FailedConsole Output

Skipping 624 KB.. Full Log
park/examples/mllib/LinearRegressionWithSGDExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LogisticRegressionWithLBFGSExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MovieLensALS.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MulticlassMetricsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MultiLabelMetricsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MultivariateSummarizer.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/NaiveBayesExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/NormalizerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnRowMatrixExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnSourceVectorExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PMMLModelExportExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PowerIterationClusteringExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PrefixSpanExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestClassificationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomRDDGeneration.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RankingMetricsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RecommendationExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RegressionMetricsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SampledRDDs.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SimpleFPGrowth.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SparseNaiveBayes.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StandardScalerExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StratifiedSamplingExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingKMeansExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLinearRegressionExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLogisticRegression.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SummaryStatisticsExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SVDExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SVMWithSGDExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnyPCA.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnySVD.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TFIDFExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/Word2VecExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/MultiBroadcastTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/pythonconverters/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/pythonconverters/AvroConverters.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SimpleSkewedGroupByTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SkewedGroupByTest.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkALS.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkHdfsLR.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkKMeans.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkLR.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkPageRank.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkPi.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkTC.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/hive/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/hive/SparkHiveExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/RDDRelation.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/SparkSQLExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/SQLDataSourceExample.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredKafkaWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCountWindowed.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredSessionization.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedTypedAggregation.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedUntypedAggregation.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewGenerator.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewStream.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/CustomReceiver.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/DirectKafkaWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/HdfsWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/NetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/QueueStream.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/RawNetworkGrep.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/RecoverableNetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/SqlNetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/StatefulNetworkWordCount.scala
spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/StreamingExamples.scala
spark-2.3.3-bin-hadoop2.7/jars/
spark-2.3.3-bin-hadoop2.7/jars/activation-1.1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/aircompressor-0.8.jar
spark-2.3.3-bin-hadoop2.7/jars/antlr-2.7.7.jar
spark-2.3.3-bin-hadoop2.7/jars/antlr-runtime-3.4.jar
spark-2.3.3-bin-hadoop2.7/jars/antlr4-runtime-4.7.jar
spark-2.3.3-bin-hadoop2.7/jars/aopalliance-1.0.jar
spark-2.3.3-bin-hadoop2.7/jars/aopalliance-repackaged-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/apache-log4j-extras-1.2.17.jar
spark-2.3.3-bin-hadoop2.7/jars/apacheds-i18n-2.0.0-M15.jar
spark-2.3.3-bin-hadoop2.7/jars/apacheds-kerberos-codec-2.0.0-M15.jar
spark-2.3.3-bin-hadoop2.7/jars/api-asn1-api-1.0.0-M20.jar
spark-2.3.3-bin-hadoop2.7/jars/api-util-1.0.0-M20.jar
spark-2.3.3-bin-hadoop2.7/jars/arpack_combined_all-0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/arrow-format-0.8.0.jar
spark-2.3.3-bin-hadoop2.7/jars/arrow-memory-0.8.0.jar
spark-2.3.3-bin-hadoop2.7/jars/arrow-vector-0.8.0.jar
spark-2.3.3-bin-hadoop2.7/jars/automaton-1.11-8.jar
spark-2.3.3-bin-hadoop2.7/jars/avro-1.7.7.jar
spark-2.3.3-bin-hadoop2.7/jars/avro-ipc-1.7.7.jar
spark-2.3.3-bin-hadoop2.7/jars/avro-mapred-1.7.7-hadoop2.jar
spark-2.3.3-bin-hadoop2.7/jars/base64-2.3.8.jar
spark-2.3.3-bin-hadoop2.7/jars/bcprov-jdk15on-1.58.jar
spark-2.3.3-bin-hadoop2.7/jars/bonecp-0.8.0.RELEASE.jar
spark-2.3.3-bin-hadoop2.7/jars/breeze-macros_2.11-0.13.2.jar
spark-2.3.3-bin-hadoop2.7/jars/breeze_2.11-0.13.2.jar
spark-2.3.3-bin-hadoop2.7/jars/calcite-avatica-1.2.0-incubating.jar
spark-2.3.3-bin-hadoop2.7/jars/calcite-core-1.2.0-incubating.jar
spark-2.3.3-bin-hadoop2.7/jars/calcite-linq4j-1.2.0-incubating.jar
spark-2.3.3-bin-hadoop2.7/jars/chill-java-0.8.4.jar
spark-2.3.3-bin-hadoop2.7/jars/chill_2.11-0.8.4.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-beanutils-1.7.0.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-beanutils-core-1.8.0.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-cli-1.2.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-codec-1.10.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-collections-3.2.2.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-compiler-3.0.8.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-compress-1.4.1.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-configuration-1.6.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-crypto-1.0.0.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-dbcp-1.4.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-digester-1.8.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-httpclient-3.1.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-io-2.4.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-lang-2.6.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-lang3-3.5.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-logging-1.1.3.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-math3-3.4.1.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-net-2.2.jar
spark-2.3.3-bin-hadoop2.7/jars/commons-pool-1.5.4.jar
spark-2.3.3-bin-hadoop2.7/jars/compress-lzf-1.0.3.jar
spark-2.3.3-bin-hadoop2.7/jars/core-1.1.2.jar
spark-2.3.3-bin-hadoop2.7/jars/curator-client-2.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/curator-framework-2.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/curator-recipes-2.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/datanucleus-api-jdo-3.2.6.jar
spark-2.3.3-bin-hadoop2.7/jars/datanucleus-core-3.2.10.jar
spark-2.3.3-bin-hadoop2.7/jars/datanucleus-rdbms-3.2.9.jar
spark-2.3.3-bin-hadoop2.7/jars/derby-10.12.1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/eigenbase-properties-1.1.5.jar
spark-2.3.3-bin-hadoop2.7/jars/flatbuffers-1.2.0-3f79e055.jar
spark-2.3.3-bin-hadoop2.7/jars/generex-1.0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/gson-2.2.4.jar
spark-2.3.3-bin-hadoop2.7/jars/guava-14.0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/guice-3.0.jar
spark-2.3.3-bin-hadoop2.7/jars/guice-servlet-3.0.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-annotations-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-auth-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-client-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-common-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-hdfs-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-app-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-common-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-core-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-jobclient-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-shuffle-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-api-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-client-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-common-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-server-common-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-server-web-proxy-2.7.3.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-beeline-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-cli-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-exec-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-jdbc-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hive-metastore-1.2.1.spark2.jar
spark-2.3.3-bin-hadoop2.7/jars/hk2-api-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/hk2-locator-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/hk2-utils-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/hppc-0.7.2.jar
spark-2.3.3-bin-hadoop2.7/jars/htrace-core-3.1.0-incubating.jar
spark-2.3.3-bin-hadoop2.7/jars/httpclient-4.5.4.jar
spark-2.3.3-bin-hadoop2.7/jars/httpcore-4.4.8.jar
spark-2.3.3-bin-hadoop2.7/jars/ivy-2.4.0.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-annotations-2.6.7.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-core-2.6.7.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-core-asl-1.9.13.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-databind-2.6.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-dataformat-yaml-2.6.7.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-jaxrs-1.9.13.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-mapper-asl-1.9.13.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-module-jaxb-annotations-2.6.7.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-module-paranamer-2.7.9.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-module-scala_2.11-2.6.7.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jackson-xc-1.9.13.jar
spark-2.3.3-bin-hadoop2.7/jars/janino-3.0.8.jar
spark-2.3.3-bin-hadoop2.7/jars/java-xmlbuilder-1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/JavaEWAH-0.3.2.jar
spark-2.3.3-bin-hadoop2.7/jars/javassist-3.18.1-GA.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.annotation-api-1.2.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.inject-1.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.inject-2.4.0-b34.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.servlet-api-3.1.0.jar
spark-2.3.3-bin-hadoop2.7/jars/javax.ws.rs-api-2.0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/javolution-5.5.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jaxb-api-2.2.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jcl-over-slf4j-1.7.16.jar
spark-2.3.3-bin-hadoop2.7/jars/jdo-api-3.0.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-client-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-common-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-container-servlet-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-container-servlet-core-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-guava-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-media-jaxb-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jersey-server-2.22.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jets3t-0.9.4.jar
spark-2.3.3-bin-hadoop2.7/jars/jetty-6.1.26.jar
spark-2.3.3-bin-hadoop2.7/jars/jetty-util-6.1.26.jar
spark-2.3.3-bin-hadoop2.7/jars/jline-2.12.1.jar
spark-2.3.3-bin-hadoop2.7/jars/joda-time-2.9.3.jar
spark-2.3.3-bin-hadoop2.7/jars/jodd-core-3.5.2.jar
spark-2.3.3-bin-hadoop2.7/jars/jpam-1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/json4s-ast_2.11-3.2.11.jar
spark-2.3.3-bin-hadoop2.7/jars/json4s-core_2.11-3.2.11.jar
spark-2.3.3-bin-hadoop2.7/jars/json4s-jackson_2.11-3.2.11.jar
spark-2.3.3-bin-hadoop2.7/jars/jsp-api-2.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jsr305-1.3.9.jar
spark-2.3.3-bin-hadoop2.7/jars/jta-1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/jtransforms-2.4.0.jar
spark-2.3.3-bin-hadoop2.7/jars/jul-to-slf4j-1.7.16.jar
spark-2.3.3-bin-hadoop2.7/jars/kryo-shaded-3.0.3.jar
spark-2.3.3-bin-hadoop2.7/jars/kubernetes-client-3.0.0.jar
spark-2.3.3-bin-hadoop2.7/jars/kubernetes-model-2.0.0.jar
spark-2.3.3-bin-hadoop2.7/jars/leveldbjni-all-1.8.jar
spark-2.3.3-bin-hadoop2.7/jars/libfb303-0.9.3.jar
spark-2.3.3-bin-hadoop2.7/jars/libthrift-0.9.3.jar
spark-2.3.3-bin-hadoop2.7/jars/log4j-1.2.17.jar
spark-2.3.3-bin-hadoop2.7/jars/logging-interceptor-3.8.1.jar
spark-2.3.3-bin-hadoop2.7/jars/lz4-java-1.4.0.jar
spark-2.3.3-bin-hadoop2.7/jars/machinist_2.11-0.6.1.jar
spark-2.3.3-bin-hadoop2.7/jars/macro-compat_2.11-1.1.1.jar
spark-2.3.3-bin-hadoop2.7/jars/mesos-1.4.0-shaded-protobuf.jar
spark-2.3.3-bin-hadoop2.7/jars/metrics-core-3.1.5.jar
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spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/c=0/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/c=0/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=0/c=0/part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/c=1/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/c=1/.part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/orc_partitioned/b=1/c=1/part-r-00000-829af031-b970-49d6-ad39-30460a0be2c8.orc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/_common_metadata
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/_metadata
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/_SUCCESS
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/.part-r-00008.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2014/month=9/day=1/part-r-00008.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/.part-r-00002.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/.part-r-00004.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/part-r-00002.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=25/part-r-00004.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/.part-r-00005.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=10/day=26/part-r-00005.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/.part-r-00007.gz.parquet.crc
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/part-r-00007.gz.parquet
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/people.json
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/people1.json
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/people_array.json
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/streaming/
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/streaming/text-test.txt
spark-2.3.3-bin-hadoop2.7/python/test_support/sql/text-test.txt
spark-2.3.3-bin-hadoop2.7/python/test_support/userlib-0.1.zip
spark-2.3.3-bin-hadoop2.7/python/test_support/userlibrary.py
spark-2.3.3-bin-hadoop2.7/R/
spark-2.3.3-bin-hadoop2.7/R/lib/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/DESCRIPTION
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/index.html
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/sparkr-vignettes.html
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/sparkr-vignettes.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/sparkr-vignettes.Rmd
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/aliases.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/AnIndex
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/paths.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdb
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdx
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/html/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/html/00Index.html
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/html/R.css
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/INDEX
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/features.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/hsearch.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/links.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/nsInfo.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/package.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/Rd.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/vignette.rds
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/NAMESPACE
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/profile/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/profile/general.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/profile/shell.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/SparkR
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdb
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdx
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/tests/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/tests/testthat/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/tests/testthat/test_basic.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/worker/
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/worker/daemon.R
spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/worker/worker.R
spark-2.3.3-bin-hadoop2.7/R/lib/sparkr.zip
spark-2.3.3-bin-hadoop2.7/README.md
spark-2.3.3-bin-hadoop2.7/RELEASE
spark-2.3.3-bin-hadoop2.7/sbin/
spark-2.3.3-bin-hadoop2.7/sbin/slaves.sh
spark-2.3.3-bin-hadoop2.7/sbin/spark-config.sh
spark-2.3.3-bin-hadoop2.7/sbin/spark-daemon.sh
spark-2.3.3-bin-hadoop2.7/sbin/spark-daemons.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-all.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-history-server.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-master.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-mesos-dispatcher.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-mesos-shuffle-service.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-shuffle-service.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-slave.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-slaves.sh
spark-2.3.3-bin-hadoop2.7/sbin/start-thriftserver.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-all.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-history-server.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-master.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-mesos-dispatcher.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-mesos-shuffle-service.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-shuffle-service.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-slave.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-slaves.sh
spark-2.3.3-bin-hadoop2.7/sbin/stop-thriftserver.sh
spark-2.3.3-bin-hadoop2.7/yarn/
spark-2.3.3-bin-hadoop2.7/yarn/spark-2.3.3-yarn-shuffle.jar
+ export SPARK_HOME=/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7
+ SPARK_HOME=/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7
ls -1 "${SPARK_HOME}/python/lib" | grep py4j
++ ls -1 /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python/lib
++ grep py4j
+ PY4J_ZIP=py4j-0.10.7-src.zip
+ export PYTHONPATH=/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python:/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip:
+ PYTHONPATH=/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python:/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip:
+ ASSEMBLY_DIR=/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target
ls -1 "$ASSEMBLY_DIR" | grep "^mango-assembly[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true
++ ls -1 /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target
++ grep '^mango-assembly[0-9A-Za-z\_\.-]*\.jar$'
++ grep -v javadoc
++ grep -v sources
+ ASSEMBLY_JAR=mango-assembly-0.0.3-SNAPSHOT.jar
+ export 'PYSPARK_SUBMIT_ARGS=--jars /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar --driver-class-path /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar pyspark-shell'
+ PYSPARK_SUBMIT_ARGS='--jars /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar --driver-class-path /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar pyspark-shell'
+ pythons=(2.7 3.6)
+ for python in '${pythons[*]}'
uuidgen
++ uuidgen
+ uuid=8732a22c-7259-449a-a9e7-536587529ab9
+ conda create -y -q -n mango-build-8732a22c-7259-449a-a9e7-536587529ab9 python=2.7


