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spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/aft_survival_regression.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/kmeans_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/decision_tree_classification_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/linear_regression_with_elastic_net.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/lda_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/string_indexer_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/estimator_transformer_param_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/imputer_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/isotonic_regression_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/als_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/sql_transformer.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/summarizer_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/multilayer_perceptron_classification.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/prefixspan_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/normalizer_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/bucketed_random_projection_lsh_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/feature_hasher_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/random_forest_regressor_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/chi_square_test_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/tf_idf_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/vector_indexer_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/onehot_encoder_estimator_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/pipeline_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/word2vec_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/ml/gradient_boosted_tree_regressor_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/summary_statistics_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/decision_tree_regression_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/stratified_sampling_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/multi_class_metrics_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/elementwise_product_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/streaming_k_means_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/binary_classification_metrics_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/svd_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/random_forest_classification_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/correlations_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/pca_rowmatrix_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/hypothesis_testing_kolmogorov_smirnov_test_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/sampled_rdds.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/correlations.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/regression_metrics_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/logistic_regression.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/linear_regression_with_sgd_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/logistic_regression_with_lbfgs_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/fpgrowth_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/svm_with_sgd_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/standard_scaler_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/naive_bayes_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/power_iteration_clustering_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/k_means_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/kmeans.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/kernel_density_estimation_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/gaussian_mixture_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/word2vec.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/random_rdd_generation.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/multi_label_metrics_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/bisecting_k_means_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/gradient_boosting_classification_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/hypothesis_testing_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/decision_tree_classification_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/recommendation_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/gaussian_mixture_model.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/isotonic_regression_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/gradient_boosting_regression_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/normalizer_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/random_forest_regression_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/tf_idf_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/latent_dirichlet_allocation_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/ranking_metrics_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/word2vec_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/mllib/streaming_linear_regression_example.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/als.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/sort.py
spark-2.4.7-bin-hadoop2.7/examples/src/main/python/avro_inputformat.py
spark-2.4.7-bin-hadoop2.7/examples/jars/
spark-2.4.7-bin-hadoop2.7/examples/jars/spark-examples_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/examples/jars/scopt_2.11-3.7.0.jar
spark-2.4.7-bin-hadoop2.7/R/
spark-2.4.7-bin-hadoop2.7/R/lib/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/tests/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/tests/testthat/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/tests/testthat/test_basic.R
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/html/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/html/R.css
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/html/00Index.html
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/NAMESPACE
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/profile/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/profile/shell.R
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/profile/general.R
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/Meta/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/Meta/Rd.rds
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/Meta/features.rds
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/Meta/hsearch.rds
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/Meta/links.rds
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/Meta/nsInfo.rds
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/Meta/package.rds
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/worker/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/worker/daemon.R
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/worker/worker.R
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/help/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/help/paths.rds
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/help/aliases.rds
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdx
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/help/AnIndex
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdb
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/DESCRIPTION
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/INDEX
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/R/
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/R/SparkR
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdx
spark-2.4.7-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdb
spark-2.4.7-bin-hadoop2.7/R/lib/sparkr.zip
spark-2.4.7-bin-hadoop2.7/RELEASE
spark-2.4.7-bin-hadoop2.7/jars/
spark-2.4.7-bin-hadoop2.7/jars/hadoop-client-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/compress-lzf-1.0.3.jar
spark-2.4.7-bin-hadoop2.7/jars/activation-1.1.1.jar
spark-2.4.7-bin-hadoop2.7/jars/json4s-scalap_2.11-3.5.3.jar
spark-2.4.7-bin-hadoop2.7/jars/chill-java-0.9.3.jar
spark-2.4.7-bin-hadoop2.7/jars/hk2-locator-2.4.0-b34.jar
spark-2.4.7-bin-hadoop2.7/jars/validation-api-1.1.0.Final.jar
spark-2.4.7-bin-hadoop2.7/jars/super-csv-2.2.0.jar
spark-2.4.7-bin-hadoop2.7/jars/leveldbjni-all-1.8.jar
spark-2.4.7-bin-hadoop2.7/jars/arrow-format-0.10.0.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-common-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-hive_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/javassist-3.18.1-GA.jar
spark-2.4.7-bin-hadoop2.7/jars/oro-2.0.8.jar
spark-2.4.7-bin-hadoop2.7/jars/jersey-client-2.22.2.jar
spark-2.4.7-bin-hadoop2.7/jars/parquet-encoding-1.10.1.jar
spark-2.4.7-bin-hadoop2.7/jars/janino-3.0.16.jar
spark-2.4.7-bin-hadoop2.7/jars/arrow-memory-0.10.0.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-mapreduce-client-core-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/logging-interceptor-3.12.0.jar
spark-2.4.7-bin-hadoop2.7/jars/flatbuffers-1.2.0-3f79e055.jar
spark-2.4.7-bin-hadoop2.7/jars/slf4j-log4j12-1.7.16.jar
spark-2.4.7-bin-hadoop2.7/jars/guava-14.0.1.jar
spark-2.4.7-bin-hadoop2.7/jars/datanucleus-core-3.2.10.jar
spark-2.4.7-bin-hadoop2.7/jars/calcite-core-1.2.0-incubating.jar
spark-2.4.7-bin-hadoop2.7/jars/antlr-2.7.7.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-core-2.6.7.jar
spark-2.4.7-bin-hadoop2.7/jars/jaxb-api-2.2.2.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-configuration-1.6.jar
spark-2.4.7-bin-hadoop2.7/jars/json4s-ast_2.11-3.5.3.jar
spark-2.4.7-bin-hadoop2.7/jars/hive-jdbc-1.2.1.spark2.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-module-jaxb-annotations-2.6.7.jar
spark-2.4.7-bin-hadoop2.7/jars/bonecp-0.8.0.RELEASE.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-hive-thriftserver_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-yarn-client-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/machinist_2.11-0.6.1.jar
spark-2.4.7-bin-hadoop2.7/jars/kubernetes-model-common-4.6.1.jar
spark-2.4.7-bin-hadoop2.7/jars/hive-beeline-1.2.1.spark2.jar
spark-2.4.7-bin-hadoop2.7/jars/libthrift-0.9.3.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-pool-1.5.4.jar
spark-2.4.7-bin-hadoop2.7/jars/metrics-graphite-3.1.5.jar
spark-2.4.7-bin-hadoop2.7/jars/libfb303-0.9.3.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-lang-2.6.jar
spark-2.4.7-bin-hadoop2.7/jars/pyrolite-4.13.jar
spark-2.4.7-bin-hadoop2.7/jars/lz4-java-1.4.0.jar
spark-2.4.7-bin-hadoop2.7/jars/orc-core-1.5.5-nohive.jar
spark-2.4.7-bin-hadoop2.7/jars/calcite-linq4j-1.2.0-incubating.jar
spark-2.4.7-bin-hadoop2.7/jars/hk2-api-2.4.0-b34.jar
spark-2.4.7-bin-hadoop2.7/jars/snakeyaml-1.15.jar
spark-2.4.7-bin-hadoop2.7/jars/shapeless_2.11-2.3.2.jar
