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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/commons/commons-compress/1.9/commons-compress-1.9.jar (378 kB at 4.2 MB/s)
[INFO] Installing artifact /root/.m2/repository/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar
[INFO] Installing artifact /root/.m2/repository/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar
[INFO] Installing artifact /root/.m2/repository/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar
[INFO] Installing artifact /root/.m2/repository/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/avro/avro/1.8.2/avro-1.8.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro/1.8.2/avro-1.8.2.jar
[INFO] Installing artifact /root/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar
[INFO] Installing artifact /root/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar
[INFO] Installing artifact /root/.m2/repository/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar
[INFO] Installing artifact /root/.m2/repository/org/tukaani/xz/1.5/xz-1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar
[INFO] Installing artifact /root/.m2/repository/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar
[INFO] Installing artifact /root/.m2/repository/commons-codec/commons-codec/1.4/commons-codec-1.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/commons-codec/commons-codec/1.4/commons-codec-1.4.jar
[INFO] Installing artifact /root/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
[INFO] Installing artifact /root/.m2/repository/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.10.1/parquet-column-1.10.1.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.10.1/parquet-common-1.10.1.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.10.1/parquet-encoding-1.10.1.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.10.1/parquet-hadoop-1.10.1.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.10.1/parquet-jackson-1.10.1.jar
[INFO] Installing artifact /root/.m2/repository/commons-pool/commons-pool/1.6/commons-pool-1.6.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/commons-pool/commons-pool/1.6/commons-pool-1.6.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.4.0/parquet-format-2.4.0.jar
[INFO] Installing artifact /root/.m2/repository/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/it/unimi/dsi/fastutil/7.0.13/fastutil-7.0.13.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.10.1/parquet-scala_2.10-1.10.1.jar
[INFO] Installing artifact /root/.m2/repository/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar
[INFO] Installing artifact /root/.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/adam/adam-cli-spark2_2.11/0.30.0/adam-cli-spark2_2.11-0.30.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli-spark2_2.11/0.30.0/adam-cli-spark2_2.11-0.30.0.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/adam/adam-apis-spark2_2.11/0.30.0/adam-apis-spark2_2.11-0.30.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis-spark2_2.11/0.30.0/adam-apis-spark2_2.11-0.30.0.jar
[INFO] Installing artifact /root/.m2/repository/args4j/args4j/2.33/args4j-2.33.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/args4j/args4j/2.33/args4j-2.33.jar
[INFO] Installing artifact /root/.m2/repository/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar
[INFO] Installing artifact /root/.m2/repository/com/google/inject/guice/4.2.0/guice-4.2.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/google/inject/guice/4.2.0/guice-4.2.0.jar
[INFO] Installing artifact /root/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/javax/inject/javax.inject/1/javax.inject-1.jar
[INFO] Installing artifact /root/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/aopalliance/aopalliance/1.0/aopalliance-1.0.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/adam/adam-core-spark2_2.11/0.30.0/adam-core-spark2_2.11-0.30.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core-spark2_2.11/0.30.0/adam-core-spark2_2.11-0.30.0.jar
[INFO] Installing artifact /root/.m2/repository/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar
[INFO] Installing artifact /root/.m2/repository/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar
[INFO] Installing artifact /root/.m2/repository/org/objenesis/objenesis/2.1/objenesis-2.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/objenesis/objenesis/2.1/objenesis-2.1.jar
[INFO] Installing artifact /root/.m2/repository/commons-io/commons-io/2.6/commons-io-2.6.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/commons-io/commons-io/2.6/commons-io-2.6.jar
[INFO] Installing artifact /root/.m2/repository/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/clapper/grizzled-slf4j_2.11/1.3.3/grizzled-slf4j_2.11-1.3.3.jar
[INFO] Installing artifact /root/.m2/repository/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar
[INFO] Installing artifact /root/.m2/repository/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar
[INFO] Installing artifact /root/.m2/repository/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[INFO] Installing artifact /root/.m2/repository/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.5.7/httpclient-4.5.7.jar
[INFO] Installing artifact /root/.m2/repository/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.4.11/httpcore-4.4.11.jar
[INFO] Installing artifact /root/.m2/repository/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar
[INFO] Installing artifact /root/.m2/repository/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar
[INFO] Installing artifact /root/.m2/repository/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar
[INFO] Installing artifact /root/.m2/repository/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar
[INFO] Installing artifact /root/.m2/repository/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar
[INFO] Installing artifact /root/.m2/repository/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar
[INFO] Installing artifact /root/.m2/repository/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.30.0/adam-codegen-spark2_2.11-0.30.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.30.0/adam-codegen-spark2_2.11-0.30.0.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.15.0/bdg-formats-0.15.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.15.0/bdg-formats-0.15.0.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.15/utils-cli-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.15/utils-misc-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.15/utils-intervalrdd-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.15/utils-metrics-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /root/.m2/repository/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.12.25/servo-core-0.12.25.jar
[INFO] Installing artifact /root/.m2/repository/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/spectator/spectator-api/0.67.0/spectator-api-0.67.0.jar
[INFO] Installing artifact /root/.m2/repository/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-server/9.4.17.v20190418/jetty-server-9.4.17.v20190418.jar
[INFO] Installing artifact /root/.m2/repository/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-http/9.4.17.v20190418/jetty-http-9.4.17.v20190418.jar
[INFO] Installing artifact /root/.m2/repository/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util/9.4.17.v20190418/jetty-util-9.4.17.v20190418.jar
[INFO] Installing artifact /root/.m2/repository/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-io/9.4.17.v20190418/jetty-io-9.4.17.v20190418.jar
[INFO] Installing artifact /root/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-webapp/9.4.17.v20190418/jetty-webapp-9.4.17.v20190418.jar
[INFO] Installing artifact /root/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-xml/9.4.17.v20190418/jetty-xml-9.4.17.v20190418.jar
[INFO] Installing artifact /root/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-servlet/9.4.17.v20190418/jetty-servlet-9.4.17.v20190418.jar
[INFO] Installing artifact /root/.m2/repository/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-security/9.4.17.v20190418/jetty-security-9.4.17.v20190418.jar
[INFO] Installing artifact /root/.m2/repository/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-reflect/2.11.12/scala-reflect-2.11.12.jar
[INFO] Installing artifact /root/.m2/repository/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-xml_2.11/1.1.0/scala-xml_2.11-1.1.0.jar
[INFO] Installing artifact /root/.m2/repository/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar
[INFO] Installing artifact /root/.m2/repository/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar
[INFO] Installing artifact /root/.m2/repository/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar
[INFO] Installing artifact /root/.m2/repository/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar
[INFO] Installing artifact /root/.m2/repository/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar
[INFO] Installing artifact /root/.m2/repository/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar
[INFO] Installing artifact /root/.m2/repository/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar
[INFO] Installing artifact /root/.m2/repository/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar
[INFO] Installing artifact /root/.m2/repository/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar
[INFO] Installing artifact /root/.m2/repository/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar
[INFO] Installing artifact /root/.m2/repository/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar
[INFO] Installing artifact /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-core/target/mango-core-0.0.4-SNAPSHOT.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core/0.0.4-SNAPSHOT/mango-core-0.0.4-SNAPSHOT.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.15/utils-io-spark2_2.11-0.2.15.jar
[INFO] Installing artifact /root/.m2/repository/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/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 /root/.m2/repository/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/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 /root/.m2/repository/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/convert/convert-ga4gh/0.9.0/convert-ga4gh-0.9.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.9.0/convert-ga4gh-0.9.0.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.9.0/convert-htsjdk-0.9.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.9.0/convert-htsjdk-0.9.0.jar
[INFO] Installing artifact /root/.m2/repository/com/google/inject/extensions/guice-assistedinject/4.2.2/guice-assistedinject-4.2.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/com/google/inject/extensions/guice-assistedinject/4.2.2/guice-assistedinject-4.2.2.jar
[INFO] Installing artifact /root/.m2/repository/org/bdgenomics/convert/convert/0.9.0/convert-0.9.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.9.0/convert-0.9.0.jar