Package plan for installation in environment /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9:

The following NEW packages will be INSTALLED:

    ca-certificates: 2019.1.23-0            
    certifi:         2019.3.9-py27_0        
    libedit:         3.1.20181209-hc058e9b_0
    libffi:          3.2.1-hd88cf55_4       
    libgcc-ng:       8.2.0-hdf63c60_1       
    libstdcxx-ng:    8.2.0-hdf63c60_1       
    ncurses:         6.1-he6710b0_1         
    openssl:         1.1.1b-h7b6447c_1      
    pip:             19.1.1-py27_0          
    python:          2.7.16-h9bab390_0      
    readline:        7.0-h7b6447c_5         
    setuptools:      41.0.1-py27_0          
    sqlite:          3.28.0-h7b6447c_0      
    tk:              8.6.8-hbc83047_0       
    wheel:           0.33.2-py27_0          
    zlib:            1.2.11-h7b6447c_3      


+ source activate mango-build-8732a22c-7259-449a-a9e7-536587529ab9
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ _SCRIPT_LOCATION=/home/anaconda/bin/activate
++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
+++ dirname /home/anaconda/bin/activate
++ _CONDA_DIR=/home/anaconda/bin

if [ $# -gt 1 ]; then
    (>&2 echo "Error: did not expect more than one argument.")
    (>&2 echo "    (Got $@)")
    return 1
fi
++ '[' 1 -gt 1 ']'