spark-2.4.7-bin-hadoop2.7/jars/arrow-vector-0.10.0.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-tags_2.11-2.4.7-tests.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-module-paranamer-2.7.9.jar
spark-2.4.7-bin-hadoop2.7/jars/api-asn1-api-1.0.0-M20.jar
spark-2.4.7-bin-hadoop2.7/jars/minlog-1.3.0.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-yarn_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/curator-framework-2.7.1.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-compress-1.8.1.jar
spark-2.4.7-bin-hadoop2.7/jars/javax.ws.rs-api-2.0.1.jar
spark-2.4.7-bin-hadoop2.7/jars/scala-compiler-2.11.12.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-xc-1.9.13.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-databind-2.6.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/jersey-media-jaxb-2.22.2.jar
spark-2.4.7-bin-hadoop2.7/jars/arpack_combined_all-0.1.jar
spark-2.4.7-bin-hadoop2.7/jars/gson-2.2.4.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-yarn-api-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/parquet-hadoop-1.10.1.jar
spark-2.4.7-bin-hadoop2.7/jars/apacheds-i18n-2.0.0-M15.jar
spark-2.4.7-bin-hadoop2.7/jars/metrics-json-3.1.5.jar
spark-2.4.7-bin-hadoop2.7/jars/hk2-utils-2.4.0-b34.jar
spark-2.4.7-bin-hadoop2.7/jars/log4j-1.2.17.jar
spark-2.4.7-bin-hadoop2.7/jars/javolution-5.5.1.jar
spark-2.4.7-bin-hadoop2.7/jars/macro-compat_2.11-1.1.1.jar
spark-2.4.7-bin-hadoop2.7/jars/aopalliance-repackaged-2.4.0-b34.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-graphx_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-beanutils-1.9.4.jar
spark-2.4.7-bin-hadoop2.7/jars/xz-1.5.jar
spark-2.4.7-bin-hadoop2.7/jars/xmlenc-0.52.jar
spark-2.4.7-bin-hadoop2.7/jars/jersey-container-servlet-2.22.2.jar
spark-2.4.7-bin-hadoop2.7/jars/jcl-over-slf4j-1.7.16.jar
spark-2.4.7-bin-hadoop2.7/jars/parquet-format-2.4.0.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-streaming_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-sql_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/jdo-api-3.0.1.jar
spark-2.4.7-bin-hadoop2.7/jars/jpam-1.1.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-tags_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/json4s-core_2.11-3.5.3.jar
spark-2.4.7-bin-hadoop2.7/jars/core-1.1.2.jar
spark-2.4.7-bin-hadoop2.7/jars/hppc-0.7.2.jar
spark-2.4.7-bin-hadoop2.7/jars/datanucleus-api-jdo-3.2.6.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-math3-3.4.1.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-network-common_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-net-3.1.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-compiler-3.0.16.jar
spark-2.4.7-bin-hadoop2.7/jars/spire_2.11-0.13.0.jar
spark-2.4.7-bin-hadoop2.7/jars/aircompressor-0.10.jar
spark-2.4.7-bin-hadoop2.7/jars/derby-10.12.1.1.jar
spark-2.4.7-bin-hadoop2.7/jars/datanucleus-rdbms-3.2.9.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-mapreduce-client-jobclient-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/avro-1.8.2.jar
spark-2.4.7-bin-hadoop2.7/jars/chill_2.11-0.9.3.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-auth-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/stream-2.7.0.jar
spark-2.4.7-bin-hadoop2.7/jars/apacheds-kerberos-codec-2.0.0-M15.jar
spark-2.4.7-bin-hadoop2.7/jars/antlr4-runtime-4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/osgi-resource-locator-1.0.1.jar
spark-2.4.7-bin-hadoop2.7/jars/httpcore-4.4.10.jar
spark-2.4.7-bin-hadoop2.7/jars/ivy-2.4.0.jar
spark-2.4.7-bin-hadoop2.7/jars/kryo-shaded-4.0.2.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-module-scala_2.11-2.6.7.1.jar
spark-2.4.7-bin-hadoop2.7/jars/orc-shims-1.5.5.jar
spark-2.4.7-bin-hadoop2.7/jars/curator-recipes-2.7.1.jar
spark-2.4.7-bin-hadoop2.7/jars/json4s-jackson_2.11-3.5.3.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-cli-1.2.jar
spark-2.4.7-bin-hadoop2.7/jars/slf4j-api-1.7.16.jar
spark-2.4.7-bin-hadoop2.7/jars/jetty-6.1.26.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-catalyst_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/stax-api-1.0.1.jar
spark-2.4.7-bin-hadoop2.7/jars/eigenbase-properties-1.1.5.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-unsafe_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-io-2.4.jar
spark-2.4.7-bin-hadoop2.7/jars/javax.inject-1.jar
spark-2.4.7-bin-hadoop2.7/jars/guice-3.0.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-logging-1.1.3.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-mllib_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-mapreduce-client-common-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/zjsonpatch-0.3.0.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-sketch_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/univocity-parsers-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/scala-reflect-2.11.12.jar
spark-2.4.7-bin-hadoop2.7/jars/jsp-api-2.1.jar
spark-2.4.7-bin-hadoop2.7/jars/kubernetes-model-4.6.1.jar
spark-2.4.7-bin-hadoop2.7/jars/parquet-jackson-1.10.1.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-core-asl-1.9.13.jar
spark-2.4.7-bin-hadoop2.7/jars/aopalliance-1.0.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-yarn-server-web-proxy-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/metrics-jvm-3.1.5.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-mesos_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/hive-cli-1.2.1.spark2.jar
spark-2.4.7-bin-hadoop2.7/jars/apache-log4j-extras-1.2.17.jar
spark-2.4.7-bin-hadoop2.7/jars/guice-servlet-3.0.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-dbcp-1.4.jar
spark-2.4.7-bin-hadoop2.7/jars/netty-all-4.1.47.Final.jar
spark-2.4.7-bin-hadoop2.7/jars/protobuf-java-2.5.0.jar
spark-2.4.7-bin-hadoop2.7/jars/jta-1.1.jar
spark-2.4.7-bin-hadoop2.7/jars/netty-3.9.9.Final.jar
spark-2.4.7-bin-hadoop2.7/jars/orc-mapreduce-1.5.5-nohive.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-core_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/scala-xml_2.11-1.0.5.jar
spark-2.4.7-bin-hadoop2.7/jars/javax.annotation-api-1.2.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-yarn-common-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-mapper-asl-1.9.13.jar
spark-2.4.7-bin-hadoop2.7/jars/jul-to-slf4j-1.7.16.jar
spark-2.4.7-bin-hadoop2.7/jars/spire-macros_2.11-0.13.0.jar
spark-2.4.7-bin-hadoop2.7/jars/javax.servlet-api-3.1.0.jar
spark-2.4.7-bin-hadoop2.7/jars/hive-exec-1.2.1.spark2.jar
spark-2.4.7-bin-hadoop2.7/jars/mesos-1.4.0-shaded-protobuf.jar
spark-2.4.7-bin-hadoop2.7/jars/jodd-core-3.5.2.jar
spark-2.4.7-bin-hadoop2.7/jars/curator-client-2.7.1.jar
spark-2.4.7-bin-hadoop2.7/jars/zookeeper-3.4.6.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-digester-1.8.jar
spark-2.4.7-bin-hadoop2.7/jars/xbean-asm6-shaded-4.8.jar
spark-2.4.7-bin-hadoop2.7/jars/scala-parser-combinators_2.11-1.1.0.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-launcher_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/jsr305-1.3.9.jar
spark-2.4.7-bin-hadoop2.7/jars/scala-library-2.11.12.jar
spark-2.4.7-bin-hadoop2.7/jars/jersey-container-servlet-core-2.22.2.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-repl_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-jaxrs-1.9.13.jar
spark-2.4.7-bin-hadoop2.7/jars/opencsv-2.3.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-lang3-3.5.jar
spark-2.4.7-bin-hadoop2.7/jars/jetty-util-6.1.26.jar
spark-2.4.7-bin-hadoop2.7/jars/generex-1.0.2.jar
spark-2.4.7-bin-hadoop2.7/jars/joda-time-2.9.3.jar
spark-2.4.7-bin-hadoop2.7/jars/shims-0.7.45.jar
spark-2.4.7-bin-hadoop2.7/jars/objenesis-2.5.1.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-codec-1.10.jar
spark-2.4.7-bin-hadoop2.7/jars/py4j-0.10.7.jar
spark-2.4.7-bin-hadoop2.7/jars/avro-mapred-1.8.2-hadoop2.jar
spark-2.4.7-bin-hadoop2.7/jars/RoaringBitmap-0.7.45.jar
spark-2.4.7-bin-hadoop2.7/jars/zstd-jni-1.3.2-2.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-annotations-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-collections-3.2.2.jar
spark-2.4.7-bin-hadoop2.7/jars/parquet-column-1.10.1.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-crypto-1.0.0.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-kvstore_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/snappy-java-1.1.7.5.jar
spark-2.4.7-bin-hadoop2.7/jars/httpclient-4.5.6.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-mllib-local_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/okio-1.15.0.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-hdfs-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/breeze_2.11-0.13.2.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-yarn-server-common-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/paranamer-2.8.jar
spark-2.4.7-bin-hadoop2.7/jars/commons-httpclient-3.1.jar
spark-2.4.7-bin-hadoop2.7/jars/jersey-server-2.22.2.jar
spark-2.4.7-bin-hadoop2.7/jars/jline-2.14.6.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-network-shuffle_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/spark-kubernetes_2.11-2.4.7.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-annotations-2.6.7.jar
spark-2.4.7-bin-hadoop2.7/jars/parquet-common-1.10.1.jar
spark-2.4.7-bin-hadoop2.7/jars/ST4-4.0.4.jar
spark-2.4.7-bin-hadoop2.7/jars/htrace-core-3.1.0-incubating.jar
spark-2.4.7-bin-hadoop2.7/jars/JavaEWAH-0.3.2.jar
spark-2.4.7-bin-hadoop2.7/jars/api-util-1.0.0-M20.jar
spark-2.4.7-bin-hadoop2.7/jars/parquet-hadoop-bundle-1.6.0.jar
spark-2.4.7-bin-hadoop2.7/jars/breeze-macros_2.11-0.13.2.jar
spark-2.4.7-bin-hadoop2.7/jars/snappy-0.2.jar
spark-2.4.7-bin-hadoop2.7/jars/stringtemplate-3.2.1.jar
spark-2.4.7-bin-hadoop2.7/jars/kubernetes-client-4.6.1.jar
spark-2.4.7-bin-hadoop2.7/jars/automaton-1.11-8.jar
spark-2.4.7-bin-hadoop2.7/jars/hive-metastore-1.2.1.spark2.jar
spark-2.4.7-bin-hadoop2.7/jars/jersey-common-2.22.2.jar
spark-2.4.7-bin-hadoop2.7/jars/javax.inject-2.4.0-b34.jar
spark-2.4.7-bin-hadoop2.7/jars/okhttp-3.12.0.jar
spark-2.4.7-bin-hadoop2.7/jars/antlr-runtime-3.4.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-mapreduce-client-app-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/xercesImpl-2.9.1.jar
spark-2.4.7-bin-hadoop2.7/jars/jersey-guava-2.22.2.jar
spark-2.4.7-bin-hadoop2.7/jars/jtransforms-2.4.0.jar
spark-2.4.7-bin-hadoop2.7/jars/hadoop-mapreduce-client-shuffle-2.7.3.jar
spark-2.4.7-bin-hadoop2.7/jars/stax-api-1.0-2.jar
spark-2.4.7-bin-hadoop2.7/jars/metrics-core-3.1.5.jar
spark-2.4.7-bin-hadoop2.7/jars/jackson-dataformat-yaml-2.6.7.jar
spark-2.4.7-bin-hadoop2.7/jars/avro-ipc-1.8.2.jar
spark-2.4.7-bin-hadoop2.7/jars/calcite-avatica-1.2.0-incubating.jar
+ export SPARK_HOME=/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7
+ SPARK_HOME=/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7

