Started by upstream project "mango-prb" build number 836 originally caused by: GitHub pull request #494 of commit 87ab87b3ddca47e6e1d51d639bafcdf9e6ff9b59 automatically merged. [EnvInject] - Loading node environment variables. Building remotely on amp-jenkins-staging-worker-01 (ubuntu ubuntu-gpu staging staging-01) in workspace /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu Cloning the remote Git repository Cloning repository https://github.com/bigdatagenomics/mango.git > git init /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/mango.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/mango.git +refs/heads/*:refs/remotes/origin/* > git config remote.origin.url https://github.com/bigdatagenomics/mango.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/mango.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/mango.git > git fetch --tags --progress https://github.com/bigdatagenomics/mango.git +refs/pull/*:refs/remotes/origin/pr/* Checking out Revision 39e095d1cc3b0ea513f36068cc65cb51ea6f3015 (origin/pr/494/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 39e095d1cc3b0ea513f36068cc65cb51ea6f3015 > git rev-list 947143833269f805a6056320b28b14c521f11375 # timeout=10 First time build. Skipping changelog. [ubuntu] $ /bin/bash /tmp/hudson8599041980018522033.sh + set -e + export JAVA_HOME=/usr/lib/jvm/java-8-oracle + JAVA_HOME=/usr/lib/jvm/java-8-oracle + export CONDA_BIN=/home/anaconda/bin/ + CONDA_BIN=/home/anaconda/bin/ + export PATH=/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + set +x + /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to MANGO_MVN_TMP_DIR=$(mktemp -d -t mangoTestMvnXXXXXXX) mktemp -d -t mangoTestMvnXXXXXXX ++ mktemp -d -t mangoTestMvnXXXXXXX + MANGO_MVN_TMP_DIR=/tmp/mangoTestMvnYNWYORu # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${MANGO_MVN_TMP_DIR}:g" \ {} \; + find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/mangoTestMvnYNWYORu:g' '{}' ';' find . -name "*.bak" -exec rm {} \; + find . -name '*.bak' -exec rm '{}' ';' # variable declarations export PATH=${JAVA_HOME}/bin/:${PATH} + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8" + export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' + MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd ) cd $( dirname ${BASH_SOURCE[0]} ) && pwd dirname ${BASH_SOURCE[0]} +++ dirname /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/.. VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g') grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g' ++ grep '<version>' /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/../pom.xml ++ sed 's/ *<version>//g' ++ head -2 ++ sed 's/<\/version>//g' ++ tail -1 + VERSION=0.0.3-SNAPSHOT # is the hadoop version set? if ! [[ ${HADOOP_VERSION} ]]; then echo "HADOOP_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.7.5 ]] # is the spark version set? if ! [[ ${SPARK_VERSION} ]]; then echo "SPARK_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.3.3 ]] set -e + set -e # are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first if [ ${SCALAVER} == 2.11 ]; then # shouldn't be able to move to scala 2.11 twice set +e ./scripts/move_to_scala_2.11.sh if [[ $? == 0 ]]; then echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)." exit 1 fi set -e fi + '[' 2.11 == 2.11 ']' + set +e + ./scripts/move_to_scala_2.11.sh Scala version is already set to 2.11 (Scala artifacts have _2.11 version suffix in artifact name). Cowardly refusing to move to Scala 2.11 a second time... + [[ 1 == 0 ]] + set -e # print versions echo "Testing MANGO version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing MANGO version 0.0.3-SNAPSHOT on Spark 2.3.3 and Hadoop 2.7.5' Testing MANGO version 0.0.3-SNAPSHOT on Spark 2.3.3 and Hadoop 2.7.5 # clean the targets first mvn clean + mvn clean Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-cli:[unknown-version], /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/pom.xml, line 39, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] mango [INFO] mango: CORE [INFO] mango: CLI [INFO] Mango: Assembly [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.0.0:clean (default-clean) @ mango-parent --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango: CORE 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.0.0:clean (default-clean) @ mango-core --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango: CLI 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.0.0:clean (default-clean) @ mango-cli --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Mango: Assembly 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:3.0.0:clean (default-clean) @ mango-assembly --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] mango .............................................. SUCCESS [ 0.274 s] [INFO] mango: CORE ........................................ SUCCESS [ 0.010 s] [INFO] mango: CLI ......................................... SUCCESS [ 0.020 s] [INFO] Mango: Assembly .................................... SUCCESS [ 0.013 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.552 s [INFO] Finished at: 2019-05-13T18:01:06-07:00 [INFO] Final Memory: 23M/1472M [INFO] ------------------------------------------------------------------------ # clear distribution in case there are residual jars rm -rf mango-distribution/target/ + rm -rf mango-distribution/target/ # if this is a pull request, we need to set the coveralls pr id if [[ ! -z $ghprbPullId ]]; then COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}" fi + [[ ! -z 494 ]] + COVERALLS_PRB_OPTION=-DpullRequest=494 # coveralls token should not be visible set +x +v + set +x +v Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-cli:[unknown-version], /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/pom.xml, line 39, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] mango [INFO] mango: CORE [INFO] mango: CLI [INFO] Mango: Assembly [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent --- [INFO] Modified 1 of 39 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-parent >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent --- [INFO] Modified 0 of 39 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-parent --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-parent --- [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-parent <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-parent --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango: CORE 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.pom 3/8 KB 5/8 KB 8/8 KB 8/8 KB Downloaded: https://repo.maven.apache.org/maven2/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.pom (8 KB at 25.6 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scalap/2.11.11/scalap-2.11.11.pom 2/2 KB Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scalap/2.11.11/scalap-2.11.11.pom (2 KB at 127.6 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.11/scala-compiler-2.11.11.pom 3/3 KB 3/3 KB Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.11/scala-compiler-2.11.11.pom (3 KB at 192.9 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.11.11/scala-reflect-2.11.11.pom 2/2 KB Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-reflect/2.11.11/scala-reflect-2.11.11.pom (2 KB at 139.6 KB/sec) Downloading: https://repository.apache.org/snapshots/commons-codec/commons-codec/maven-metadata.xml Downloading: https://oss.sonatype.org/content/repositories/snapshots/commons-codec/commons-codec/maven-metadata.xml Downloading: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml 672/672 B Downloaded: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml (672 B at 54.7 KB/sec) Downloading: https://repo.maven.apache.org/maven2/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar Downloading: 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15065/15235 KB 15069/15235 KB 15073/15235 KB 15077/15235 KB 15081/15235 KB 15085/15235 KB 15089/15235 KB 15093/15235 KB 15097/15235 KB 15101/15235 KB 15105/15235 KB 15109/15235 KB 15113/15235 KB 15117/15235 KB 15121/15235 KB 15125/15235 KB 15129/15235 KB 15133/15235 KB 15137/15235 KB 15141/15235 KB 15145/15235 KB 15149/15235 KB 15153/15235 KB 15157/15235 KB 15161/15235 KB 15165/15235 KB 15169/15235 KB 15173/15235 KB 15177/15235 KB 15181/15235 KB 15185/15235 KB 15189/15235 KB 15193/15235 KB 15197/15235 KB 15201/15235 KB 15205/15235 KB 15209/15235 KB 15213/15235 KB 15217/15235 KB 15221/15235 KB 15225/15235 KB 15229/15235 KB 15233/15235 KB 15235/15235 KB Downloaded: https://repo.maven.apache.org/maven2/org/scala-lang/scala-compiler/2.11.11/scala-compiler-2.11.11.jar (15235 KB at 19333.7 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core --- [INFO] Modified 0 of 30 .scala files [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala:-1: info: compiling [INFO] Compiling 17 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/classes at 1557795679634 [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class AlignmentRecordMaterialization(@transient sc: SparkContext, [WARNING] ^ [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class FeatureMaterialization(@transient sc: SparkContext, [WARNING] ^ [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] @transient sc: SparkContext, [WARNING] ^ [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class VariantContextMaterialization(@transient sc: SparkContext, [WARNING] ^ [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled. [WARNING] try { [WARNING] ^ [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/converters/SAMRecordConverter.scala:145: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information. [WARNING] builder.setPrimaryAlignment(!samRecord.getNotPrimaryAlignmentFlag) [WARNING] ^ [WARNING] warning: there were four feature warnings; re-run with -feature for details [WARNING] warning: there were three inliner warnings; re-run with -Yinline-warnings for details [WARNING] 8 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 15 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core --- [INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 24 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/test/scala:-1: info: compiling [INFO] Compiling 13 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes at 1557795697724 [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/test/scala/org/bdgenomics/mango/models/LazyMaterializationSuite.scala:77: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class LazyDummy(@transient sc: SparkContext, [WARNING] ^ [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-core --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-core --- Discovery starting. Discovery completed in 620 milliseconds. Run starting. Expected test count is: 72 DiscoverySuite: 2019-05-13 18:01:47 WARN Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1) 2019-05-13 18:01:47 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-13 18:01:47 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-05-13 18:01:49 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed.idx... - correctly gathers regions of occupancy from Feature file - does not fail when no regions discovered VariantContextMaterializationSuite: 2019-05-13 18:01:49 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx... - Fetch from 1 vcf file with genotypes - gets sample information - Can extract json 2019-05-13 18:01:56 WARN Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf. - Can read Partitioned Parquet Genotypes - correctly reassigns referenceName 2019-05-13 18:02:03 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf.idx... - returns from file without genotypes - more than 1 vcf file - Should handle chromosomes with different prefixes - fetches multiple regions from load GenomeConfigSuite: - Should read in genome path - Should parse chrom sizes file - Should parse refSeq.txt file - Should fail when genome file does not exist - should build genome BamReaderSuite: - Should load local bam file - Gets file header - loads all data when region is not specified - Fails on files that are not bam or sam - Should return empty on invalid chromosome - Should return no data on empty dictionary - Should load local sam file - Should load local bam files with