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        # ignore any windows backup paths from bat-based activation
        if [ "${CONDA_PATH_BACKUP:0:1}" != "/"  ]; then
           unset CONDA_PATH_BACKUP
        fi
        export _CONDA_PYTHON="$_CONDA_DIR/../python"
        ;;
    *)
        EXT=""
        export _CONDA_PYTHON="$_CONDA_DIR/python"
        ;;
esac
++ case "$(uname -s)" in
uname -s
+++ uname -s
++ EXT=
++ export _CONDA_PYTHON=/home/anaconda/bin/python
++ _CONDA_PYTHON=/home/anaconda/bin/python

# Ensure that this script is sourced, not executed
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "activate" ]]; then
    (>&2 echo "Error: activate must be sourced. Run 'source activate envname'
instead of 'activate envname'.
")
    "$_CONDA_DIR/conda" ..activate $_SHELL$EXT -h
    exit 1
fi
++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
+++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test
++ [[ jenkins-test == \a\c\t\i\v\a\t\e ]]

if [ "$#" -eq "0" ]; then
    args=('root')
else
    args=$@
fi
++ '[' 1 -eq 0 ']'
++ args=mango-build-8732a22c-7259-449a-a9e7-536587529ab9

"$_CONDA_DIR/conda" ..checkenv $_SHELL$EXT "$args"
++ /home/anaconda/bin/conda ..checkenv bash mango-build-8732a22c-7259-449a-a9e7-536587529ab9
if (( $? != 0 )); then
    return 1
fi
++ ((  0 != 0  ))

# Ensure we deactivate any scripts from the old env
_CONDA_HOLD=true
++ _CONDA_HOLD=true
source "$_CONDA_DIR/deactivate"
++ source /home/anaconda/bin/deactivate
#!/bin/bash

# Determine the directory containing this script
if [[ -n $BASH_VERSION ]]; then
    _SCRIPT_LOCATION=${BASH_SOURCE[0]}
    _SHELL="bash"
elif [[ -n $ZSH_VERSION ]]; then
    _SCRIPT_LOCATION=${funcstack[1]}
    _SHELL="zsh"
else
    echo "Only bash and zsh are supported"
    return 1
fi
+++ [[ -n 4.3.48(1)-release ]]
+++ _SCRIPT_LOCATION=/home/anaconda/bin/deactivate
+++ _SHELL=bash
_CONDA_DIR=$(dirname "$_SCRIPT_LOCATION")
dirname "$_SCRIPT_LOCATION"
++++ dirname /home/anaconda/bin/deactivate
+++ _CONDA_DIR=/home/anaconda/bin

case "$(uname -s)" in
    CYGWIN*|MINGW*|MSYS*)
        EXT=".exe"
        export MSYS2_ENV_CONV_EXCL=CONDA_PATH
        ;;
    *)
        EXT=""
        ;;
esac
+++ case "$(uname -s)" in
uname -s
++++ uname -s
+++ EXT=

# shift over all args.  We don't accept any, so it's OK that we ignore them all here.
while [[ $# > 0 ]]
do
    key="$1"
    case $key in
        -h|--help)
            "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
            if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
                exit 0
            else
                return 0
            fi
            ;;
    esac
    shift # past argument or value
done
+++ [[ 1 > 0 ]]
+++ key=mango-build-8732a22c-7259-449a-a9e7-536587529ab9
+++ case $key in
+++ shift
+++ [[ 0 > 0 ]]

# Ensure that this script is sourced, not executed
# Note that if the script was executed, we're running inside bash!
# Also note that errors are ignored as `activate foo` doesn't generate a bad
# value for $0 which would cause errors.
if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
    (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate'
instead of 'deactivate'.
")
    "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h
    exit 1
fi
+++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
++++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test
+++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]

if [[ -z "$CONDA_PATH_BACKUP" ]]; then
    if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then
        exit 0
    else
        return 0
    fi
fi
+++ [[ -z '' ]]
+++ [[ -n 4.3.48(1)-release ]]
basename "$0" 2> /dev/null
++++ basename /home/jenkins/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test
+++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]]
+++ return 0
unset _CONDA_HOLD
++ unset _CONDA_HOLD

_NEW_PART=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$args")
"$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$args"
+++ /home/anaconda/bin/conda ..activate bash mango-build-8732a22c-7259-449a-a9e7-536587529ab9
++ _NEW_PART=/home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/bin
if (( $? == 0 )); then
    export CONDA_PATH_BACKUP="$PATH"
    # export this to restore it upon deactivation
    export CONDA_PS1_BACKUP="$PS1"

    # look if the deactivate script left a placeholder for us
    if [[ $PATH == *"CONDA_PATH_PLACEHOLDER"* ]]; then
        # If it did, replace it with our _NEW_PART
        export PATH="$($_CONDA_PYTHON -c "import re; print(re.sub(r'CONDA_PATH_PLACEHOLDER', r'$_NEW_PART', '$PATH', 1))")"
    else
        export PATH="$_NEW_PART:$PATH"
    fi

    # CONDA_DEFAULT_ENV is the shortest representation of how conda recognizes your env.
    #    It can be an env name, or a full path.
    #    Last date of change: 2016-06-21
    # If the string contains / it's a path
    if [[ "$@" == */* ]]; then
        export CONDA_DEFAULT_ENV=$(get_abs_filename "$args")
    else
        export CONDA_DEFAULT_ENV="$args"
    fi
    # CONDA_PREFIX is always the full path to the activated environment.  It is not set
    #    when no environment is active.
    # Legacy support: CONDA_DEFAULT_ENV is either env name or full path if given as path.
    #    CONDA_PREFIX is always the full path, for consistency.
    #    Last date of change: 2016-06-21
    firstpath=${_NEW_PART%%:*}
    export CONDA_PREFIX="$(echo ${firstpath} | sed "s|/bin$||")" &>/dev/null

    # if CONDA_DEFAULT_ENV not in PS1, prepend it with parentheses
    if [ $("$_CONDA_DIR/conda" ..changeps1) = "1" ]; then
        if ! $(grep -q CONDA_DEFAULT_ENV <<<$PS1); then
            if ! $(grep -q "POWERLINE" <<<$PS1); then
                export PS1="(${CONDA_DEFAULT_ENV}) $PS1"
            fi
        fi
    fi

    # Load any of the scripts found $PREFIX/etc/conda/activate.d AFTER activation
    _CONDA_D="${CONDA_PREFIX}/etc/conda/activate.d"
    if [[ -d "$_CONDA_D" ]]; then
        eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;)
    fi
    unset _CONDA_PYTHON
else
    unset _CONDA_PYTHON
    return $?
fi
++ ((  0 == 0  ))
++ export CONDA_PATH_BACKUP=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ CONDA_PATH_BACKUP=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ export CONDA_PS1_BACKUP=
++ CONDA_PS1_BACKUP=
++ [[ /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games == *\C\O\N\D\A\_\P\A\T\H\_\P\L\A\C\E\H\O\L\D\E\R* ]]
++ export PATH=/home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ PATH=/home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
++ [[ '' == */* ]]
++ export CONDA_DEFAULT_ENV=mango-build-8732a22c-7259-449a-a9e7-536587529ab9
++ CONDA_DEFAULT_ENV=mango-build-8732a22c-7259-449a-a9e7-536587529ab9
++ firstpath=/home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/bin
echo ${firstpath} | sed "s|/bin$||"
+++ echo /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9
"$_CONDA_DIR/conda" ..changeps1
+++ /home/anaconda/bin/conda ..changeps1
++ '[' 1 = 1 ']'
grep -q CONDA_DEFAULT_ENV <<<$PS1
+++ grep -q CONDA_DEFAULT_ENV
grep -q "POWERLINE" <<<$PS1
+++ grep -q POWERLINE
++ export 'PS1=(mango-build-8732a22c-7259-449a-a9e7-536587529ab9) '
++ PS1='(mango-build-8732a22c-7259-449a-a9e7-536587529ab9) '
++ _CONDA_D=/home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/etc/conda/activate.d
++ [[ -d /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/etc/conda/activate.d ]]
++ unset _CONDA_PYTHON

unset CONDA_PATH
++ unset CONDA_PATH

if [[ -n $BASH_VERSION ]]; then
    hash -r
elif [[ -n $ZSH_VERSION ]]; then
    rehash
else
    echo "Only bash and zsh are supported"
    return 1
fi
++ [[ -n 4.3.48(1)-release ]]
++ hash -r
+ conda install -y nodejs
Fetching package metadata ...........
Solving package specifications: .