[INFO] Installing artifact /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/mango-cli-0.0.4-SNAPSHOT.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli/0.0.4-SNAPSHOT/mango-cli-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] ----------------< org.bdgenomics.mango:mango-assembly >-----------------
[INFO] Building Mango: Assembly 0.0.4-SNAPSHOT                            [4/5]
[INFO] --------------------------------[ jar ]---------------------------------
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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.jar
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/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 ---
[INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[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 ---
[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 ---
[INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ mango-assembly ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[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 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ mango-assembly ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly ---
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ mango-assembly ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly ---
[INFO] Request to add '/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/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 ---
[INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
model contains 6 documentable templates
[INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-assembly/target/mango-assembly-0.0.4-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ mango-assembly ---
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-common-artifact-filters/3.0.1/maven-common-artifact-filters-3.0.1.jar
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[INFO] Including org.bdgenomics.mango:mango-cli:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:7.0.13 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.10.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.30.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.30.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.30.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.3 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.30.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
[INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.17.v20190418 in the shaded jar.
[INFO] Including org.scalatra:scalatra_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra:scalatra-common_2.11:jar:2.4.1 in the shaded jar.
[INFO] Including org.scalatra.rl:rl_2.11:jar:0.4.10 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 joda-time:joda-time:jar:2.9.1 in the shaded jar.
[INFO] Including org.joda:joda-convert:jar:1.8.1 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.5 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-core_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.11.12 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.9.1 in the shaded jar.
[INFO] Including org.bdgenomics.mango:mango-core:jar:0.0.4-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.15 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.
[INFO] Including org.apache.commons:commons-lang3:jar:3.9 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /root/.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 /root/.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$1.class from jar /root/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] mango-cli-0.0.4-SNAPSHOT.jar, adam-cli-spark2_2.11-0.30.0.jar define 3 overlapping classes: 
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup
[WARNING]   - org.bdgenomics.adam.cli.InitArgs
[WARNING]   - org.bdgenomics.adam.cli.CommandGroup$
[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.
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[INFO] 
[INFO] --------------< org.bdgenomics.mango:mango-distribution >---------------
[INFO] Building mango: Distribution 0.0.4-SNAPSHOT                        [5/5]
[INFO] --------------------------------[ pom ]---------------------------------
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution ---
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[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.2-beta-5:single (default) @ mango-distribution ---
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[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar : /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
[INFO] Building tar : /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for mango 0.0.4-SNAPSHOT:
[INFO] 
[INFO] mango .............................................. SUCCESS [  6.616 s]
[INFO] mango: CORE ........................................ SUCCESS [ 19.638 s]
[INFO] mango: CLI ......................................... SUCCESS [ 25.390 s]
[INFO] Mango: Assembly .................................... SUCCESS [ 25.540 s]
[INFO] mango: Distribution ................................ SUCCESS [01:01 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:18 min
[INFO] Finished at: 2020-08-05T17:15:19Z
[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 tzvf mango-distribution/target/mango-distribution*-bin.tar.gz | \
    grep mango-assembly | \
    grep jar | \
    grep -v -e sources -e javadoc
+ grep mango-assembly
+ grep jar
+ tar tzvf mango-distribution/target/mango-distribution-0.0.4-SNAPSHOT-bin.tar.gz
+ grep -v -e sources -e javadoc
-rw-r--r-- 0/0        93867645 2020-08-05 17:14 mango-distribution-0.0.4-SNAPSHOT/repo/mango-assembly-0.0.4-SNAPSHOT.jar