incorrect prefixes file - Should load data from HDFS using Spark - Should load http bam file RefSeqSuite: - Should convert refseq file to GA4GH genes GA4GHutilSuite: - create JSON from AlignmentRecordDataset - create JSON from AlignmentRecordDataset with 1 sample - create JSON from AlignmentRecordDataset with more than 1 sample - create JSON with genotypes from VCF using GenotypeDataset - create JSON without genotypes from VCF using VariantDataset - create JSON from FeatureDataset LazyMaterializationSuite: - Should correctly reassigns chr prefix 2019-05-13 18:02:18 WARN Bookkeep:66 - bookkeeping queue is empty 2019-05-13 18:02:18 WARN LazyDummy:247 - memory limit exceeded. Dropping null from cache 2019-05-13 18:02:18 WARN LazyDummy:247 - memory limit exceeded. Dropping chrM from cache - Should check and clear memory FeatureMaterializationSuite: - assert raw data returns from one block 2019-05-13 18:02:18 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed.idx... - can fetch multiple files - Should handle chromosomes with different prefixes - fetches multiple regions from load BookkeepSuite: - remembers new regions - adds new regions to existing chromosomes - adds new chromosome - merges regions - saves sequence dictionary - get and put region where region equals chunk size AlignmentRecordMaterializationSuite: - create new AlignmentRecordMaterialization - return raw data from AlignmentRecordMaterialization - can process stringified data - Read Partitioned Data - fetches multiple regions from load - Should handle chromosomes with different prefixes - should get data from unindexed file when referenceName predicates do not match 2019-05-13 18:02:42 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak.idx... BedReaderSuite: - Should load local bed file - Should load all records when region is not specified - Fails on files that are not bed format - Should return empty on invalid chromosome - Should load local narrowPeak file - Should load local bed files with incorrect prefixes file - Should load data from HDFS using Spark - Should load remote bed file VcfReaderSuite: - Should load local vcf file 2019-05-13 18:02:43 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz.tbi... - Gets file header 2019-05-13 18:02:43 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz.tbi... 2019-05-13 18:02:43 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.idx... - Should load bgz file 2019-05-13 18:02:43 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz.tbi... - Should load compressed bgz file - Should load all records when region is not defined - Fails on files that are not vcf or vcf.gz - Should return empty on invalid chromosome - Should load local vcf files with incorrect prefixes file - Should load genotypes - loads gzipped vcfs 2019-05-13 18:02:43 WARN VCFInputFormat:410 - No tabix index file found for file:/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.tbi, splits will not be filtered, which may be very inefficient - Should load data from HDFS using Spark - Should load http vcf file Run completed in 1 minute, 2 seconds. Total number of tests run: 72 Suites: completed 13, aborted 0 Tests: succeeded 72, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-core >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core --- [INFO] Modified 0 of 30 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-core --- [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala:-1: info: compiling [INFO] Compiling 17 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/scoverage-classes at 1557795771511 [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class AlignmentRecordMaterialization(@transient sc: SparkContext, [WARNING] ^ [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class FeatureMaterialization(@transient sc: SparkContext, [WARNING] ^ [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] @transient sc: SparkContext, [WARNING] ^ [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class VariantContextMaterialization(@transient sc: SparkContext, [WARNING] ^ [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled. [WARNING] try { [WARNING] ^ [INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [INFO] [info] Instrumentation completed [1614 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scoverage-data] [WARNING] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/converters/SAMRecordConverter.scala:145: warning: method getNotPrimaryAlignmentFlag in class SAMRecord is deprecated: see corresponding Javadoc for more information. [WARNING] builder.setPrimaryAlignment(!samRecord.getNotPrimaryAlignmentFlag) [WARNING] ^ [WARNING] warning: there were four feature warnings; re-run with -feature for details [WARNING] warning: there were three inliner warnings; re-run with -Yinline-warnings for details [WARNING] 8 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 27 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-core --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core --- [INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 24 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-core --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-core --- Discovery starting. Discovery completed in 619 milliseconds. Run starting. Expected test count is: 72 DiscoverySuite: 2019-05-13 18:03:21 WARN Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1) 2019-05-13 18:03:21 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-13 18:03:22 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-05-13 18:03:23 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest.bed.idx... - correctly gathers regions of occupancy from Feature file - does not fail when no regions discovered VariantContextMaterializationSuite: 2019-05-13 18:03:24 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx... - Fetch from 1 vcf file with genotypes - gets sample information - Can extract json 2019-05-13 18:03:30 WARN Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf. - Can read Partitioned Parquet Genotypes - correctly reassigns referenceName 2019-05-13 18:03:38 