# set the path to the adam submit script
ADAM=./bin/adam-submit
+ ADAM=./bin/adam-submit

# test running adam-shell
./bin/adam-shell -i scripts/jenkins-test-adam-shell.scala
+ ./bin/adam-shell -i scripts/jenkins-test-adam-shell.scala
Using SPARK_SHELL=/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/bin/spark-shell
20/11/18 07:31:56 WARN Utils: Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0)
20/11/18 07:31:56 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/11/18 07:31:57 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
Spark context Web UI available at http://192.168.10.31:4040
Spark context available as 'sc' (master = local[*], app id = local-1605713523807).
Spark session available as 'spark'.

[Stage 0:>                                                          (0 + 1) / 1]
                                                                                
    
# add pyspark to the python path
PY4J_ZIP="$(ls -1 "${SPARK_HOME}/python/lib" | grep py4j)"
ls -1 "${SPARK_HOME}/python/lib" | grep py4j
++ ls -1 /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python/lib
++ grep py4j
+ PY4J_ZIP=py4j-0.10.7-src.zip
export PYTHONPATH=${SPARK_HOME}/python:${SPARK_HOME}/python/lib/${PY4J_ZIP}:${PYTHONPATH}
+ export PYTHONPATH=/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python:/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip:
+ PYTHONPATH=/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python:/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip:

# put adam jar on the pyspark path
ASSEMBLY_DIR="${ADAM_TMP_DIR}/adam-assembly/target"
+ ASSEMBLY_DIR=/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target
ASSEMBLY_JAR="$(ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)"
ls -1 "$ASSEMBLY_DIR" | grep "^adam[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true
++ ls -1 /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target
++ grep '^adam[0-9A-Za-z\_\.-]*\.jar$'
++ grep -v javadoc
++ grep -v sources
+ ASSEMBLY_JAR=adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar
export PYSPARK_SUBMIT_ARGS="--conf spark.driver.memory=4g --conf spark.executor.memory=4g --jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} pyspark-shell"
+ export 'PYSPARK_SUBMIT_ARGS=--conf spark.driver.memory=4g --conf spark.executor.memory=4g --jars /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar pyspark-shell'
+ PYSPARK_SUBMIT_ARGS='--conf spark.driver.memory=4g --conf spark.executor.memory=4g --jars /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar --driver-class-path /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar pyspark-shell'

# create a conda environment for python build, if necessary
pythons=( 3.6 )
+ pythons=(3.6)

for python in ${pythons[*]}
do
    uuid=$(uuidgen)
    conda create -y -q -n adam-build-${uuid} python=${python}
    source activate adam-build-${uuid}

    # prepare adam python
    pushd adam-python
    make prepare
    popd
    	    
    # we can run the python build, now that we have a spark executable
    # -DskipTests appears to skip the python/r tests?
    mvn -U \
    	-P python,distribution \
    	package \
    	-Dsuites=select.no.suites\* \
    	-Dhadoop.version=${HADOOP_VERSION}

    # make sure that the distribution package contains an egg
    # if no assembly jar is found, this will exit with code 1 and fail the build
    tar tzvf adam-distribution/target/adam-distribution*-bin.tar.gz | \
    	grep bdgenomics.adam | \
    	grep egg
    	
    # run pyadam test
    ./bin/pyadam < scripts/jenkins-test-pyadam.py
    	
    # deactivate and remove the conda env
    source deactivate
    conda remove -y -n adam-build-${uuid} --all

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

    # clean after each python version
    pushd adam-python
    make clean
    make clean_sdist
    popd

done
+ for python in '${pythons[*]}'
uuidgen
++ uuidgen
+ uuid=5474ce40-9c0e-4dd0-92be-873345b47411
+ conda create -y -q -n adam-build-5474ce40-9c0e-4dd0-92be-873345b47411 python=3.6


Package plan for installation in environment /home/jenkins/anaconda2/envs/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411:

The following NEW packages will be INSTALLED:

    _libgcc_mutex:    0.1-main               
    ca-certificates:  2020.10.14-0           
    certifi:          2020.6.20-pyhd3eb1b0_3 
    ld_impl_linux-64: 2.33.1-h53a641e_7      
    libedit:          3.1.20191231-h14c3975_1
    libffi:           3.3-he6710b0_2         
    libgcc-ng:        9.1.0-hdf63c60_0       
    libstdcxx-ng:     9.1.0-hdf63c60_0       
    ncurses:          6.2-he6710b0_1         
    openssl:          1.1.1h-h7b6447c_0      
    pip:              20.2.4-py36h06a4308_0  
    python:           3.6.12-hcff3b4d_2      
    readline:         8.0-h7b6447c_0         
    setuptools:       50.3.1-py36h06a4308_1  
    sqlite:           3.33.0-h62c20be_0      
    tk:               8.6.10-hbc83047_0      
    wheel:            0.35.1-pyhd3eb1b0_0    
    xz:               5.2.5-h7b6447c_0       
    zlib:             1.2.11-h7b6447c_3      


+ source activate adam-build-5474ce40-9c0e-4dd0-92be-873345b47411
#!/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/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/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=adam-build-5474ce40-9c0e-4dd0-92be-873345b47411