Package plan for installation in environment /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9:

The following NEW packages will be INSTALLED:

    nodejs: 10.13.0-he6710b0_0

+ pushd mango-python
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ make prepare
pip install pytest==3.9.1
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting pytest==3.9.1
  Using cached https://files.pythonhosted.org/packages/bf/14/a16e1ac03aeb9776d98374bb76495a6623d56dff0f7b815ed5a1e04d893e/pytest-3.9.1-py2.py3-none-any.whl
Collecting atomicwrites>=1.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/52/90/6155aa926f43f2b2a22b01be7241be3bfd1ceaf7d0b3267213e8127d41f4/atomicwrites-1.3.0-py2.py3-none-any.whl
Collecting more-itertools>=4.0.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/2f/9d/dcfe59e213093695f108508af1214cf9cd95cc5489e46877ec5cb56369e5/more_itertools-5.0.0-py2-none-any.whl
Collecting pluggy>=0.7 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/cc/e4/2003a5e4e445424602c8f06a436eeed9e78bcae4947128f64741c66c7216/pluggy-0.11.0-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from pytest==3.9.1) (41.0.1)
Collecting attrs>=17.4.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/23/96/d828354fa2dbdf216eaa7b7de0db692f12c234f7ef888cc14980ef40d1d2/attrs-19.1.0-py2.py3-none-any.whl
Collecting pathlib2>=2.2.0; python_version < "3.6" (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/2a/46/c696dcf1c7aad917b39b875acdc5451975e3a9b4890dca8329983201c97a/pathlib2-2.3.3-py2.py3-none-any.whl
Collecting py>=1.5.0 (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/76/bc/394ad449851729244a97857ee14d7cba61ddb268dce3db538ba2f2ba1f0f/py-1.8.0-py2.py3-none-any.whl
Requirement already satisfied: six>=1.10.0 in /home/jenkins/.local/lib/python2.7/site-packages (from pytest==3.9.1) (1.11.0)
Collecting funcsigs; python_version < "3.0" (from pytest==3.9.1)
  Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl
Collecting scandir; python_version < "3.5" (from pathlib2>=2.2.0; python_version < "3.6"->pytest==3.9.1)
Installing collected packages: atomicwrites, more-itertools, pluggy, attrs, scandir, pathlib2, py, funcsigs, pytest
Successfully installed atomicwrites-1.3.0 attrs-19.1.0 funcsigs-1.0.2 more-itertools-5.0.0 pathlib2-2.3.3 pluggy-0.11.0 py-1.8.0 pytest-3.9.1 scandir-1.10.0
# ipython version required for python 2.7
pip install jupyter_contrib_nbextensions
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting jupyter_contrib_nbextensions
  Using cached https://files.pythonhosted.org/packages/33/f0/6e2c00afda860f655fbf0f795f7310bdbf12122846344dfdc803fc7455d5/jupyter_contrib_nbextensions-0.5.1-py2.py3-none-any.whl
Collecting notebook>=4.0 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/f6/36/89ebfffc9dd8c8dbd81c1ffb53e3d4233ee666414c143959477cb07cc5f5/notebook-5.7.8-py2.py3-none-any.whl
Collecting traitlets>=4.1 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/93/d6/abcb22de61d78e2fc3959c964628a5771e47e7cc60d53e9342e21ed6cc9a/traitlets-4.3.2-py2.py3-none-any.whl
Collecting ipython-genutils (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl
Collecting nbconvert>=4.2 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/35/e7/f46c9d65f149271e47fca6ab084ef5c6e4cb1870f4c5cce6690feac55231/nbconvert-5.5.0-py2.py3-none-any.whl
Collecting pyyaml (from jupyter_contrib_nbextensions)
Collecting jupyter-latex-envs>=1.3.8 (from jupyter_contrib_nbextensions)
Collecting jupyter-core (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/1d/44/065d2d7bae7bebc06f1dd70d23c36da8c50c0f08b4236716743d706762a8/jupyter_core-4.4.0-py2.py3-none-any.whl
Collecting lxml (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/89/51/a8a6cdb8a084d32dbc9bda94623dc35310ae2002be57de8702a1703c0026/lxml-4.3.3-cp27-cp27mu-manylinux1_x86_64.whl
Collecting tornado (from jupyter_contrib_nbextensions)
Collecting jupyter-contrib-core>=0.3.3 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/e6/8f/04a752a8b66a66e7092c035e5d87d2502ac7ec07f9fb6059059b6c0dc272/jupyter_contrib_core-0.3.3-py2.py3-none-any.whl
Collecting jupyter-nbextensions-configurator>=0.4.0 (from jupyter_contrib_nbextensions)
Collecting jupyter-highlight-selected-word>=0.1.1 (from jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/50/d7/19ab7cfd60bf268d2abbacc52d4295a40f52d74dfc0d938e4761ee5e598b/jupyter_highlight_selected_word-0.2.0-py2.py3-none-any.whl
Collecting jupyter-client>=5.2.0 (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/3b/c3/3043fe9ffd140d03c9d091a056794ccdc427c56ec19b8eea74f9ea0a498f/jupyter_client-5.2.4-py2.py3-none-any.whl
Collecting nbformat (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/da/27/9a654d2b6cc1eaa517d1c5a4405166c7f6d72f04f6e7eea41855fe808a46/nbformat-4.4.0-py2.py3-none-any.whl
Collecting terminado>=0.8.1 (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/a7/56/80ea7fa66565fa75ae21ce0c16bc90067530e5d15e48854afcc86585a391/terminado-0.8.2-py2.py3-none-any.whl
Collecting Send2Trash (from notebook>=4.0->jupyter_contrib_nbextensions)
Collecting pyzmq>=17 (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/91/f5/c9bef3768d6f8d71aae8f44f1ddbee90162dad909560fa6c13e4872e28c9/pyzmq-18.0.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting prometheus-client (from notebook>=4.0->jupyter_contrib_nbextensions)
Collecting jinja2 (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl
Collecting ipykernel (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/00/47/764e4fa1b1b89598426b8d79b1c4fbe8042432621b0f8e1991aeb3c24806/ipykernel-4.10.0-py2-none-any.whl
Collecting ipaddress; python_version == "2.7" (from notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl
Collecting enum34; python_version == "2.7" (from traitlets>=4.1->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl
Requirement already satisfied: six in /home/jenkins/.local/lib/python2.7/site-packages (from traitlets>=4.1->jupyter_contrib_nbextensions) (1.11.0)
Collecting decorator (from traitlets>=4.1->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl
Collecting entrypoints>=0.2.2 (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl
Collecting pandocfilters>=1.4.1 (from nbconvert>=4.2->jupyter_contrib_nbextensions)
Collecting pygments (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/6e/00/c5cb5fc7c047da4af049005d0146b3a961b1a25d9cefbbe24bf0882a11ad/Pygments-2.4.0-py2.py3-none-any.whl
Collecting bleach (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/ab/05/27e1466475e816d3001efb6e0a85a819be17411420494a1e602c36f8299d/bleach-3.1.0-py2.py3-none-any.whl
Collecting testpath (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/be/a4/162f9ebb6489421fe46dcca2ae420369edfee4b563c668d93cb4605d12ba/testpath-0.4.2-py2.py3-none-any.whl
Collecting defusedxml (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/06/74/9b387472866358ebc08732de3da6dc48e44b0aacd2ddaa5cb85ab7e986a2/defusedxml-0.6.0-py2.py3-none-any.whl
Collecting mistune>=0.8.1 (from nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl
Collecting ipython (from jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/b0/88/d996ab8be22cea1eaa18baee3678a11265e18cf09974728d683c51102148/ipython-5.8.0-py2-none-any.whl
Requirement already satisfied: futures in /home/jenkins/.local/lib/python2.7/site-packages (from tornado->jupyter_contrib_nbextensions) (3.2.0)
Collecting singledispatch (from tornado->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/c5/10/369f50bcd4621b263927b0a1519987a04383d4a98fb10438042ad410cf88/singledispatch-3.4.0.3-py2.py3-none-any.whl
Collecting backports-abc>=0.4 (from tornado->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/7d/56/6f3ac1b816d0cd8994e83d0c4e55bc64567532f7dc543378bd87f81cebc7/backports_abc-0.5-py2.py3-none-any.whl
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jupyter-contrib-core>=0.3.3->jupyter_contrib_nbextensions) (41.0.1)
Requirement already satisfied: python-dateutil>=2.1 in /home/jenkins/.local/lib/python2.7/site-packages (from jupyter-client>=5.2.0->notebook>=4.0->jupyter_contrib_nbextensions) (2.7.4)
Collecting jsonschema!=2.5.0,>=2.4 (from nbformat->notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/aa/69/df679dfbdd051568b53c38ec8152a3ab6bc533434fc7ed11ab034bf5e82f/jsonschema-3.0.1-py2.py3-none-any.whl
Collecting ptyprocess; os_name != "nt" (from terminado>=0.8.1->notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from jinja2->notebook>=4.0->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/fb/40/f3adb7cf24a8012813c5edb20329eb22d5d8e2a0ecf73d21d6b85865da11/MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl
Collecting configparser>=3.5; python_version == "2.7" (from entrypoints>=0.2.2->nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/ba/05/6c96328e92e625fc31445d24d75a2c92ef9ba34fc5b037fe69693c362a0d/configparser-3.7.4-py2.py3-none-any.whl
Collecting webencodings (from bleach->nbconvert>=4.2->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (2.3.3)
Collecting backports.shutil-get-terminal-size; python_version == "2.7" (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/7d/cd/1750d6c35fe86d35f8562091737907f234b78fdffab42b29c72b1dd861f4/backports.shutil_get_terminal_size-1.0.0-py2.py3-none-any.whl
Collecting simplegeneric>0.8 (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
Collecting pexpect; sys_platform != "win32" (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/0e/3e/377007e3f36ec42f1b84ec322ee12141a9e10d808312e5738f52f80a232c/pexpect-4.7.0-py2.py3-none-any.whl
Collecting prompt-toolkit<2.0.0,>=1.0.4 (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/4e/4e/e5545e8bebf89790455b31112a0f886580c7b3624a05abec416efa5c3a08/prompt_toolkit-1.0.16-py2-none-any.whl
Collecting pickleshare (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl
Collecting functools32; python_version < "3" (from jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions)
Collecting pyrsistent>=0.14.0 (from jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->notebook>=4.0->jupyter_contrib_nbextensions) (19.1.0)
Requirement already satisfied: scandir; python_version < "3.5" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (1.10.0)
Collecting wcwidth (from prompt-toolkit<2.0.0,>=1.0.4->ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions)
  Using cached https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl
