.0 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:2.8.0 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:4.5.13 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.13 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:30.1.1-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0.1 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:3.8.0 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.5.1 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.3 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark3_2.12:jar:0.35.0 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-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_2.12:jar:0.3.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.41.v20210516 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:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.41.v20210516 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util-ajax:jar:9.4.41.v20210516 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-spark3_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:0.11.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.11.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-assistedinject:jar:5.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.11.0 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$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] mango-cli-spark3_2.12-0.0.6-SNAPSHOT.jar, adam-cli-spark3_2.12-0.35.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[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/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-spark3_2.12-0.0.6-SNAPSHOT.jar with /tmp/mangoTestftHpKkB/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:1.2:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2: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:4.4.1:compile (scala-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-distribution-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar-no-fork (attach-sources) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.2.0:jar (attach-javadocs) @ mango-distribution-spark3_2.12 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] >>> scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-distribution-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1: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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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-plugin-api/2.0.4/maven-plugin-api-2.0.4.jar (8.3 kB at 130 kB/s)
Progress (3): 48 kB | 41/109 kB | 12/30 kB
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Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/2.0.1/plexus-utils-2.0.1.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-io/1.0-alpha-4/plexus-io-1.0-alpha-4.jar (48 kB at 733 kB/s)
Progress (3): 53/109 kB | 30 kB | 20 kB
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-artifact/2.0.4/maven-artifact-2.0.4.jar
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Progress (4): 98/109 kB | 30 kB | 20 kB | 25/222 kB
                                                   
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-profile/2.0.4/maven-profile-2.0.4.jar (30 kB at 432 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-archiver/2.4/maven-archiver-2.4.jar (20 kB at 280 kB/s)
Progress (2): 102/109 kB | 25/222 kB
                                    
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-model/2.0.4/maven-model-2.0.4.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-repository-builder/1.0-alpha-2/maven-repository-builder-1.0-alpha-2.jar
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Progress (4): 109 kB | 82/222 kB | 53/80 kB | 12/80 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 (3): 82/222 kB | 57/80 kB | 12/80 kB
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Progress (3): 152/222 kB | 80 kB | 66/80 kB
                                           
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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 901 kB/s)
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 2.4 MB/s)
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /tmp/mangoTestftHpKkB/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/mangoTestftHpKkB/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/mangoTestftHpKkB/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:1.2:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2: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:4.4.1:compile (scala-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1:testCompile (scala-test-compile-first) @ mango-parent-spark3_2.12 ---
[INFO] compile in 0.0 s
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar-no-fork (attach-sources) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.2.0:jar (attach-javadocs) @ mango-parent-spark3_2.12 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] >>> scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) > generate-sources @ mango-parent-spark3_2.12 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-versions) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ mango-parent-spark3_2.12 ---
[INFO] 
[INFO] <<< scala-maven-plugin:4.4.1:doc-jar (attach-scaladocs) < generate-sources @ mango-parent-spark3_2.12 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:4.4.1: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 [ 42.340 s]
[INFO] mango_2.12: CLI .................................... SUCCESS [ 54.026 s]
[INFO] Mango_2.12: Assembly ............................... SUCCESS [ 30.462 s]
[INFO] mango_2.12: Distribution ........................... SUCCESS [01:02 min]
[INFO] mango_2.12 ......................................... SUCCESS [  0.917 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  03:10 min
[INFO] Finished at: 2021-12-06T13:58:05Z
[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
+ grep mango-assembly
+ tar tzf mango-distribution/target/mango-distribution-spark3_2.12-0.0.6-SNAPSHOT-bin.tar.gz
+ grep -v -e sources -e javadoc
+ grep jar
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/mangoTestMvnUG3U0j6
/tmp/mangoTestMvnUG3U0j6
/tmp/mangoTestMvnUG3U0j6/genomes6763387086626184307
/tmp/mangoTestMvnUG3U0j6/genomes6763387086626184307/hg19.genome
/tmp/mangoTestMvnUG3U0j6/fake-690846205113668387.sh
/tmp/mangoTestMvnUG3U0j6/fake-523148040139843237.txt
/tmp/mangoTestMvnUG3U0j6/genomes8093687009003962816
/tmp/mangoTestMvnUG3U0j6/genomes8093687009003962816/hg19.genome
/tmp/mangoTestMvnUG3U0j6/518487858366411836
/tmp/mangoTestMvnUG3U0j6/518487858366411836/anoGam1.genome
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/._references.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/_header
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/_references.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/._samples.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/_samples.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/referenceName=1
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/referenceName=1/positionBin=0/.part-00000-52cd7977-875a-489f-9f2c-9c1e7ce0352d.c000.snappy.parquet.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/referenceName=1/positionBin=0/part-00000-52cd7977-875a-489f-9f2c-9c1e7ce0352d.c000.snappy.parquet
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/._SUCCESS.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/_SUCCESS
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/_partitionedByStartPos
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668.adam/._header.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819
/tmp/mangoTestMvnUG3U0j6/mmbroken6085280564160484374.genome
/tmp/mangoTestMvnUG3U0j6/invalidBuild.genome8726016569434469622
/tmp/mangoTestMvnUG3U0j6/invalidBuild.genome8726016569434469622/properties.txt
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/._samples.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/._SUCCESS.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/_partitionedByStartPos
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/._references.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/_header
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/_samples.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/_references.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/_SUCCESS
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/._header.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/referenceName=1
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/referenceName=1/positionBin=0/part-00000-f9783480-bd7a-4e5f-9e63-85c975b2b9cb.c000.snappy.parquet
/tmp/mangoTestMvnUG3U0j6/TempSuite7709396178153494819.adam/referenceName=1/positionBin=0/.part-00000-f9783480-bd7a-4e5f-9e63-85c975b2b9cb.c000.snappy.parquet.crc
/tmp/mangoTestMvnUG3U0j6/mmbroken2593528516672861010.genome
/tmp/mangoTestMvnUG3U0j6/fake-6262450552891606668.sh
/tmp/mangoTestMvnUG3U0j6/9058554689864763873
/tmp/mangoTestMvnUG3U0j6/5939986393893996206
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=1
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=1/positionBin=240/part-00000-5b6410cd-7b48-49c9-9c07-49b1f33ca286.c000.snappy.parquet
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=1/positionBin=240/.part-00000-5b6410cd-7b48-49c9-9c07-49b1f33ca286.c000.snappy.parquet.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=1/positionBin=26/.part-00000-5b6410cd-7b48-49c9-9c07-49b1f33ca286.c000.snappy.parquet.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=1/positionBin=26/part-00000-5b6410cd-7b48-49c9-9c07-49b1f33ca286.c000.snappy.parquet
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/_references.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/_processingSteps.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=2
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=2/positionBin=189/part-00000-5b6410cd-7b48-49c9-9c07-49b1f33ca286.c000.snappy.parquet
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/referenceName=2/positionBin=189/.part-00000-5b6410cd-7b48-49c9-9c07-49b1f33ca286.c000.snappy.parquet.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/._references.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/._readGroups.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/_SUCCESS
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/_readGroups.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/_partitionedByStartPos
/tmp/mangoTestMvnUG3U0j6/TempSuite5728879318271821939.adam/._SUCCESS.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=1
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=1/positionBin=240/part-00000-c65c6486-478d-485e-8ecb-6a3717dbff41.c000.snappy.parquet
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=1/positionBin=240/.part-00000-c65c6486-478d-485e-8ecb-6a3717dbff41.c000.snappy.parquet.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=1/positionBin=26/part-00000-c65c6486-478d-485e-8ecb-6a3717dbff41.c000.snappy.parquet
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=1/positionBin=26/.part-00000-c65c6486-478d-485e-8ecb-6a3717dbff41.c000.snappy.parquet.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/._SUCCESS.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/._readGroups.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=2
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=2/positionBin=189/.part-00000-c65c6486-478d-485e-8ecb-6a3717dbff41.c000.snappy.parquet.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/referenceName=2/positionBin=189/part-00000-c65c6486-478d-485e-8ecb-6a3717dbff41.c000.snappy.parquet
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/_references.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/._references.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/._processingSteps.avro.crc
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/_readGroups.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/_processingSteps.avro
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/_SUCCESS
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011.adam/_partitionedByStartPos
/tmp/mangoTestMvnUG3U0j6/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvnUG3U0j6/TempSuite9155215657060588011
/tmp/mangoTestMvnUG3U0j6/TempSuite2816673493400370668
/tmp/mangoTestMvnUG3U0j6/fake-2828173956259621221.txt
/tmp/mangoTestMvnUG3U0j6/6166239629657154293
/tmp/mangoTestMvnUG3U0j6/6166239629657154293/anoGam1.genome
/tmp/mangoTestMvnUG3U0j6/invalidBuild.genome8220401199222524896
/tmp/mangoTestMvnUG3U0j6/invalidBuild.genome8220401199222524896/properties.txt
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvnUG3U0j6