"$_CONDA_DIR/conda" ..checkenv $_SHELL$EXT "$args"
++ /home/anaconda/bin/conda ..checkenv bash adam-build-5474ce40-9c0e-4dd0-92be-873345b47411
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=adam-build-5474ce40-9c0e-4dd0-92be-873345b47411
+++ 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/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/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/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/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 adam-build-5474ce40-9c0e-4dd0-92be-873345b47411
++ _NEW_PART=/home/jenkins/anaconda2/envs/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411/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/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/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/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/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/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/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/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/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/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/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=adam-build-5474ce40-9c0e-4dd0-92be-873345b47411
++ CONDA_DEFAULT_ENV=adam-build-5474ce40-9c0e-4dd0-92be-873345b47411
++ firstpath=/home/jenkins/anaconda2/envs/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411/bin
echo ${firstpath} | sed "s|/bin$||"
+++ echo /home/jenkins/anaconda2/envs/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411/bin
+++ sed 's|/bin$||'
++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411
"$_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=(adam-build-5474ce40-9c0e-4dd0-92be-873345b47411) '
++ PS1='(adam-build-5474ce40-9c0e-4dd0-92be-873345b47411) '
++ _CONDA_D=/home/jenkins/anaconda2/envs/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411/etc/conda/activate.d
++ [[ -d /home/jenkins/anaconda2/envs/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411/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
+ pushd adam-python
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-python /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu
+ make prepare
pip install pytest==3.9.1
Collecting pytest==3.9.1
  Using cached pytest-3.9.1-py2.py3-none-any.whl (213 kB)
Collecting py>=1.5.0
  Using cached py-1.9.0-py2.py3-none-any.whl (99 kB)
Collecting pluggy>=0.7
  Using cached pluggy-0.13.1-py2.py3-none-any.whl (18 kB)
Collecting more-itertools>=4.0.0
  Using cached more_itertools-8.6.0-py3-none-any.whl (45 kB)
Collecting attrs>=17.4.0
  Using cached attrs-20.3.0-py2.py3-none-any.whl (49 kB)
Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411/lib/python3.6/site-packages (from pytest==3.9.1) (50.3.1.post20201107)
Collecting atomicwrites>=1.0
  Using cached atomicwrites-1.4.0-py2.py3-none-any.whl (6.8 kB)
Collecting six>=1.10.0
  Using cached six-1.15.0-py2.py3-none-any.whl (10 kB)
Collecting importlib-metadata>=0.12; python_version < "3.8"
  Using cached importlib_metadata-2.0.0-py2.py3-none-any.whl (31 kB)
Collecting zipp>=0.5
  Using cached zipp-3.4.0-py3-none-any.whl (5.2 kB)
Installing collected packages: py, zipp, importlib-metadata, pluggy, more-itertools, attrs, atomicwrites, six, pytest
Successfully installed atomicwrites-1.4.0 attrs-20.3.0 importlib-metadata-2.0.0 more-itertools-8.6.0 pluggy-0.13.1 py-1.9.0 pytest-3.9.1 six-1.15.0 zipp-3.4.0
+ popd
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu
+ mvn -U -P python,distribution package '-Dsuites=select.no.suites*' -Dhadoop.version=2.7.5
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ADAM_2.11                                                          [pom]
[INFO] ADAM_2.11: Shader workaround                                       [jar]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils                           [jar]
[INFO] ADAM_2.11: Core                                                    [jar]
[INFO] ADAM_2.11: APIs for Java, Python                                   [jar]
[INFO] ADAM_2.11: CLI                                                     [jar]
[INFO] ADAM_2.11: Assembly                                                [jar]
[INFO] ADAM_2.11: Python APIs                                             [jar]
[INFO] ADAM_2.11: Distribution                                            [pom]
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-parent-spark2_2.11 >-------------
[INFO] Building ADAM_2.11 0.33.0-SNAPSHOT                                 [1/9]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark2_2.11 ---
[INFO] Modified 128 of 435 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-parent-spark2_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-parent-spark2_2.11 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-parent-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark2_2.11 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-parent-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-parent-spark2_2.11 ---
[INFO] No source files found
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-shade-spark2_2.11 >-------------
[INFO] Building ADAM_2.11: Shader workaround 0.33.0-SNAPSHOT              [2/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark2_2.11 ---
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/main/java:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.11.12/classes at 1605713572657
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/2.11.12/classes
[INFO] 
[INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark2_2.11 ---
[INFO] Discovered 1 component descriptors(s)
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark2_2.11 ---
[INFO] No tests to run.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-shade-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.11-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-shade-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.11-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-shade-spark2_2.11 ---
[INFO] 
Loading source files for package org.bdgenomics.adam.shade...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-frame.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-summary.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-tree.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/constant-values.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/class-use/ParquetAvroWorkaroundShader.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/org/bdgenomics/adam/shade/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/overview-tree.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index-all.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/index.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-shade-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark2_2.11 ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-shade-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-shade-spark2_2.11 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-shade/target/adam-shade-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-codegen-spark2_2.11 >------------
[INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.33.0-SNAPSHOT  [3/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark2_2.11 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark2_2.11 ---
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/2.11.12/classes at 1605713578298
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark2_2.11 ---
Discovery starting.
Discovery completed in 40 milliseconds.
Run starting. Expected test count is: 0
Run completed in 44 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-codegen-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-codegen-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-codegen-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-codegen-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-codegen-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-codegen-spark2_2.11 ---
model contains 11 documentable templates
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/adam-codegen-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-core-spark2_2.11 >--------------
[INFO] Building ADAM_2.11: Core 0.33.0-SNAPSHOT                           [4/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.11 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.11 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark2_2.11 ---
[INFO] Modified 2 of 204 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.11 ---
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/java:-1: info: compiling
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala:-1: info: compiling
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 140 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/classes at 1605713592039
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3091: warning: no valid targets for annotation on value uTag - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @getter)
[WARNING]   @transient val uTag: TypeTag[U]
[WARNING]    ^
[WARNING] warning: there were 53 deprecation warnings; re-run with -deprecation for details
[WARNING] warning: there were 5 feature warnings; re-run with -feature for details
[WARNING] three warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 29 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-core-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 6 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-core-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 153 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-core-spark2_2.11 ---
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala:-1: info: compiling
[INFO] Compiling 70 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/2.11.12/test-classes at 1605713622767
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:59: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]       .build()
[WARNING]             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:61: warning: method richRecordToRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val new_cigar = NormalizationUtils.leftAlignIndel(read)
[WARNING]                                                       ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/NormalizationUtilsSuite.scala:66: warning: method richRecordToRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(RichAlignment(read).samtoolsCigar.getReadLength === new_cigar.getReadLength)
[WARNING]                          ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:54: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala:89: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(!testAlignment.getPrimaryAlignment === testSAMRecord.getNotPrimaryAlignmentFlag)
[WARNING]                                                                 ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala:53: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     SequenceDictionary(SAMSequenceDictionaryExtractor.extractDictionary(new File(path)))
[WARNING]                                                       ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:37: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.start == featureToConvert.start)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:38: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.end == featureToConvert.end)
[WARNING]                                                            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:40: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.count == featureToConvert.score)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:57: warning: variable start in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.start == featureToConvert.start)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:58: warning: variable end in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.end == featureToConvert.end)
[WARNING]                                                            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:60: warning: variable score in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.count == featureToConvert.score)
[WARNING]                                                              ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/CoverageSuite.scala:61: warning: variable sampleId in class Feature is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(coverageAfterConversion.optSampleId == Some(featureToConvert.sampleId))
[WARNING]                                                                         ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:194: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(read.mdTag.get.end === read.getEnd)
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:475: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:482: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:495: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val tag = read.mdTag.get
[WARNING]               ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:496: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(tag.getReference(read, withGaps = true) === "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGAAAAAAAAAAA")
[WARNING]                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:510: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar)
[WARNING]                                      ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:526: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:544: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "GGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:562: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/MdTagSuite.scala:580: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newTag = MdTag.moveAlignment(read, newCigar, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA", 100L)
[WARNING]                                      ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:48: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
[WARNING]                                              ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:62: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
[WARNING]                                              ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/models/SequenceDictionarySuite.scala:75: warning: method extractDictionary in object SAMSequenceDictionaryExtractor is deprecated: see corresponding Javadoc for more information.
[WARNING]     val ssd = SAMSequenceDictionaryExtractor.extractDictionary(new File(path))
[WARNING]                                              ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:83: warning: method richRecordToRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(TargetOrdering.contains(targets.head, read))
[WARNING]                                                  ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:191: warning: method richRecordToRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]         if (read.getStart < 105) {