Installing collected packages: enum34, ipython-genutils, decorator, traitlets, pyzmq, jupyter-core, singledispatch, backports-abc, tornado, jupyter-client, functools32, pyrsistent, jsonschema, nbformat, ptyprocess, terminado, Send2Trash, configparser, entrypoints, pandocfilters, MarkupSafe, jinja2, pygments, webencodings, bleach, testpath, defusedxml, mistune, nbconvert, prometheus-client, backports.shutil-get-terminal-size, simplegeneric, pexpect, wcwidth, prompt-toolkit, pickleshare, ipython, ipykernel, ipaddress, notebook, pyyaml, jupyter-latex-envs, lxml, jupyter-contrib-core, jupyter-nbextensions-configurator, jupyter-highlight-selected-word, jupyter-contrib-nbextensions
Successfully installed MarkupSafe-1.1.1 Send2Trash-1.5.0 backports-abc-0.5 backports.shutil-get-terminal-size-1.0.0 bleach-3.1.0 configparser-3.7.4 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 enum34-1.1.6 functools32-3.2.3.post2 ipaddress-1.0.22 ipykernel-4.10.0 ipython-5.8.0 ipython-genutils-0.2.0 jinja2-2.10.1 jsonschema-3.0.1 jupyter-client-5.2.4 jupyter-contrib-core-0.3.3 jupyter-contrib-nbextensions-0.5.1 jupyter-core-4.4.0 jupyter-highlight-selected-word-0.2.0 jupyter-latex-envs-1.4.6 jupyter-nbextensions-configurator-0.4.1 lxml-4.3.3 mistune-0.8.4 nbconvert-5.5.0 nbformat-4.4.0 notebook-5.7.8 pandocfilters-1.4.2 pexpect-4.7.0 pickleshare-0.7.5 prometheus-client-0.6.0 prompt-toolkit-1.0.16 ptyprocess-0.6.0 pygments-2.4.0 pyrsistent-0.15.1 pyyaml-5.1 pyzmq-18.0.1 simplegeneric-0.8.1 singledispatch-3.4.0.3 terminado-0.8.2 testpath-0.4.2 tornado-5.1.1 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1
pip install -r requirements.txt
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Collecting cigar==0.1.3 (from -r requirements.txt (line 1))
Collecting matplotlib==2.0.2 (from -r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/2c/69/362c0a5eca37225c7d451e6c57f07c4fee85a5b6cb3aedf16fe649f411ea/matplotlib-2.0.2-cp27-cp27mu-manylinux1_x86_64.whl
Collecting ipython==5.5.0 (from -r requirements.txt (line 3))
  Using cached https://files.pythonhosted.org/packages/08/2c/6285504003b4eadce5540f3ee3adc081468b26723f3eef07d9d5d7d97ed8/ipython-5.5.0-py2-none-any.whl
Collecting jupyter==1.0.0 (from -r requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl
Collecting bdgenomics.mango.pileup==0.0.2a0 (from -r requirements.txt (line 5))
Collecting bdgenomics.adam==0.26.0 (from -r requirements.txt (line 6))
Collecting ipywidgets==7.0.0 (from -r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/14/ea/793f6588d5be295d103fb868e26ba8671686b70bd855a21d02302f8dcd37/ipywidgets-7.0.0-py2.py3-none-any.whl
Collecting psutil (from -r requirements.txt (line 8))
Collecting subprocess32 (from matplotlib==2.0.2->-r requirements.txt (line 2))
Collecting cycler>=0.10 (from matplotlib==2.0.2->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl
Requirement already satisfied: functools32 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (3.2.3.post2)
Requirement already satisfied: six>=1.10 in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.11.0)
Requirement already satisfied: pytz in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2018.9)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib==2.0.2->-r requirements.txt (line 2))
  Using cached https://files.pythonhosted.org/packages/dd/d9/3ec19e966301a6e25769976999bd7bbe552016f0d32b577dc9d63d2e0c49/pyparsing-2.4.0-py2.py3-none-any.whl
Requirement already satisfied: numpy>=1.7.1 in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.15.3)
Requirement already satisfied: python-dateutil in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.7.4)
Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (2.3.3)
Requirement already satisfied: traitlets>=4.2 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (4.3.2)
Requirement already satisfied: backports.shutil-get-terminal-size; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (1.0.0)
Requirement already satisfied: simplegeneric>0.8 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (0.8.1)
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (2.4.0)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (4.7.0)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (41.0.1)
Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (1.0.16)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (0.7.5)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (4.4.0)
Collecting qtconsole (from jupyter==1.0.0->-r requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/c7/45/1a50288305797fbca7c2039f9baefff1a9df603322874743fbb8408d8ec2/qtconsole-4.4.4-py2.py3-none-any.whl
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.7.8)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.5.0)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (4.10.0)
Collecting jupyter-console (from jupyter==1.0.0->-r requirements.txt (line 4))
  Using cached https://files.pythonhosted.org/packages/77/82/6469cd7fccf7958cbe5dce2e623f1e3c5e27f1bb1ad36d90519bc2d5d370/jupyter_console-5.2.0-py2.py3-none-any.whl
Requirement already satisfied: pyspark>=1.6.0 in /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python (from bdgenomics.adam==0.26.0->-r requirements.txt (line 6)) (2.3.3)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 7)) (4.4.0)
Collecting widgetsnbextension~=3.0.0 (from ipywidgets==7.0.0->-r requirements.txt (line 7))
  Using cached https://files.pythonhosted.org/packages/8d/f2/c8bcccccbed39d51d3e237fb0c0f0c9bbc845d12afc41f5ca5f5728fffc7/widgetsnbextension-3.0.8-py2.py3-none-any.whl
Requirement already satisfied: scandir; python_version < "3.5" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython==5.5.0->-r requirements.txt (line 3)) (1.10.0)
Requirement already satisfied: enum34; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->-r requirements.txt (line 3)) (1.1.6)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->-r requirements.txt (line 3)) (0.2.0)
Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from pexpect; sys_platform != "win32"->ipython==5.5.0->-r requirements.txt (line 3)) (0.6.0)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython==5.5.0->-r requirements.txt (line 3)) (0.1.7)
Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (4.4.0)
Requirement already satisfied: jupyter-client>=4.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (5.2.4)
Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.2)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.6.0)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.5.0)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (18.0.1)
Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (2.10.1)
Requirement already satisfied: tornado<7,>=4.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (5.1.1)
Requirement already satisfied: ipaddress; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.0.22)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.3)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.4.2)
Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.1.0)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.4.2)
Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.6.0)
Requirement already satisfied: mistune>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.4)
Collecting py4j==0.10.7 (from pyspark>=1.6.0->bdgenomics.adam==0.26.0->-r requirements.txt (line 6))
  Using cached https://files.pythonhosted.org/packages/e3/53/c737818eb9a7dc32a7cd4f1396e787bd94200c3997c72c1dbe028587bd76/py4j-0.10.7-py2.py3-none-any.whl
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (3.0.1)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jinja2->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.1.1)
Requirement already satisfied: futures in /home/jenkins/.local/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (3.2.0)
Requirement already satisfied: singledispatch in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (3.4.0.3)
Requirement already satisfied: backports-abc>=0.4 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5)
Requirement already satisfied: configparser>=3.5; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from entrypoints>=0.2.2->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.7.4)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5.1)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (0.15.1)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (19.1.0)
Installing collected packages: cigar, subprocess32, cycler, pyparsing, matplotlib, ipython, qtconsole, widgetsnbextension, ipywidgets, jupyter-console, jupyter, bdgenomics.mango.pileup, bdgenomics.adam, psutil, py4j
  Found existing installation: ipython 5.8.0
    Uninstalling ipython-5.8.0:
      Successfully uninstalled ipython-5.8.0
Successfully installed bdgenomics.adam-0.26.0 bdgenomics.mango.pileup-0.0.2a0 cigar-0.1.3 cycler-0.10.0 ipython-5.5.0 ipywidgets-7.0.0 jupyter-1.0.0 jupyter-console-5.2.0 matplotlib-2.0.2 psutil-5.6.2 py4j-0.10.7 pyparsing-2.4.0 qtconsole-4.4.4 subprocess32-3.5.3 widgetsnbextension-3.0.8
+ popd
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu
+ mvn -U -P python,distribution package -DskipTests -Dhadoop.version=2.7.5 -Dspark.version=2.3.3
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-python:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-python:[unknown-version], /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-python/pom.xml, line 21, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-cli:[unknown-version], /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-cli/pom.xml, line 39, column 15
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] mango
[INFO] mango: CORE
[INFO] Mango: Python APIs
[INFO] mango: CLI
[INFO] Mango: Assembly
[INFO] mango: Distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent ---
[INFO] Modified 144 of 218 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-parent ---
[INFO] Replacing original artifact with shaded artifact.
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building mango: CORE 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml
Downloading: https://repository.apache.org/snapshots/commons-codec/commons-codec/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/repositories/snapshots/commons-codec/commons-codec/maven-metadata.xml
672/672 B   
            