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/bqsr1.vcf.idx... - returns from file without genotypes - more than 1 vcf file - Should handle chromosomes with different prefixes - fetches multiple regions from load GenomeConfigSuite: - Should read in genome path - Should parse chrom sizes file - Should parse refSeq.txt file - Should fail when genome file does not exist - should build genome BamReaderSuite: - Should load local bam file - Gets file header - loads all data when region is not specified - Fails on files that are not bam or sam - Should return empty on invalid chromosome - Should return no data on empty dictionary - Should load local sam file - Should load local bam files with incorrect prefixes file - Should load data from HDFS using Spark - Should load http bam file RefSeqSuite: - Should convert refseq file to GA4GH genes GA4GHutilSuite: - create JSON from AlignmentRecordDataset - create JSON from AlignmentRecordDataset with 1 sample - create JSON from AlignmentRecordDataset with more than 1 sample - create JSON with genotypes from VCF using GenotypeDataset - create JSON without genotypes from VCF using VariantDataset - create JSON from FeatureDataset LazyMaterializationSuite: - Should correctly reassigns chr prefix 2019-05-13 18:03:55 WARN Bookkeep:66 - bookkeeping queue is empty 2019-05-13 18:03:55 WARN LazyDummy:247 - memory limit exceeded. Dropping null from cache 2019-05-13 18:03:55 WARN LazyDummy:247 - memory limit exceeded. Dropping chrM from cache - Should check and clear memory FeatureMaterializationSuite: - assert raw data returns from one block 2019-05-13 18:03:55 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/smalltest2.bed.idx... - can fetch multiple files - Should handle chromosomes with different prefixes - fetches multiple regions from load BookkeepSuite: - remembers new regions - adds new regions to existing chromosomes - adds new chromosome - merges regions - saves sequence dictionary - get and put region where region equals chunk size AlignmentRecordMaterializationSuite: - create new AlignmentRecordMaterialization - return raw data from AlignmentRecordMaterialization - can process stringified data - Read Partitioned Data - fetches multiple regions from load - Should handle chromosomes with different prefixes - should get data from unindexed file when referenceName predicates do not match 2019-05-13 18:04:33 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.1.sorted.narrowPeak.idx... BedReaderSuite: - Should load local bed file - Should load all records when region is not specified - Fails on files that are not bed format - Should return empty on invalid chromosome - Should load local narrowPeak file - Should load local bed files with incorrect prefixes file - Should load data from HDFS using Spark - Should load remote bed file VcfReaderSuite: - Should load local vcf file 2019-05-13 18:04:34 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/small.vcf.gz.tbi... - Gets file header 2019-05-13 18:04:34 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgz.tbi... 2019-05-13 18:04:34 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.idx... - Should load bgz file 2019-05-13 18:04:34 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/test.vcf.bgzf.gz.tbi... - Should load compressed bgz file - Should load all records when region is not defined - Fails on files that are not vcf or vcf.gz - Should return empty on invalid chromosome - Should load local vcf files with incorrect prefixes file - Should load genotypes - loads gzipped vcfs 2019-05-13 18:04:34 WARN VCFInputFormat:410 - No tabix index file found for file:/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.tbi, splits will not be filtered, which may be very inefficient - Should load data from HDFS using Spark - Should load http vcf file Run completed in 1 minute, 20 seconds. Total number of tests run: 72 Suites: completed 13, aborted 0 Tests: succeeded 72, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-core <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-core --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango: CLI 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml 741/741 B Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml (741 B at 65.8 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.pom 3/6 KB 5/6 KB 6/6 KB Downloaded: https://repo.maven.apache.org/maven2/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.pom (6 KB at 456.1 KB/sec) Downloading: https://repo.maven.apache.org/maven2/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.pom 3/5 KB 5/5 KB Downloaded: https://repo.maven.apache.org/maven2/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.pom 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[INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-cli --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 23 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/classes at 1557795884469 [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- exec-maven-plugin:1.6.0:exec (Run `npm install`) @ mango-cli --- WARN engine har-validator@5.1.3: wanted: {"node":">=6"} (current: {"node":"4.2.6","npm":"3.5.2"}) WARN engine punycode@2.1.1: wanted: {"node":">=6"} (current: {"node":"4.2.6","npm":"3.5.2"}) npm WARN deprecated core-js@1.2.7: core-js@<2.6.5 is no longer maintained. Please, upgrade to core-js@3 or at least to actual version of core-js@2. mango-cli@0.0.2 /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/webapp/resources └─┬ pileup@0.6.11 ├── backbone@1.1.2 ├── d3@3.5.17 ├── data-canvas@0.1.1 ├─┬ jbinary@2.1.3 │ ├── es6-promise@4.2.6 │ └─┬ request@2.88.0 │ ├── aws-sign2@0.7.0 │ ├── aws4@1.8.0 │ ├── caseless@0.12.0 │ ├─┬ combined-stream@1.0.8 │ │ └── delayed-stream@1.0.0 │ ├── extend@3.0.2 │ ├── forever-agent@0.6.1 │ ├─┬ form-data@2.3.3 │ │ └── asynckit@0.4.0 │ ├─┬ har-validator@5.1.3 │ │ ├─┬ ajv@6.10.0 │ │ │ ├── fast-deep-equal@2.0.1 │ │ │ ├── fast-json-stable-stringify@2.0.0 │ │ │ ├── json-schema-traverse@0.4.1 │ │ │ └─┬ uri-js@4.2.2 │ │ │ └── punycode@2.1.1 │ │ └── har-schema@2.0.0 │ ├─┬ http-signature@1.2.0 │ │ ├── assert-plus@1.0.0 │ │ ├─┬ jsprim@1.4.1 │ │ │ ├── extsprintf@1.3.0 │ │ │ ├── json-schema@0.2.3 │ │ │ └─┬ verror@1.10.0 │ │ │ └── core-util-is@1.0.2 │ │ └─┬ sshpk@1.16.1 │ │ ├── asn1@0.2.4 │ │ ├── bcrypt-pbkdf@1.0.2 │ │ ├── dashdash@1.14.1 │ │ ├── ecc-jsbn@0.1.2 │ │ ├── getpass@0.1.7 │ │ ├── jsbn@0.1.1 │ │ ├── safer-buffer@2.1.2 │ │ └── tweetnacl@0.14.5 │ ├── is-typedarray@1.0.0 │ ├── isstream@0.1.2 │ ├── json-stringify-safe@5.0.1 │ ├─┬ mime-types@2.1.24 │ │ └── mime-db@1.40.0 │ ├── oauth-sign@0.9.0 │ ├── performance-now@2.1.0 │ ├── qs@6.5.2 │ ├── safe-buffer@5.1.2 │ ├─┬ tough-cookie@2.4.3 │ │ ├── psl@1.1.31 │ │ └── punycode@1.4.1 │ ├── tunnel-agent@0.6.0 │ └── uuid@3.3.2 ├── jdataview@2.5.0 ├── memory-cache@0.1.6 ├── pako@0.2.9 ├── q@1.5.1 ├─┬ react@0.14.9 │ ├─┬ envify@3.4.1 │ │ ├─┬ jstransform@11.0.3 │ │ │ ├── base62@1.2.8 │ │ │ ├─┬ commoner@0.10.8 │ │ │ │ ├── commander@2.20.0 │ │ │ │ ├─┬ detective@4.7.1 │ │ │ │ │ ├── acorn@5.7.3 │ │ │ │ │ └── defined@1.0.0 │ │ │ │ ├─┬ glob@5.0.15 │ │ │ │ │ ├─┬ inflight@1.0.6 │ │ │ │ │ │ └── wrappy@1.0.2 │ │ │ │ │ ├── inherits@2.0.3 │ │ │ │ │ ├─┬ minimatch@3.0.4 │ │ │ │ │ │ └─┬ brace-expansion@1.1.11 │ │ │ │ │ │ ├── balanced-match@1.0.0 │ │ │ │ │ │ └── concat-map@0.0.1 │ │ │ │ │ ├── once@1.4.0 │ │ │ │ │ └── path-is-absolute@1.0.1 │ │ │ │ ├── graceful-fs@4.1.15 │ │ │ │ ├── iconv-lite@0.4.24 │ │ │ │ ├─┬ mkdirp@0.5.1 │ │ │ │ │ └── minimist@0.0.8 │ │ │ │ ├── private@0.1.8 │ │ │ │ └─┬ recast@0.11.23 │ │ │ │ ├── ast-types@0.9.6 │ │ │ │ ├── esprima@3.1.3 │ │ │ │ └── source-map@0.5.7 │ │ │ ├── esprima-fb@15001.1.0-dev-harmony-fb │ │ │ ├── object-assign@2.1.1 │ │ │ └─┬ source-map@0.4.4 │ │ │ └── amdefine@1.0.1 │ │ └── through@2.3.8 │ └─┬ fbjs@0.6.1 │ ├── core-js@1.2.7 │ ├─┬ loose-envify@1.4.0 │ │ └── js-tokens@4.0.0 │ ├─┬ promise@7.3.1 │ │ └── asap@2.0.6 │ ├── ua-parser-js@0.7.19 │ └── whatwg-fetch@0.9.0 ├── react-dom@0.14.9 ├── shallow-equals@0.0.0 └── underscore@1.9.1 npm WARN mango-cli@0.0.2 No repository field. [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-cli --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli --- [INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-cli --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/test/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes at 1557795902240 [INFO] prepare-compile in 0 s [INFO] compile in 7 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-cli --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-cli --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-cli --- Discovery starting. Discovery completed in 613 milliseconds. Run starting. Expected test count is: 31 MangoMainSuite: - default command groups is non empty - module provides default command groups - inject default command groups when called via main - command groups is empty when called via apply - single command group - add new command group to default command groups - module restores default command groups when called via apply - custom module with single command group - custom module with new command group added to default command groups VizReadsSuite: 2019-05-13 18:05:12 WARN Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1) 2019-05-13 18:05:12 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-13 18:05:13 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-05-13 18:05:16 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx... 2019-05-13 18:05:16 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx... 2019-05-13 18:05:16 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx... - Should pass for discovery mode scala/reflect/io/JavaToolsPlatformArchive scala/reflect/io/JavaToolsPlatformArchive - Should get browser and overall template information - should return reads - Should throw error when reads do not exist - Reads should throw NotFound error on invalid reference - should not return reads with invalid key - /variants/:key/:ref - should not return variants with invalid key - Should throw error when variants do not exist - /features/:key/:ref - should not return features with invalid key - Should throw error when features do not exist - Features should throw out of bounds error on invalid reference - gets coverage from feature endpoint - should not return coverage with invalid key - Should return coverage and features - gets genes - Coverage should throw out of bounds error on invalid reference - Should trigger requests for http files 2019-05-13 18:06:00 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.idx... - should run example files MakeGenomeSuite: Exception in thread "Thread-100" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492) at java.net.URL.openStream(URL.java:1045) at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31) at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31) at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45) at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45) at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58) at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23) Exception in thread "Thread-112" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492) at java.net.URL.openStream(URL.java:1045) at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31) at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31) at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45) at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45) at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58) at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23) 2019-05-13 18:06:04 WARN GenomeConfig:141 - No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1 - creates genome - fails with invalid genome Run completed in 56 seconds, 218 milliseconds. Total number of tests run: 31 Suites: completed 4, aborted 0 Tests: succeeded 31, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-cli >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-cli --- [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-cli --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2854 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/scoverage-classes at 1557795970921 