[WARNING]             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:194: warning: method richRecordToRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.start === read.getStart)
[WARNING]                                                   ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:195: warning: method richRecordToRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]           assert(targets.head.readRange.end === read.getEnd)
[WARNING]                                                 ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala:196: warning: method richRecordToRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]           assert(check_indel(targets.head, read))
[WARNING]                                            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:697: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:698: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                          ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:698: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:699: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation === null)
[WARNING]                          ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:699: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation === null)
[WARNING]                  ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:710: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:712: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                                     ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:712: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:714: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation === null)
[WARNING]                                     ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:714: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation === null)
[WARNING]                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:745: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:746: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                          ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:746: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.end === 16157602L)
[WARNING]                  ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable attributes in class VariantAnnotation is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                                     ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                          ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:747: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(first.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                  ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:758: warning: variable end in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:759: warning: variable end in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                                     ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:759: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.end === 16157602L)
[WARNING]                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable attributes in class VariantAnnotation is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                                                ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable annotation in class Variant is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                                     ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala:760: warning: variable variant in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     assert(firstVcfGenotype.variant.annotation.attributes.get("END") === "16157602")
[WARNING]                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantContextDatasetSuite.scala:181: warning: variable start in class Genotype is deprecated: see corresponding Javadoc for more information.
[WARNING]     val filtered = vcs.toGenotypes().rdd.filter(_.start == 66631043)
[WARNING]                                                   ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:31: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithoutClipping.unclippedStart == 42L)
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:32: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithClipping.unclippedStart == 40L)
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:33: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithHardClipping.unclippedStart == 37L)
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:41: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithoutClipping.unclippedEnd == 20L)
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:42: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithClipping.unclippedEnd == 20L)
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:43: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(recordWithHardClipping.unclippedEnd == 20L)
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:49: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(rec.tags.size === 2)
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:50: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(rec.tags(0) === Attribute("XX", TagType.Integer, 3))
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:51: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(rec.tags(1) === Attribute("YY", TagType.String, "foo"))
[WARNING]            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichAlignmentSuite.scala:57: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val overlaps = unmappedRead.overlapsReferencePosition(ReferencePosition("chr1", 10))
[WARNING]                    ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:34: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:37: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar2.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:49: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:52: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar2.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                             ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:64: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:66: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                            ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:78: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     val newCigar = RichCigar(new Cigar(read.samtoolsCigar.getCigarElements)).moveLeft(1)
[WARNING]                                        ^
[WARNING] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichCigarSuite.scala:80: warning: method recordToRichRecord in object RichAlignment is deprecated: Use explicit conversion wherever possible in new development.
[WARNING]     assert(newCigar.cigar.getReadLength == read.samtoolsCigar.getReadLength)
[WARNING]                                            ^
[WARNING] 72 warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 33 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-core-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-core-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-core-spark2_2.11 ---
Discovery starting.
Discovery completed in 1 second, 355 milliseconds.
Run starting. Expected test count is: 0
Run completed in 1 second, 361 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-core-spark2_2.11 ---
[ERROR] Error fetching link: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-codegen/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.apache.parquet.avro...
Loading source files for package org.bdgenomics.adam.io...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/AvroSchemaConverter.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqInputFormat.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/FastqRecordReader.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/SingleFastqInputFormat.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-frame.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-frame.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-summary.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-tree.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-frame.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-summary.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-tree.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/constant-values.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/class-use/AvroSchemaConverter.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/SingleFastqInputFormat.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/InterleavedFastqInputFormat.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqRecordReader.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/class-use/FastqInputFormat.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/apache/parquet/avro/package-use.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/org/bdgenomics/adam/io/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-tree.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index-all.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/index.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/overview-summary.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-core-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-core-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-core-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala added.
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/generated-sources/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-products) @ adam-core-spark2_2.11 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:java (generate-scala-projection-fields) @ adam-core-spark2_2.11 ---
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-core-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-core-spark2_2.11 ---
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverters.scala:274: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentDataset.scala:846: warning: Octal escape literals are deprecated, use \u0001 instead.
      binaryCodec.writeBytes("BAM\001".getBytes())
                                 ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichCigar.scala:43: warning: discarding unmoored doc comment
    /**
    ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3091: warning: no valid targets for annotation on value uTag - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @getter)
  @transient val uTag: TypeTag[U]
   ^
warning: there were 5 feature warnings; re-run with -feature for details
model contains 283 documentable templates
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/util/AttributeUtils.scala:70: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/projections/Projection.scala:45: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1810: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1839: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:1859: warning: Could not find any member to link for "FileNotFoundException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:75: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala:178: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:474: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3464: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:429: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:747: warning: Variable x undefined in comment for method pipe in trait GenomicDataset
   * Files are substituted in to the command with a $x syntax. E.g., to invoke
                                                     ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:748: warning: Variable 0 undefined in comment for method pipe in trait GenomicDataset
   * a command that uses the first file from the files Seq, use $0. To access
                                                                 ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:749: warning: Variable root undefined in comment for method pipe in trait GenomicDataset
   * the path to the directory where the files are copied, use $root.
                                                                ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala:47: warning: Could not find any member to link for "IllegalArgumentException".
/**
^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/Alphabet.scala:44: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:258: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:242: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:444: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala:354: warning: Could not find any member to link for "IllegalArgumentException".
  /**
  ^
24 warnings found
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-core-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-core/target/adam-core-spark2_2.11-0.33.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-apis-spark2_2.11 >--------------
[INFO] Building ADAM_2.11: APIs for Java, Python 0.33.0-SNAPSHOT          [5/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark2_2.11 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-apis-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-apis-spark2_2.11 ---
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/classes at 1605713691300
[WARNING] warning: there were two feature warnings; re-run with -feature for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-apis-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-apis-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-apis-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-apis-spark2_2.11 ---
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/java:-1: info: compiling
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/test/scala:-1: info: compiling
[INFO] Compiling 9 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/test-classes at 1605713697591
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-apis-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 8 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/2.11.12/test-classes
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-apis-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-apis-spark2_2.11 ---
Discovery starting.
Discovery completed in 148 milliseconds.
Run starting. Expected test count is: 0
Run completed in 154 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-apis-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-apis-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-apis-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-apis-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-apis-spark2_2.11 ---
warning: there were two feature warnings; re-run with -feature for details
model contains 192 documentable templates
one warning found
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:test-jar (default) @ adam-apis-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/adam-apis-spark2_2.11-0.33.0-SNAPSHOT-tests.jar