# we are done with maven, so clean up the maven temp dir
find ${MANGO_MVN_TMP_DIR}
+ find /tmp/mangoTestMvn4dV6yrP
/tmp/mangoTestMvn4dV6yrP
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460
/tmp/mangoTestMvn4dV6yrP/mmbroken7330248960047263090.genome
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/_samples.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/_partitionedByStartPos
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/._header.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/_header
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/_references.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/_SUCCESS
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/referenceName=1
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/referenceName=1/positionBin=0/part-00000-bdaf20d7-ca40-4b7a-b070-79a9f722d0f3.c000.snappy.parquet
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/referenceName=1/positionBin=0/.part-00000-bdaf20d7-ca40-4b7a-b070-79a9f722d0f3.c000.snappy.parquet.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/._SUCCESS.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/._samples.avro.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997.adam/._references.avro.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275
/tmp/mangoTestMvn4dV6yrP/9138160083003144695
/tmp/mangoTestMvn4dV6yrP/8208399782086757978
/tmp/mangoTestMvn4dV6yrP/8208399782086757978/anoGam1.genome
/tmp/mangoTestMvn4dV6yrP/genomes316201363837720033
/tmp/mangoTestMvn4dV6yrP/genomes316201363837720033/hg19.genome
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832
/tmp/mangoTestMvn4dV6yrP/invalidBuild.genome2170685467095677201
/tmp/mangoTestMvn4dV6yrP/mmbroken5727375505293187982.genome
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/_processingSteps.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/_partitionedByStartPos
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=2
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=2/positionBin=189/.part-00000-194461a8-6b9d-4ad9-9870-6473a5a55c42.c000.snappy.parquet.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=2/positionBin=189/part-00000-194461a8-6b9d-4ad9-9870-6473a5a55c42.c000.snappy.parquet
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/._SUCCESS.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/_references.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/_SUCCESS
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/._references.avro.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=1
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=1/positionBin=240/part-00000-194461a8-6b9d-4ad9-9870-6473a5a55c42.c000.snappy.parquet
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=1/positionBin=240/.part-00000-194461a8-6b9d-4ad9-9870-6473a5a55c42.c000.snappy.parquet.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=1/positionBin=26/part-00000-194461a8-6b9d-4ad9-9870-6473a5a55c42.c000.snappy.parquet
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/referenceName=1/positionBin=26/.part-00000-194461a8-6b9d-4ad9-9870-6473a5a55c42.c000.snappy.parquet.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/_readGroups.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite1290617254349170832.adam/._readGroups.avro.crc
/tmp/mangoTestMvn4dV6yrP/9012520046213625728
/tmp/mangoTestMvn4dV6yrP/9012520046213625728/anoGam1.genome
/tmp/mangoTestMvn4dV6yrP/snappy-1.0.5-libsnappyjava.so
/tmp/mangoTestMvn4dV6yrP/8218921237081309386
/tmp/mangoTestMvn4dV6yrP/invalidBuild.genome8360472495671867435
/tmp/mangoTestMvn4dV6yrP/TempSuite5657102397453408997
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/._references.avro.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/._samples.avro.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/_samples.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/_header
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/_partitionedByStartPos
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/_references.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/._SUCCESS.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/_SUCCESS
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/referenceName=1
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/referenceName=1/positionBin=0
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/referenceName=1/positionBin=0/.part-00000-de641843-58ec-4ccb-8191-fcb0931e4be7.c000.snappy.parquet.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/referenceName=1/positionBin=0/part-00000-de641843-58ec-4ccb-8191-fcb0931e4be7.c000.snappy.parquet
/tmp/mangoTestMvn4dV6yrP/TempSuite60963437579858460.adam/._header.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=1
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=1/positionBin=26
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=1/positionBin=26/part-00000-8cec6458-e66e-4551-b2ae-298f0807c79d.c000.snappy.parquet
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=1/positionBin=26/.part-00000-8cec6458-e66e-4551-b2ae-298f0807c79d.c000.snappy.parquet.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=1/positionBin=240
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=1/positionBin=240/.part-00000-8cec6458-e66e-4551-b2ae-298f0807c79d.c000.snappy.parquet.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=1/positionBin=240/part-00000-8cec6458-e66e-4551-b2ae-298f0807c79d.c000.snappy.parquet
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/._partitionedByStartPos.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/._readGroups.avro.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=2
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=2/positionBin=189
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=2/positionBin=189/.part-00000-8cec6458-e66e-4551-b2ae-298f0807c79d.c000.snappy.parquet.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/referenceName=2/positionBin=189/part-00000-8cec6458-e66e-4551-b2ae-298f0807c79d.c000.snappy.parquet
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/_references.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/._references.avro.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/._SUCCESS.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/_SUCCESS
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/._processingSteps.avro.crc
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/_readGroups.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/_processingSteps.avro
/tmp/mangoTestMvn4dV6yrP/TempSuite3724306708613889275.adam/_partitionedByStartPos
/tmp/mangoTestMvn4dV6yrP/genomes8924047838601995775
/tmp/mangoTestMvn4dV6yrP/genomes8924047838601995775/hg19.genome
rm -rf ${MANGO_MVN_TMP_DIR}
+ rm -rf /tmp/mangoTestMvn4dV6yrP