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [INFO] [info] Instrumentation completed [872 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- exec-maven-plugin:1.6.0:exec (Run `npm install`) @ mango-cli --- npm WARN mango-cli@0.0.2 No repository field. [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-cli --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-cli --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli --- [INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-cli --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-cli --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-cli --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-cli --- Discovery starting. Discovery completed in 762 milliseconds. Run starting. Expected test count is: 31 MangoMainSuite: - default command groups is non empty - module provides default command groups - inject default command groups when called via main - command groups is empty when called via apply - single command group - add new command group to default command groups - module restores default command groups when called via apply - custom module with single command group - custom module with new command group added to default command groups VizReadsSuite: 2019-05-13 18:06:24 WARN Utils:66 - Your hostname, amp-jenkins-staging-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface eno1) 2019-05-13 18:06:24 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2019-05-13 18:06:24 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2019-05-13 18:06:28 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/truetest.genotypes.vcf.idx... 2019-05-13 18:06:28 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/smalltest.bed.idx... 2019-05-13 18:06:28 WARN BedReader:158 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/scala-2.11.12/test-classes/mouse_chrM.coverage.bed.idx... - Should pass for discovery mode scala/reflect/io/JavaToolsPlatformArchive scala/reflect/io/JavaToolsPlatformArchive - Should get browser and overall template information - should return reads - Should throw error when reads do not exist - Reads should throw NotFound error on invalid reference - should not return reads with invalid key - /variants/:key/:ref - should not return variants with invalid key - Should throw error when variants do not exist - /features/:key/:ref - should not return features with invalid key - Should throw error when features do not exist - Features should throw out of bounds error on invalid reference - gets coverage from feature endpoint - should not return coverage with invalid key - Should return coverage and features - gets genes - Coverage should throw out of bounds error on invalid reference - Should trigger requests for http files 2019-05-13 18:07:44 WARN VcfReader:205 - No index file for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf found. Generating /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/../example-files/ALL.chr17.7500000-7515000.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.idx... - should run example files MakeGenomeSuite: Exception in thread "Thread-101" java.io.FileNotFoundException: http://hgdownload.soe.ucsc.edu/goldenPath/anoGam1/database/refGene.txt.gz at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492) at java.net.URL.openStream(URL.java:1045) at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31) at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31) at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45) at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45) at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58) at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23) Exception in thread "Thread-113" java.io.FileNotFoundException: http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1890) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1492) at java.net.URL.openStream(URL.java:1045) at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31) at scala.sys.process.ProcessBuilderImpl$URLInput$$anonfun$$lessinit$greater$1.apply(ProcessBuilderImpl.scala:31) at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45) at scala.sys.process.ProcessBuilderImpl$IStreamBuilder$$anonfun$$lessinit$greater$5.apply(ProcessBuilderImpl.scala:45) at scala.sys.process.ProcessBuilderImpl$ThreadBuilder$$anonfun$1.apply$mcV$sp(ProcessBuilderImpl.scala:58) at scala.sys.process.ProcessImpl$Spawn$$anon$1.run(ProcessImpl.scala:23) 2019-05-13 18:07:48 WARN GenomeConfig:141 - No refGene file found at http://hgdownload.cse.ucsc.edu/goldenpath/anoGam1/database/cytoBand.txt.gz for genome anoGam1 - creates genome - fails with invalid genome Run completed in 1 minute, 29 seconds. Total number of tests run: 31 Suites: completed 4, aborted 0 Tests: succeeded 31, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-cli <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-cli --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Mango: Assembly 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ mango-assembly --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly --- [INFO] Request to add '/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-assembly --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/scala-2.11.12/classes at 1557796084510 [INFO] prepare-compile in 0 s [INFO] compile in 1 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-assembly --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly --- [INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-assembly --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-assembly --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-assembly --- [INFO] Tests are skipped. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ mango-assembly >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ mango-assembly --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly --- [INFO] Request to add '/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ mango-assembly --- [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-assembly --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/scala-2.11.12/scoverage-classes at 1557796105180 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [0 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-assembly --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ mango-assembly --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly --- [INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-assembly --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from cloudera [INFO] artifact commons-codec:commons-codec: checking for updates from apache.snapshots.https [INFO] artifact commons-codec:commons-codec: checking for updates from repository.jboss.org [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-assembly --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-assembly --- [INFO] Tests are skipped. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ mango-assembly <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ mango-assembly --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ mango-parent --- [INFO] Starting Coveralls job for jenkins (836 / https://amplab.cs.berkeley.edu/jenkins/job/mango-prb/HADOOP_VERSION=2.7.5,SCALAVER=2.11,SPARK_VERSION=2.3.3,label=ubuntu/836/) [INFO] Using repository token <secret> [INFO] Git commit 39e095d in optimize_http [INFO] Writing Coveralls data to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/target/coveralls.json... [INFO] Processing coverage report from /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/target/cobertura.xml [INFO] Successfully wrote Coveralls data in 131ms [INFO] Gathered code coverage metrics for 21 source files with 3983 lines of code: [INFO] - 1100 relevant lines [INFO] - 883 covered lines [INFO] - 217 missed lines [INFO] Submitting Coveralls data to API [INFO] Successfully submitted Coveralls data in 798ms for Job #836.1 [INFO] https://coveralls.io/jobs/48447437 [INFO] *** It might take hours for Coveralls to update the actual coverage numbers for a job [INFO] If you see question marks in the report, please be patient [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] mango .............................................. SUCCESS [ 1.377 s] [INFO] mango: CORE ........................................ SUCCESS [03:30 min] [INFO] mango: CLI ......................................... SUCCESS [03:09 min] [INFO] Mango: Assembly .................................... SUCCESS [ 45.094 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 07:30 min [INFO] Finished at: 2019-05-13T18:08:39-07:00 [INFO] Final Memory: 66M/1495M [INFO] ------------------------------------------------------------------------ # if those pass, build the distribution package mvn -U \ -P distribution \ package \ -DskipTests \ -Dhadoop.version=${HADOOP_VERSION} \ -Dspark.version=${SPARK_VERSION} \ -DargLine=${MANGO_MVN_TMP_DIR} + mvn -U -P distribution package -DskipTests -Dhadoop.version=2.7.5 -Dspark.version=2.3.3 -DargLine=/tmp/mangoTestMvnYNWYORu Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-cli:[unknown-version], /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/pom.xml, line 39, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] mango [INFO] mango: CORE [INFO] mango: CLI [INFO] Mango: Assembly [INFO] mango: Distribution [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent --- [INFO] Modified 0 of 39 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent --- [INFO] No sources to compile [INFO] [INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-parent --- [INFO] Replacing original artifact with shaded artifact. [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent --- [INFO] No source files found [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango: CORE 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repository.apache.org/snapshots/commons-codec/commons-codec/maven-metadata.xml Downloading: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml Downloading: https://oss.sonatype.org/content/repositories/snapshots/commons-codec/commons-codec/maven-metadata.xml 672/672 B Downloaded: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml (672 B at 3.2 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core --- [INFO] Modified 0 of 30 .scala files [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core --- [INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 24 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-core --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-core --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-core --- [INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar [INFO] [INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-core --- [INFO] Including com.github.samtools:htsjdk:jar:2.16.1 in the shaded jar. [INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar. [INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar. [INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar. [INFO] Including org.scala-lang:scala-compiler:jar:2.11.11 in the shaded jar. [INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar. [INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar. [INFO] Including org.apache.curator:curator-client:jar:2.7.1 in the shaded jar. [INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar. [INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar. [INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar. [INFO] Including