[INFO] 
[INFO] --------------< org.bdgenomics.adam:adam-cli-spark2_2.11 >--------------
[INFO] Building ADAM_2.11: CLI 0.33.0-SNAPSHOT                            [6/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark2_2.11 ---
[INFO] Modified 0 of 29 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-cli-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-cli-spark2_2.11 ---
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 18 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/classes at 1605713712462
[WARNING] warning: there was one deprecation warning; re-run with -deprecation for details
[WARNING] one warning found
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-cli-spark2_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-cli-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-cli-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 15 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-cli-spark2_2.11 ---
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 12 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/2.11.12/test-classes at 1605713720258
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-cli-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-cli-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-cli-spark2_2.11 ---
Discovery starting.
Discovery completed in 137 milliseconds.
Run starting. Expected test count is: 0
Run completed in 143 milliseconds.
Total number of tests run: 0
Suites: completed 0, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-cli-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-cli-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-cli-spark2_2.11 ---
[ERROR] Error fetching link: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-apis/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.adam.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_222
Building tree for all the packages and classes...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/About.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-frame.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-summary.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-tree.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/constant-values.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/class-use/About.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/org/bdgenomics/adam/cli/package-use.html...
Building index for all the packages and classes...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/overview-tree.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index-all.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-frame.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/allclasses-noframe.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/index.html...
Generating /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-cli-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-cli-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-cli-spark2_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-cli-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-cli-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-cli-spark2_2.11 ---
model contains 55 documentable templates
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-cli/target/adam-cli-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] -----------< org.bdgenomics.adam:adam-assembly-spark2_2.11 >------------
[INFO] Building ADAM_2.11: Assembly 0.33.0-SNAPSHOT                       [7/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 ---
[INFO] Request to add '/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark2_2.11 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-assembly-spark2_2.11 ---
[INFO] /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala:-1: info: compiling
[INFO] Compiling 1 source files to /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/2.11.12/classes at 1605713737251
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-assembly-spark2_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-assembly-spark2_2.11 ---
[INFO] Test Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-assembly-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-assembly-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-assembly-spark2_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.2.0:jar (default-jar) @ adam-assembly-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ adam-assembly-spark2_2.11 ---
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadoc) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ adam-assembly-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ adam-assembly-spark2_2.11 ---
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ adam-assembly-spark2_2.11 ---
[INFO] Request to add '/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/java-templates' folder. Not added since it does not exist.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-assembly-spark2_2.11 ---
[INFO] Source directory: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ adam-assembly-spark2_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ adam-assembly-spark2_2.11 ---
model contains 6 documentable templates
[INFO] Building jar: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ adam-assembly-spark2_2.11 ---
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.3.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.12 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.3.0 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.3.0 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.4 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.30 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 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 com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.3.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.19.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 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:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.33.0-SNAPSHOT in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] 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/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT-shaded.jar
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-python-spark2_2.11 >-------------
[INFO] Building ADAM_2.11: Python APIs 0.33.0-SNAPSHOT                    [8/9]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-python-spark2_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-python-spark2_2.11 ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-python-spark2_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-python-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-python/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-python-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (dev-python) @ adam-python-spark2_2.11 ---
pip install -e .
Obtaining file:///tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-python
Requirement already satisfied: pyspark>=1.6.0 in /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python (from bdgenomics.adam==0.32.0a0) (2.4.7)
Collecting py4j==0.10.7
  Using cached py4j-0.10.7-py2.py3-none-any.whl (197 kB)
Installing collected packages: bdgenomics.adam, py4j
  Running setup.py develop for bdgenomics.adam
Successfully installed bdgenomics.adam py4j-0.10.7
python setup.py bdist_egg
running bdist_egg
running egg_info
writing bdgenomics.adam.egg-info/PKG-INFO
writing dependency_links to bdgenomics.adam.egg-info/dependency_links.txt
writing requirements to bdgenomics.adam.egg-info/requires.txt
writing top-level names to bdgenomics.adam.egg-info/top_level.txt
package init file 'deps/jars/__init__.py' not found (or not a regular file)
package init file 'deps/bin/__init__.py' not found (or not a regular file)
reading manifest file 'bdgenomics.adam.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
writing manifest file 'bdgenomics.adam.egg-info/SOURCES.txt'
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/adam
copying bdgenomics/adam/stringency.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/adamContext.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/rdd.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/models.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/__init__.py -> build/lib/bdgenomics/adam
copying bdgenomics/adam/find_adam_home.py -> build/lib/bdgenomics/adam
creating build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/variantDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/alignmentDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/coverageDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/__init__.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/adamContext_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/featureDataset_test.py -> build/lib/bdgenomics/adam/test
copying bdgenomics/adam/test/genotypeDataset_test.py -> build/lib/bdgenomics/adam/test
creating build/lib/bdgenomics/adam/jars
copying deps/jars/adam.jar -> build/lib/bdgenomics/adam/jars
creating build/lib/bdgenomics/adam/bin
copying deps/bin/adam-shell -> build/lib/bdgenomics/adam/bin
copying deps/bin/adam-submit -> build/lib/bdgenomics/adam/bin
copying deps/bin/adamR -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-assembly.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-egg.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-adam-home -> build/lib/bdgenomics/adam/bin
copying deps/bin/find-spark.sh -> build/lib/bdgenomics/adam/bin
copying deps/bin/pyadam -> build/lib/bdgenomics/adam/bin
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/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-spark.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-submit -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adam-shell -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/adamR -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/pyadam -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/bin/find-adam-home -> build/bdist.linux-x86_64/egg/bdgenomics/adam/bin
copying build/lib/bdgenomics/adam/stringency.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/adamContext.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/rdd.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/jars/adam.jar -> build/bdist.linux-x86_64/egg/bdgenomics/adam/jars
copying build/lib/bdgenomics/adam/models.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
copying build/lib/bdgenomics/adam/find_adam_home.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam
creating build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/variantDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/alignmentDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/coverageDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/adamContext_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/featureDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/adam/test/genotypeDataset_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/adam/test
copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/stringency.py to stringency.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/adamContext.py to adamContext.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/rdd.py to rdd.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/models.py to models.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/find_adam_home.py to find_adam_home.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/variantDataset_test.py to variantDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/alignmentDataset_test.py to alignmentDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/coverageDataset_test.py to coverageDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/__init__.py to __init__.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/adamContext_test.py to adamContext_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/featureDataset_test.py to featureDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/adam/test/genotypeDataset_test.py to genotypeDataset_test.cpython-36.pyc
byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.cpython-36.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/scripts-3.6
copying deps/bin/find-spark.sh -> build/scripts-3.6
copying deps/bin/find-adam-assembly.sh -> build/scripts-3.6
copying deps/bin/adam-submit -> build/scripts-3.6
copying deps/bin/adam-shell -> build/scripts-3.6
copying deps/bin/find-adam-egg.sh -> build/scripts-3.6
copying deps/bin/adamR -> build/scripts-3.6
copying deps/bin/pyadam -> build/scripts-3.6
copying deps/bin/find-adam-home -> build/scripts-3.6
copying and adjusting bdgenomics/adam/find_adam_home.py -> build/scripts-3.6
changing mode of build/scripts-3.6/find_adam_home.py from 664 to 775
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-spark.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-assembly.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adam-submit -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adam-shell -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-egg.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/adamR -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find_adam_home.py -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/pyadam -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-3.6/find-adam-home -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-spark.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-assembly.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-submit to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adam-shell to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-egg.sh to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/adamR to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find_adam_home.py to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/pyadam to 775
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/find-adam-home to 775
copying bdgenomics.adam.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying bdgenomics.adam.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
bdgenomics.__pycache__.__init__.cpython-36: module references __path__
bdgenomics.adam.__pycache__.find_adam_home.cpython-36: module references __file__
creating dist
creating 'dist/bdgenomics.adam-0.32.0a0-py3.6.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
[INFO] 
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[INFO] 
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[INFO] No sources to compile
[INFO] 
[INFO] --- exec-maven-plugin:1.5.0:exec (test-python) @ adam-python-spark2_2.11 ---
mkdir -p target
python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics
============================= test session starts ==============================
platform linux -- Python 3.6.12, pytest-3.9.1, py-1.9.0, pluggy-0.13.1 -- /home/jenkins/anaconda2/envs/adam-build-5474ce40-9c0e-4dd0-92be-873345b47411/bin/python
cachedir: .pytest_cache
rootdir: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-python, inifile:
collecting ... collected 63 items

bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_alignments PASSED [  1%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_bed PASSED [  3%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_coverage PASSED [  4%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_dna_sequences PASSED [  6%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_genotypes PASSED [  7%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_gtf PASSED [  9%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_indexed_bam PASSED [ 11%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_interval_list PASSED [ 12%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_narrowPeak PASSED [ 14%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_slices PASSED [ 15%]
bdgenomics/adam/test/adamContext_test.py::ADAMContextTest::test_load_variants PASSED [ 17%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_broadcast_inner_join PASSED [ 19%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_broadcast_right_outer_join PASSED [ 20%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_caching PASSED [ 22%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_count_kmers PASSED [ 23%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_filterByOverlappingRegion PASSED [ 25%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_filterByOverlappingRegions PASSED [ 26%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_load_indexed_bam PASSED [ 28%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_persisting PASSED [ 30%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_pipe_as_sam PASSED [ 31%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_realignIndels_known_indels PASSED [ 33%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_realignIndels_reads PASSED [ 34%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_save_as_bam PASSED [ 36%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_save_sorted_sam PASSED [ 38%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_save_unordered_sam PASSED [ 39%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_full_outer_join PASSED [ 41%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_inner_join PASSED [ 42%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_inner_join_groupBy_left PASSED [ 44%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_left_outer_join PASSED [ 46%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_right_outer_join PASSED [ 47%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_shuffle_right_outer_join_groupBy_left PASSED [ 49%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_to_coverage PASSED [ 50%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_to_fragments FAILED [ 52%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_transform PASSED [ 53%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_transmute_to_coverage PASSED [ 55%]
bdgenomics/adam/test/alignmentDataset_test.py::AlignmentDatasetTest::test_union PASSED [ 57%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_aggregatedCoverage PASSED [ 58%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_collapse PASSED [ 60%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_flatten PASSED [ 61%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_save PASSED [ 63%]
bdgenomics/adam/test/coverageDataset_test.py::CoverageDatasetTest::test_toFeatures PASSED [ 65%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_bed PASSED [ 66%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_gtf PASSED [ 68%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_interval_list PASSED [ 69%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_round_trip_narrowPeak PASSED [ 71%]
bdgenomics/adam/test/featureDataset_test.py::FeatureDatasetTest::test_transform PASSED [ 73%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_to_variants PASSED [ 74%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_transform PASSED [ 76%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_filter PASSED [ 77%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_all_array PASSED [ 79%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_alts_array PASSED [ 80%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_array PASSED [ 82%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_genotype_array PASSED [ 84%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_format_scalar PASSED [ 85%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_all_array PASSED [ 87%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_alts_array PASSED [ 88%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_array PASSED [ 90%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_add_info_scalar PASSED [ 92%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_round_trip PASSED [ 93%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_sort PASSED [ 95%]
bdgenomics/adam/test/genotypeDataset_test.py::GenotypeDatasetTest::test_vcf_sort_lex PASSED [ 96%]
bdgenomics/adam/test/variantDataset_test.py::VariantDatasetTest::test_transform PASSED [ 98%]
bdgenomics/adam/test/variantDataset_test.py::VariantDatasetTest::test_vcf_round_trip PASSED [100%]