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/mangoTestMvn4dV6yrP:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# run integration tests
# prebuilt spark distributions are scala 2.11 for spark 2.x
if [[ ${SCALAVER} == 2.11 ]];
then

    # set the TMPDIR envar, which is used by python to choose where to make temp directories
    export TMPDIR=${MANGO_TMP_DIR}

    pushd $PROJECT_ROOT

    # Copy the jar into our temp space for testing
    cp -r . $MANGO_TMP_DIR
    popd

    pushd $MANGO_TMP_DIR

    # what hadoop version are we on? format string for downloading spark assembly
    if [[ $HADOOP_VERSION =~ ^2\.6 ]]; then
        HADOOP=hadoop2.6
    elif [[ $HADOOP_VERSION =~ ^2\.7 ]]; then
        HADOOP=hadoop2.7
    else
        echo "Unknown Hadoop version."
        exit 1
    fi

    # set spark artifact string for downloading assembly
    SPARK=spark-${SPARK_VERSION}

    # download prepackaged spark assembly
    curl \
        -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \
        -o ${SPARK}-bin-${HADOOP}.tgz

    tar xzvf ${SPARK}-bin-${HADOOP}.tgz
    export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP}

    # create a conda environment for python build, if necessary
    pythons=( 3.6 )
    for python in ${pythons[*]}
    do
        conda create -y -q -c conda-forge -n mango-build-${PYTHON_UUID} python=${python} pip=19.3.1 jupyterlab=2.0.1
        source activate mango-build-${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
        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 tzvf 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
        bash -xv ${PROJECT_ROOT}/bin/mango-notebook  &> ${MANGO_NOTEBOOK_LOGS} &

        # sleep for 2 seconds to let mango-notebook start up
        sleep 2

        # if mango-notebook fails, then trying to kill the process will fail
        if kill $! ; then
            echo "Mango Notebook Succeeded"
        else
            echo "Mango Notebook failed with logs:"
            cat ${MANGO_NOTEBOOK_LOGS}
            exit 1
        fi

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

        # deactivate and remove the conda env
        source deactivate
        conda remove -y --name mango-build-${PYTHON_UUID} --all

    done

    # test mango submit
    MANGO_BROWSER_LOGS=${MANGO_TMP_DIR}/mango-submit.log
    bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS} &

    # sleep for 10 seconds to let mango-browser start up
    sleep 10

    # make sure server responds to POST for reads and variants
    curl -s -N \
    --header "Content-type: application/json" \
    --request POST \
    --data "{\"pageToken\":null,\"pageSize\":200,\"readGroupIds\":[\"chr17_7500000-7515000_sam\"],\"referenceId\":\"chr17\",\"start\":1,\"end\":100}"  \
    http://localhost:8080/reads/search | grep alignments

    if [[ $? != 0 ]]; then
        echo "invalid alignments"
        exit 1
    fi

    curl -s -N \
        --header "Content-type: application/json" \
        --request POST \
        --data "{\"variantSetId\":\"ALL_chr17_7500000-7515000_phase3_shapeit2_mvncall_integrated_v5a_20130502_genotypes_vcf\",\"pageToken\":null,\"pageSize\":400,\"referenceName\":\"chr17\",\"callSetIds\":[],\"start\":7500000,\"end\":7515000}"  \
        http://localhost:8080/variants/search | grep variants

    if [[ $? != 0 ]]; then
        echo "invalid variants"
        exit 1
    fi

    # get processes with mango prefix
    PROCESSES=( $(ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }') )

    # There should be processes running for mango-browser
    if [ "${#PROCESSES[@]}" -gt 0 ] ; then
        echo "Mango Browser Succeeded"
        # kill all Mango Browser related processes
        kill ${PROCESSES};
    else
        echo "Mango Browser failed with logs:"
        cat ${MANGO_BROWSER_LOGS}
        exit 1
    fi

    # test genome builds
    TEST_GENOME="anoGam1"
    bash -xv ${PROJECT_ROOT}/bin/make_genome ${TEST_GENOME} ${MANGO_TMP_DIR}

    unzip ${MANGO_TMP_DIR}/${TEST_GENOME}.genome -d ${MANGO_TMP_DIR}/${TEST_GENOME}

    pushd ${MANGO_TMP_DIR}/${TEST_GENOME}
    cat properties.txt
    cat ${TEST_GENOME}.chrom.sizes
    popd
fi
+ [[ 2.11 == 2.11 ]]
+ export TMPDIR=/tmp/mangoTest2PcnAhw/deleteMePleaseThisIsNoLongerNeeded
+ TMPDIR=/tmp/mangoTest2PcnAhw/deleteMePleaseThisIsNoLongerNeeded
+ pushd /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu/scripts/..
+ cp -r . /tmp/mangoTest2PcnAhw/deleteMePleaseThisIsNoLongerNeeded
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu /home
/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu /home
/tmp/mangoTest2PcnAhw/deleteMePleaseThisIsNoLongerNeeded /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.4.5/label/ubuntu /home
+ popd
+ pushd /tmp/mangoTest2PcnAhw/deleteMePleaseThisIsNoLongerNeeded
+ [[ 2.7.5 =~ ^2\.6 ]]
+ [[ 2.7.5 =~ ^2\.7 ]]
+ HADOOP=hadoop2.7
+ SPARK=spark-2.4.5
+ curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.4.5/spark-2.4.5-bin-hadoop2.7.tgz' -o spark-2.4.5-bin-hadoop2.7.tgz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0