Downloaded: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml (672 B at 2.2 KB/sec)
            
            
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core ---
[INFO] Modified 0 of 22 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.0.1 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala:-1: info: compiling
[INFO] Compiling 12 source files to /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/scala-2.11.12/classes at 1557576734270
[WARNING] /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:69: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class AlignmentRecordMaterialization(@transient sc: SparkContext,
[WARNING]                                       ^
[WARNING] /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:48: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class FeatureMaterialization(@transient sc: SparkContext,
[WARNING]                               ^
[WARNING] /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:56: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING]                                                              @transient sc: SparkContext,
[WARNING]                                                               ^
[WARNING] /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:45: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class VariantContextMaterialization(@transient sc: SparkContext,
[WARNING]                                      ^
[WARNING] /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
[WARNING]     try {
[WARNING]     ^
[WARNING] warning: there was one deprecation warning; re-run with -deprecation for details
[WARNING] warning: there were four feature warnings; re-run with -feature for details
[WARNING] 7 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-core ---
[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-core ---
[INFO] Test Source directory: /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.0.1 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala:-1: info: compiling
[INFO] Compiling 10 source files to /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/scala-2.11.12/test-classes at 1557576744207
[WARNING] /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala/org/bdgenomics/mango/models/LazyMaterializationSuite.scala:77: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
[WARNING] class LazyDummy(@transient sc: SparkContext,
[WARNING]                  ^
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-core ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-core ---
[INFO] Building jar: /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-core ---
[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 com.github.samtools:htsjdk:jar:2.16.1 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 org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including net.liftweb:lift-json_2.11:jar:3.0.1 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.7 in the shaded jar.
[INFO] Including org.scala-lang:scalap:jar:2.11.7 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.slf4j:slf4j-api:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.curator:curator-client:jar:2.7.1 in the shaded jar.
[INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar.
[INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar.
[INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar.
[INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0 in the shaded jar.
[INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar.
[INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar.
[INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar.
[INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar.
[INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar.
[INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar.
[INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar.
[INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar.
[INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar.
[INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar.
[INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar.
[INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar.
[INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar.
[INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar.
[INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar.
[INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar.
[INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar.
[INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar.
[INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar.
[INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar.
[INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar.
[INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar.
[INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar.
[INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar.
[INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar.
[INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar.
[INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar.
[INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar.
[INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar.
[INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar.
[INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar.
[INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar.
[INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar.
[INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar.
[INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar.
[INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar.
[INFO] Including oro:oro:jar:2.0.8 in the shaded jar.
[INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar.
[INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar.
[INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.26.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.26.0 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 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.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 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:0.26.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.15.v20190215 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar.
[INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.2 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.clapper:grizzled-slf4j_2.11:jar:1.0.2 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.scalatra.scalate:scalate-core_2.11:jar:1.8.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-compiler:jar:2.11.8 in the shaded jar.
[INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.8.0 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.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:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar.
[INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar.
[WARNING] minlog-1.2.jar, minlog-1.3.0.jar define 2 overlapping classes: 
[WARNING]   - com.esotericsoftware.minlog.Log
[WARNING]   - com.esotericsoftware.minlog.Log$Logger
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] aopalliance-1.0.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: 
[WARNING]   - org.aopalliance.intercept.ConstructorInterceptor
[WARNING]   - org.aopalliance.intercept.MethodInvocation
[WARNING]   - org.aopalliance.intercept.MethodInterceptor
[WARNING]   - org.aopalliance.intercept.Invocation
[WARNING]   - org.aopalliance.aop.AspectException
[WARNING]   - org.aopalliance.intercept.Interceptor
[WARNING]   - org.aopalliance.intercept.Joinpoint
[WARNING]   - org.aopalliance.aop.Advice
[WARNING]   - org.aopalliance.intercept.ConstructorInvocation
[WARNING] javax.inject-2.4.0-b34.jar, javax.inject-1.jar define 6 overlapping classes: 
[WARNING]   - javax.inject.Inject
[WARNING]   - javax.inject.Singleton
[WARNING]   - javax.inject.Named
[WARNING]   - javax.inject.Scope
[WARNING]   - javax.inject.Provider
[WARNING]   - javax.inject.Qualifier
[WARNING] scalate-util_2.11-1.8.0.jar, scalate-core_2.11-1.8.0.jar define 222 overlapping classes: 
[WARNING]   - org.fusesource.scalate.util.StringResource
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$12$$anonfun$apply$3$$anonfun$apply$19
[WARNING]   - org.fusesource.scalate.util.ClassPathBuilder$$anonfun$findManifestEntries$1$$anonfun$apply$3
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$18
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$12$$anonfun$apply$3$$anonfun$apply$5$$anonfun$apply$6$$anonfun$apply$9$$anonfun$apply$10
[WARNING]   - org.fusesource.scalate.util.ResourceLoader
[WARNING]   - org.fusesource.scalate.util.SourceMapStratum$$anonfun$7
[WARNING]   - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$20$$anonfun$apply$45
[WARNING]   - org.fusesource.scalate.util.ProductReflector$
[WARNING]   - org.fusesource.scalate.util.ClassFinder$$anonfun$discoverCommandClasses$1
[WARNING]   - 212 more...
[WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, spark-tags_2.11-2.3.3.jar, spark-launcher_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, spark-kvstore_2.11-2.3.3.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: 
[WARNING]   - org.apache.spark.unused.UnusedStubClass
[WARNING] commons-logging-1.1.1.jar, jcl-over-slf4j-1.7.16.jar define 6 overlapping classes: 
[WARNING]   - org.apache.commons.logging.impl.SimpleLog$1
[WARNING]   - org.apache.commons.logging.Log
[WARNING]   - org.apache.commons.logging.impl.SimpleLog
[WARNING]   - org.apache.commons.logging.LogConfigurationException
[WARNING]   - org.apache.commons.logging.impl.NoOpLog
[WARNING]   - org.apache.commons.logging.LogFactory
[WARNING] kryo-shaded-3.0.3.jar, kryo-2.24.0.jar define 193 overlapping classes: 
[WARNING]   - com.esotericsoftware.kryo.serializers.BeanSerializer$1
[WARNING]   - com.esotericsoftware.kryo.Registration
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector
[WARNING]   - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor
[WARNING]   - com.esotericsoftware.kryo.util.IntMap$Values
[WARNING]   - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer
[WARNING]   - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl
[WARNING]   - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField
[WARNING]   - com.esotericsoftware.kryo.serializers.JavaSerializer
[WARNING]   - 183 more...
[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/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar with /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT-shaded.jar
[INFO] Dependency-reduced POM written at: /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/dependency-reduced-pom.xml
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core ---
[INFO] Building jar: /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-core ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-core >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core ---
[INFO] Source directory: /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-core <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-core ---
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.0.1 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[INFO] artifact commons-codec:commons-codec: checking for updates from central
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  net.liftweb:lift-json_2.11:3.0.1 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:69: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class AlignmentRecordMaterialization(@transient sc: SparkContext,
                                      ^
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:48: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class FeatureMaterialization(@transient sc: SparkContext,
                              ^
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:56: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
                                                             @transient sc: SparkContext,
                                                              ^
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:45: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param)
class VariantContextMaterialization(@transient sc: SparkContext,
                                     ^
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled.
    try {
    ^
warning: there were four feature warnings; re-run with -feature for details
model contains 36 documentable templates
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/RefSeq.scala:29: warning: Variable GENOME undefined in comment for object RefSeqFile in object RefSeqFile
 * Processes refSeq file, downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                     ^
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                  ^
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes
                                                                                                    ^
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:51: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz
                                                                                   ^
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:52: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig
 * - refSeq.txt file: downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz
                                                                                 ^
11 warnings found
[INFO] Building jar: /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT-javadoc.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building Mango: Python APIs 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml
741/741 B   
            
Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml (741 B at 55.7 KB/sec)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-python ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-python ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-python ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-python ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-python ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (dev-python) @ mango-python ---
pip install -e .
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Obtaining file:///tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-python
Requirement already satisfied: cigar==0.1.3 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (0.1.3)
Requirement already satisfied: matplotlib==2.0.2 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (2.0.2)
Requirement already satisfied: ipython==5.5.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (5.5.0)
Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (1.0.0)
Requirement already satisfied: bdgenomics.mango.pileup==0.0.2a0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (0.0.2a0)
Requirement already satisfied: bdgenomics.adam==0.26.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (0.26.0)
Requirement already satisfied: ipywidgets==7.0.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (7.0.0)
Requirement already satisfied: psutil in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (5.6.2)
Requirement already satisfied: subprocess32 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (3.5.3)
Requirement already satisfied: cycler>=0.10 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (0.10.0)
Requirement already satisfied: functools32 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (3.2.3.post2)
Requirement already satisfied: six>=1.10 in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (1.11.0)
Requirement already satisfied: pytz in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (2018.9)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (2.4.0)
Requirement already satisfied: numpy>=1.7.1 in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (1.15.3)
Requirement already satisfied: python-dateutil in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (2.7.4)
Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (2.3.3)
Requirement already satisfied: backports.shutil-get-terminal-size; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.0.0)
Requirement already satisfied: simplegeneric>0.8 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.8.1)
Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (2.4.0)
Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (4.7.0)
Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (41.0.1)
Requirement already satisfied: traitlets>=4.2 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (4.3.2)
Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.0.16)
Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.7.5)
Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (4.4.0)
Requirement already satisfied: qtconsole in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (4.4.4)
Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.7.8)
Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.5.0)
Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (4.10.0)
Requirement already satisfied: jupyter-console in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.2.0)
Requirement already satisfied: pyspark>=1.6.0 in /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python (from bdgenomics.adam==0.26.0->bdgenomics.mango==0.0.3a0) (2.3.3)
Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (4.4.0)
Requirement already satisfied: widgetsnbextension~=3.0.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (3.0.8)
Requirement already satisfied: scandir; python_version < "3.5" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.10.0)
Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from pexpect; sys_platform != "win32"->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.6.0)
Requirement already satisfied: enum34; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.1.6)
Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.2.0)
Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.1.7)
Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (4.4.0)
Requirement already satisfied: jupyter-client>=4.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.2.4)
Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.8.2)
Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (1.5.0)
Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (18.0.1)
Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.6.0)
Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (2.10.1)
Requirement already satisfied: ipaddress; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (1.0.22)
Requirement already satisfied: tornado<7,>=4.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.1.1)
Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.3)
Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (3.1.0)
Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (1.4.2)
Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.4.2)
Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.6.0)
Requirement already satisfied: mistune>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.8.4)
Requirement already satisfied: py4j==0.10.7 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from pyspark>=1.6.0->bdgenomics.adam==0.26.0->bdgenomics.mango==0.0.3a0) (0.10.7)
Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (3.0.1)
Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jinja2->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (1.1.1)
Requirement already satisfied: futures in /home/jenkins/.local/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (3.2.0)
Requirement already satisfied: singledispatch in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (3.4.0.3)
Requirement already satisfied: backports-abc>=0.4 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.5)
Requirement already satisfied: configparser>=3.5; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from entrypoints>=0.2.2->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (3.7.4)
Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.5.1)
Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (0.15.1)
Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (19.1.0)
Installing collected packages: bdgenomics.mango
  Found existing installation: bdgenomics.mango 0.0.3a0
    Can't uninstall 'bdgenomics.mango'. No files were found to uninstall.
  Running setup.py develop for bdgenomics.mango
Successfully installed bdgenomics.mango
python setup.py sdist bdist_egg
Could not import pypandoc - required to package bdgenomics.mango
running sdist
running egg_info
writing requirements to bdgenomics.mango.egg-info/requires.txt
writing bdgenomics.mango.egg-info/PKG-INFO
writing top-level names to bdgenomics.mango.egg-info/top_level.txt
writing dependency_links to bdgenomics.mango.egg-info/dependency_links.txt
reading manifest file 'bdgenomics.mango.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no files found matching '*.jar' under directory 'deps/jars'
writing manifest file 'bdgenomics.mango.egg-info/SOURCES.txt'
running check
creating bdgenomics.mango-0.0.3a0
creating bdgenomics.mango-0.0.3a0/bdgenomics
creating bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
creating bdgenomics.mango-0.0.3a0/bdgenomics/mango
creating bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying files to bdgenomics.mango-0.0.3a0...
copying MANIFEST.in -> bdgenomics.mango-0.0.3a0
copying README.md -> bdgenomics.mango-0.0.3a0
copying requirements.txt -> bdgenomics.mango-0.0.3a0
copying setup.py -> bdgenomics.mango-0.0.3a0
copying version.py -> bdgenomics.mango-0.0.3a0
copying bdgenomics/__init__.py -> bdgenomics.mango-0.0.3a0/bdgenomics
copying bdgenomics.mango.egg-info/PKG-INFO -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/SOURCES.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/dependency_links.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/requires.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics.mango.egg-info/top_level.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info
copying bdgenomics/mango/__init__.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/alignments.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/coverage.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/distribution.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/features.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/genotypes.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/utils.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/variants.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango
copying bdgenomics/mango/test/__init__.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/alignment_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/coverage_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/distribution_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/feature_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/genotypes_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/notebook_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
copying bdgenomics/mango/test/variant_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test
Writing bdgenomics.mango-0.0.3a0/setup.cfg
creating dist
Creating tar archive
removing 'bdgenomics.mango-0.0.3a0' (and everything under it)
running bdist_egg
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/bdgenomics
copying bdgenomics/__init__.py -> build/lib/bdgenomics
creating build/lib/bdgenomics/mango
copying bdgenomics/mango/variants.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/utils.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/distribution.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/coverage.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/features.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/alignments.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/genotypes.py -> build/lib/bdgenomics/mango
copying bdgenomics/mango/__init__.py -> build/lib/bdgenomics/mango
creating build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/coverage_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/distribution_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/variant_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/feature_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/notebook_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/genotypes_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/alignment_test.py -> build/lib/bdgenomics/mango/test
copying bdgenomics/mango/test/__init__.py -> build/lib/bdgenomics/mango/test
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/bdgenomics
creating build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/variants.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/utils.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/distribution.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/coverage.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/features.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/alignments.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/genotypes.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
copying build/lib/bdgenomics/mango/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango
creating build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/coverage_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/distribution_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/variant_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/feature_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/notebook_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/genotypes_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/alignment_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/mango/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/variants.py to variants.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/utils.py to utils.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/distribution.py to distribution.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/coverage.py to coverage.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/features.py to features.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/alignments.py to alignments.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/genotypes.py to genotypes.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/coverage_test.py to coverage_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/distribution_test.py to distribution_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/variant_test.py to variant_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/feature_test.py to feature_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/notebook_test.py to notebook_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/genotypes_test.py to genotypes_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/alignment_test.py to alignment_test.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.mango.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
bdgenomics.__init__: module references __path__
bdgenomics.mango.__init__: module references __path__
creating 'dist/bdgenomics.mango-0.0.3a0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-python ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-python ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-python/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-python ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.6.0:exec (test-python) @ mango-python ---
pushd ../example-files/notebooks \
	&& jupyter nbconvert --to python mango-python-coverage.ipynb \
	&& jupyter nbconvert --to python mango-python-alignment.ipynb \
	&& jupyter nbconvert --to python mango-viz.ipynb \
    && jupyter nbconvert --to python mango-python-variants.ipynb
/tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/example-files/notebooks /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-python
[NbConvertApp] Converting notebook mango-python-coverage.ipynb to python
[NbConvertApp] Writing 1051 bytes to mango-python-coverage.py
[NbConvertApp] Converting notebook mango-python-alignment.ipynb to python
[NbConvertApp] Writing 2194 bytes to mango-python-alignment.py
[NbConvertApp] Converting notebook mango-viz.ipynb to python
[NbConvertApp] Writing 1661 bytes to mango-viz.py
[NbConvertApp] Converting notebook mango-python-variants.ipynb to python
[NbConvertApp] Writing 1941 bytes to mango-python-variants.py
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux2 -- Python 2.7.16, pytest-3.9.1, py-1.8.0, pluggy-0.11.0 -- /home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/bin/python
cachedir: .pytest_cache
rootdir: /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-python, inifile:
collecting ... collected 24 items

bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_coverage_distribution PASSED [  4%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_fragment_distribution PASSED [  8%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution PASSED [ 12%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_maximal_bin_size PASSED [ 16%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_no_elements PASSED [ 20%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_mapq_distribution PASSED [ 25%]
bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_visualize_alignments PASSED [ 29%]
bdgenomics/mango/test/coverage_test.py::CoverageTest::test_coverage_distribution PASSED [ 33%]
bdgenomics/mango/test/coverage_test.py::CoverageTest::test_example_coverage PASSED [ 37%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_cumulative_count_distribution PASSED [ 41%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_fail_on_invalid_sample PASSED [ 45%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_normalized_count_distribution PASSED [ 50%]
bdgenomics/mango/test/distribution_test.py::DistributionTest::test_sampling PASSED [ 54%]
bdgenomics/mango/test/feature_test.py::FeatureTest::test_visualize_features PASSED [ 58%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeCallRatesDistribution PASSED [ 62%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeSummary PASSED [ 66%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_HetHomRatioDistribution PASSED [ 70%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistribution PASSED [ 75%]
bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistributionSampling FAILED [ 79%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_alignment_example PASSED [ 83%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_coverage_example PASSED [ 87%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_example PASSED [ 91%]
bdgenomics/mango/test/notebook_test.py::NotebookTest::test_variants_example PASSED [ 95%]
bdgenomics/mango/test/variant_test.py::VariantTest::test_visualize_variants PASSED [100%]

=================================== FAILURES ===================================
___________ GenotypesTest.test_VariantsPerSampleDistributionSampling ___________

self = <bdgenomics.mango.test.genotypes_test.GenotypesTest testMethod=test_VariantsPerSampleDistributionSampling>

    def test_VariantsPerSampleDistributionSampling(self):
        ac = ADAMContext(self.ss)
        testFile = self.resourceFile("genodata.v3.test.vcf")
    
        genotypes = ac.loadGenotypes(testFile)
        _, data = VariantsPerSampleDistribution(self.ss, genotypes, sample=0.9).plotDistributions(testMode= True)
    
        expected = [6, 8, 8, 1, 7, 8]
    
        # estimated counts should be around real counts
        dev = 8
>       assert(sum(expected) > sum(data) - dev and sum(expected) < sum(data) + dev)
E       AssertionError: assert (38 > (28 - 8) and 38 < (28 + 8))
E        +  where 38 = sum([6, 8, 8, 1, 7, 8])
E        +  and   28 = sum([1, 5, 5, 4, 6, 7])
E        +  and   38 = sum([6, 8, 8, 1, 7, 8])
E        +  and   28 = sum([1, 5, 5, 4, 6, 7])

bdgenomics/mango/test/genotypes_test.py:49: AssertionError
----------------------------- Captured stderr call -----------------------------

[Stage 0:>                                                          (0 + 1) / 1]
                                                                                
- generated xml file: /tmp/mangoTestmkgRsVd/deleteMePleaseThisIsNoLongerNeeded/mango-python/target/pytest-reports/tests.xml -
=============================== warnings summary ===============================
/home/jenkins/anaconda2/envs/mango-build-8732a22c-7259-449a-a9e7-536587529ab9/lib/python2.7/site-packages/ipywidgets/widgets/widget.py:287: DeprecationWarning: Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator.
  warnings.warn("Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator.", DeprecationWarning)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
=============== 1 failed, 23 passed, 1 warnings in 99.72 seconds ===============
Makefile:82: recipe for target 'test' failed
make: *** [test] Error 1
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 2 (Exit value: 2)
	at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
	at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:804)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:751)
	at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:313)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] mango .............................................. SUCCESS [  5.040 s]
[INFO] mango: CORE ........................................ SUCCESS [01:00 min]
[INFO] Mango: Python APIs ................................. FAILURE [01:47 min]
[INFO] mango: CLI ......................................... SKIPPED
[INFO] Mango: Assembly .................................... SKIPPED
[INFO] mango: Distribution ................................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 02:52 min
[INFO] Finished at: 2019-05-11T05:14:56-07:00
[INFO] Final Memory: 51M/1511M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:exec (test-python) on project mango-python: Command execution failed. Process exited with an error: 2 (Exit value: 2) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :mango-python
Build step 'Execute shell' marked build as failure
Sending e-mails to: akmorrow@berkeley.edu
Finished: FAILURE