=================================== FAILURES ===================================
____________________ AlignmentDatasetTest.test_to_fragments ____________________

self = <bdgenomics.adam.test.alignmentDataset_test.AlignmentDatasetTest testMethod=test_to_fragments>

    def test_to_fragments(self):
    
        readsPath = self.resourceFile("unsorted.sam")
        ac = ADAMContext(self.ss)
    
        reads = ac.loadAlignments(readsPath)
    
>       fragments = reads.toFragments()

bdgenomics/adam/test/alignmentDataset_test.py:169: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/rdd.py:882: in toFragments
    return FragmentDataset(self._jvmRdd.toFragments(), self.sc)
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.7-bin-hadoop2.7/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xspy4j.Py4JException: Method toFragments([]) does not exist\\n\tat py4j.reflection.ReflectionEngine.getMethod(Reflect...java:79)\\n\tat py4j.GatewayConnection.run(GatewayConnection.java:238)\\n\tat java.lang.Thread.run(Thread.java:748)\\n'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7ff92b0b3630>
target_id = 'o1728', name = 'toFragments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
                        format(target_id, ".", name), value)
                else:
                    raise Py4JError(
                        "An error occurred while calling {0}{1}{2}. Trace:\n{3}\n".
>                       format(target_id, ".", name, value))
E                   py4j.protocol.Py4JError: An error occurred while calling o1728.toFragments. Trace:
E                   py4j.Py4JException: Method toFragments([]) does not exist
E                   	at py4j.reflection.ReflectionEngine.getMethod(ReflectionEngine.java:318)
E                   	at py4j.reflection.ReflectionEngine.getMethod(ReflectionEngine.java:326)
E                   	at py4j.Gateway.invoke(Gateway.java:274)
E                   	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
E                   	at py4j.commands.CallCommand.execute(CallCommand.java:79)
E                   	at py4j.GatewayConnection.run(GatewayConnection.java:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:332: Py4JError
- generated xml file: /tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml -
=============================== warnings summary ===============================
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:2020: DeprecationWarning: invalid escape sequence \*
/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:2020: DeprecationWarning: invalid escape sequence \*

source:2020: DeprecationWarning: invalid escape sequence \*

/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-python/bdgenomics/adam/test/alignmentDataset_test.py:143: DeprecationWarning: Please use assertEqual instead.
  self.assertEquals(readsAsCoverage.toDF().count(), 5)

/tmp/adamTestpvuQP4s/deleteMePleaseThisIsNoLongerNeeded/adam-python/bdgenomics/adam/test/coverageDataset_test.py:59: DeprecationWarning: Please use assertEqual instead.
  self.assertEquals(features.toDF().count(), coverage.toDF().count())

-- Docs: https://docs.pytest.org/en/latest/warnings.html
=============== 1 failed, 62 passed, 5 warnings in 67.47 seconds ===============
Makefile:83: 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:764)
    at org.codehaus.mojo.exec.ExecMojo.executeCommandLine (ExecMojo.java:711)
    at org.codehaus.mojo.exec.ExecMojo.execute (ExecMojo.java:289)
    at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156)
    at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117)
    at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81)
    at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56)
    at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305)
    at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192)
    at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105)
    at org.apache.maven.cli.MavenCli.execute (MavenCli.java:957)
    at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:289)
    at org.apache.maven.cli.MavenCli.main (MavenCli.java:193)
    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:282)
    at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225)
    at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406)
    at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.11 0.33.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  8.981 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  5.849 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  7.630 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [01:44 min]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 20.362 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 25.905 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 14.658 s]
[INFO] ADAM_2.11: Python APIs ............................. FAILURE [01:12 min]
[INFO] ADAM_2.11: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  04:20 min
[INFO] Finished at: 2020-11-18T07:37:03-08:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (test-python) on project adam-python-spark2_2.11: 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 <args> -rf :adam-python-spark2_2.11
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/1654f4582adc31c44bbf7eae908934548ba29afd
Finished: FAILURE