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/mangoTestMvnUG3U0j6: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-3.0.1

# what hadoop version are we on? format string for downloading spark assembly
if [[ $HADOOP_VERSION =~ ^3\.2 ]]; then
    HADOOP=hadoop3.2
else
    echo "Unknown Hadoop version."
    exit 1
fi
+ [[ 3.2.1 =~ ^3\.2 ]]
+ HADOOP=hadoop3.2


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
+ curl -v -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-3.0.1/spark-3.0.1-bin-hadoop3.2.tgz' -o /tmp/mangoTestftHpKkB/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop3.2.tgz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 151.101.2.132...
* TCP_NODELAY set
* Connected to www.apache.org (151.101.2.132) port 443 (#0)
* ALPN, offering h2
* ALPN, offering http/1.1
* Cipher selection: ALL:!EXPORT:!EXPORT40:!EXPORT56:!aNULL:!LOW:!RC4:@STRENGTH
* successfully set certificate verify locations:
*   CAfile: /etc/ssl/certs/ca-certificates.crt
  CApath: /etc/ssl/certs
* TLSv1.2 (OUT), TLS header, Certificate Status (22):
} [5 bytes data]
* TLSv1.2 (OUT), TLS handshake, Client hello (1):
} [512 bytes data]
* TLSv1.2 (IN), TLS handshake, Server hello (2):
{ [102 bytes data]
* TLSv1.2 (IN), TLS handshake, Certificate (11):
{ [4015 bytes data]
* TLSv1.2 (OUT), TLS alert, Server hello (2):
} [2 bytes data]
* SSL certificate problem: certificate has expired
* Curl_http_done: called premature == 1
* stopped the pause stream!

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
* Closing connection 0
curl: (60) SSL certificate problem: certificate has expired
More details here: https://curl.haxx.se/docs/sslcerts.html

curl performs SSL certificate verification by default, using a "bundle"
 of Certificate Authority (CA) public keys (CA certs). If the default
 bundle file isn't adequate, you can specify an alternate file
 using the --cacert option.
If this HTTPS server uses a certificate signed by a CA represented in
 the bundle, the certificate verification probably failed due to a
 problem with the certificate (it might be expired, or the name might
 not match the domain name in the URL).
If you'd like to turn off curl's verification of the certificate, use
 the -k (or --insecure) option.
clean_up
+ clean_up
+ set +x +v
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
Build step 'Execute shell' marked build as failure
Sending e-mails to: akmorrow@berkeley.edu
Finished: FAILURE