100   313  100   313    0     0    580      0 --:--:-- --:--:-- --:--:--   580
+ tar xzvf spark-2.4.5-bin-hadoop2.7.tgz

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
clean_up
+ clean_up
+ source deactivate
#!/bin/sh
_CONDA_ROOT="/opt/conda"
++ _CONDA_ROOT=/opt/conda
# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
\echo >&2 "DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'."
++ echo 'DeprecationWarning: '\''source deactivate'\'' is deprecated. Use '\''conda deactivate'\''.'
DeprecationWarning: 'source deactivate' is deprecated. Use 'conda deactivate'.
\. "$_CONDA_ROOT/etc/profile.d/conda.sh" || return $?
++ . /opt/conda/etc/profile.d/conda.sh
export CONDA_EXE='/opt/conda/bin/conda'
+++ export CONDA_EXE=/opt/conda/bin/conda
+++ CONDA_EXE=/opt/conda/bin/conda
export _CE_M=''
+++ export _CE_M=
+++ _CE_M=
export _CE_CONDA=''
+++ export _CE_CONDA=
+++ _CE_CONDA=
export CONDA_PYTHON_EXE='/opt/conda/bin/python'
+++ export CONDA_PYTHON_EXE=/opt/conda/bin/python
+++ CONDA_PYTHON_EXE=/opt/conda/bin/python

# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause

__add_sys_prefix_to_path() {
    # In dev-mode CONDA_EXE is python.exe and on Windows
    # it is in a different relative location to condabin.
    if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then
        SYSP=$(\dirname "${CONDA_EXE}")
    else
        SYSP=$(\dirname "${CONDA_EXE}")
        SYSP=$(\dirname "${SYSP}")
    fi

    if [ -n "${WINDIR+x}" ]; then
        PATH="${SYSP}/bin:${PATH}"
        PATH="${SYSP}/Scripts:${PATH}"
        PATH="${SYSP}/Library/bin:${PATH}"
        PATH="${SYSP}/Library/usr/bin:${PATH}"
        PATH="${SYSP}/Library/mingw-w64/bin:${PATH}"
        PATH="${SYSP}:${PATH}"
    else
        PATH="${SYSP}/bin:${PATH}"
    fi
    \export PATH
}

__conda_hashr() {
    if [ -n "${ZSH_VERSION:+x}" ]; then
        \rehash
    elif [ -n "${POSH_VERSION:+x}" ]; then
        :  # pass
    else
        \hash -r
    fi
}

__conda_activate() {
    if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
        # Handle transition from shell activated with conda <= 4.3 to a subsequent activation
        # after conda updated to >= 4.4. See issue #6173.
        PS1="$CONDA_PS1_BACKUP"
        \unset CONDA_PS1_BACKUP
    fi

    \local cmd="$1"
    shift
    \local ask_conda
    CONDA_INTERNAL_OLDPATH="${PATH}"
    __add_sys_prefix_to_path
    ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix "$cmd" "$@")" || \return $?
    rc=$?
    PATH="${CONDA_INTERNAL_OLDPATH}"
    \eval "$ask_conda"
    if [ $rc != 0 ]; then
        \export PATH
    fi
    __conda_hashr
}

__conda_reactivate() {
    \local ask_conda
    CONDA_INTERNAL_OLDPATH="${PATH}"
    __add_sys_prefix_to_path
    ask_conda="$(PS1="$PS1" "$CONDA_EXE" $_CE_M $_CE_CONDA shell.posix reactivate)" || \return $?
    PATH="${CONDA_INTERNAL_OLDPATH}"
    \eval "$ask_conda"
    __conda_hashr
}

conda() {
    if [ "$#" -lt 1 ]; then
        "$CONDA_EXE" $_CE_M $_CE_CONDA
    else
        \local cmd="$1"
        shift
        case "$cmd" in
            activate|deactivate)
                __conda_activate "$cmd" "$@"
                ;;
            install|update|upgrade|remove|uninstall)
                CONDA_INTERNAL_OLDPATH="${PATH}"
                __add_sys_prefix_to_path
                "$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
                \local t1=$?
                PATH="${CONDA_INTERNAL_OLDPATH}"
                if [ $t1 = 0 ]; then
                    __conda_reactivate
                else
                    return $t1
                fi
                ;;
            *)
                CONDA_INTERNAL_OLDPATH="${PATH}"
                __add_sys_prefix_to_path
                "$CONDA_EXE" $_CE_M $_CE_CONDA "$cmd" "$@"
                \local t1=$?
                PATH="${CONDA_INTERNAL_OLDPATH}"
                return $t1
                ;;
        esac
    fi
}

if [ -z "${CONDA_SHLVL+x}" ]; then
    \export CONDA_SHLVL=0
    # In dev-mode CONDA_EXE is python.exe and on Windows
    # it is in a different relative location to condabin.
    if [ -n "${_CE_CONDA+x}" ] && [ -n "${WINDIR+x}" ]; then
        PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
    else
        PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
    fi
    \export PATH

    # We're not allowing PS1 to be unbound. It must at least be set.
    # However, we're not exporting it, which can cause problems when starting a second shell
    # via a first shell (i.e. starting zsh from bash).
    if [ -z "${PS1+x}" ]; then
        PS1=
    fi
fi
+++ '[' -z '' ']'
+++ export CONDA_SHLVL=0
+++ CONDA_SHLVL=0
+++ '[' -n x ']'
+++ '[' -n '' ']'
+++++ dirname /opt/conda/bin/conda
++++ dirname /opt/conda/bin
+++ PATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+++ export PATH
+++ '[' -z '' ']'
+++ PS1=
conda deactivate
++ conda deactivate
++ '[' 1 -lt 1 ']'
++ local cmd=deactivate
++ shift
++ case "$cmd" in
++ __conda_activate deactivate
++ '[' -n '' ']'
++ local cmd=deactivate
++ shift
++ local ask_conda
++ CONDA_INTERNAL_OLDPATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ __add_sys_prefix_to_path
++ '[' -n '' ']'
+++ dirname /opt/conda/bin/conda
++ SYSP=/opt/conda/bin
+++ dirname /opt/conda/bin
++ SYSP=/opt/conda
++ '[' -n '' ']'
++ PATH=/opt/conda/bin:/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export PATH
+++ PS1=
+++ /opt/conda/bin/conda shell.posix deactivate
++ ask_conda=
++ rc=0
++ PATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ eval ''
++ '[' 0 '!=' 0 ']'
++ __conda_hashr
++ '[' -n '' ']'
++ '[' -n '' ']'
++ hash -r
+ conda remove -y --force --name mango-build-ed197ed8-958c-46b8-b364-9e9263a9f3ce --all
+ '[' 6 -lt 1 ']'
+ local cmd=remove
+ shift
+ case "$cmd" in
+ CONDA_INTERNAL_OLDPATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/conda/bin/conda
+ SYSP=/opt/conda/bin
++ dirname /opt/conda/bin
+ SYSP=/opt/conda
+ '[' -n '' ']'
+ PATH=/opt/conda/bin:/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
+ /opt/conda/bin/conda remove -y --force --name mango-build-ed197ed8-958c-46b8-b364-9e9263a9f3ce --all
+ local t1=0
+ PATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ '[' 0 = 0 ']'
+ __conda_reactivate
+ local ask_conda
+ CONDA_INTERNAL_OLDPATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ __add_sys_prefix_to_path
+ '[' -n '' ']'
++ dirname /opt/conda/bin/conda
+ SYSP=/opt/conda/bin
++ dirname /opt/conda/bin
+ SYSP=/opt/conda
+ '[' -n '' ']'
+ PATH=/opt/conda/bin:/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
++ PS1=
++ /opt/conda/bin/conda shell.posix reactivate
+ ask_conda=
+ PATH=/opt/conda/condabin:/docker-java-home/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ eval ''
+ __conda_hashr
+ '[' -n '' ']'
+ '[' -n '' ']'
+ hash -r
+ rm -rf /tmp/mangoTest2PcnAhw/deleteMePleaseThisIsNoLongerNeeded
+ rm -rf /tmp/mangoTestMvn4dV6yrP
Build step 'Execute shell' marked build as failure
Finished: FAILURE