it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar. [INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar. [INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar. [INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar. [INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar. [INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar. [INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar. [INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar. [INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar. [INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar. [INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar. [INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar. [INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar. [INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar. [INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar. [INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar. [INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar. [INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar. [INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar. [INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar. [INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar. [INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar. [INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar. [INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar. [INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar. [INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar. [INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar. [INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar. [INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar. [INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar. [INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar. [INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar. [INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar. [INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar. [INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar. [INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar. [INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar. [INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar. [INFO] Including oro:oro:jar:2.0.8 in the shaded jar. [INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar. [INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar. [INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar. [INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar. [INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar. [INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar. [INFO] Including org.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 org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar. [INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar. [INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar. [INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar. [INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar. [INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar. [INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar. [INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar. [INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.2 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar. [INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.2.1 in the shaded jar. [INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar. [INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar. [WARNING] minlog-1.3.0.jar, minlog-1.2.jar define 2 overlapping classes: [WARNING] - com.esotericsoftware.minlog.Log [WARNING] - com.esotericsoftware.minlog.Log$Logger [WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: [WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess [WARNING] - com.google.common.util.concurrent.internal.InternalFutures [WARNING] aopalliance-1.0.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: [WARNING] - org.aopalliance.intercept.ConstructorInterceptor [WARNING] - org.aopalliance.intercept.MethodInvocation [WARNING] - org.aopalliance.intercept.MethodInterceptor [WARNING] - org.aopalliance.intercept.Invocation [WARNING] - org.aopalliance.aop.AspectException [WARNING] - org.aopalliance.intercept.Interceptor [WARNING] - org.aopalliance.intercept.Joinpoint [WARNING] - org.aopalliance.aop.Advice [WARNING] - org.aopalliance.intercept.ConstructorInvocation [WARNING] javax.inject-2.4.0-b34.jar, javax.inject-1.jar define 6 overlapping classes: [WARNING] - javax.inject.Inject [WARNING] - javax.inject.Singleton [WARNING] - javax.inject.Named [WARNING] - javax.inject.Scope [WARNING] - javax.inject.Provider [WARNING] - javax.inject.Qualifier [WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, spark-tags_2.11-2.3.3.jar, spark-launcher_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, spark-kvstore_2.11-2.3.3.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: [WARNING] - org.apache.spark.unused.UnusedStubClass [WARNING] commons-logging-1.1.1.jar, jcl-over-slf4j-1.7.16.jar define 6 overlapping classes: [WARNING] - org.apache.commons.logging.impl.SimpleLog$1 [WARNING] - org.apache.commons.logging.Log [WARNING] - org.apache.commons.logging.impl.SimpleLog [WARNING] - org.apache.commons.logging.LogConfigurationException [WARNING] - org.apache.commons.logging.impl.NoOpLog [WARNING] - org.apache.commons.logging.LogFactory [WARNING] kryo-shaded-3.0.3.jar, kryo-2.24.0.jar define 193 overlapping classes: [WARNING] - com.esotericsoftware.kryo.serializers.BeanSerializer$1 [WARNING] - com.esotericsoftware.kryo.Registration [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor [WARNING] - com.esotericsoftware.kryo.util.IntMap$Values [WARNING] - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer [WARNING] - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl [WARNING] - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField [WARNING] - com.esotericsoftware.kryo.serializers.JavaSerializer [WARNING] - 183 more... [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar with /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT-shaded.jar [INFO] Dependency-reduced POM written at: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/dependency-reduced-pom.xml Downloading: https://repo.maven.apache.org/maven2/org/apache/httpcomponents/httpclient/4.2.5/httpclient-4.2.5.jar Downloading: https://repo.maven.apache.org/maven2/org/apache/httpcomponents/httpcore/4.2.4/httpcore-4.2.4.jar 3/222 KB 5/222 KB 8/222 KB 11/222 KB 13/222 KB 16/222 KB 19/222 KB 21/222 KB 24/222 KB 27/222 KB 29/222 KB 32/222 KB 36/222 KB 40/222 KB 44/222 KB 48/222 KB 52/222 KB 56/222 KB 60/222 KB 64/222 KB 68/222 KB 72/222 KB 76/222 KB 80/222 KB 84/222 KB 3/424 KB 84/222 KB 3/424 KB 88/222 KB 3/424 KB 92/222 KB 3/424 KB 96/222 KB 3/424 KB 96/222 KB 5/424 KB 96/222 KB 8/424 KB 96/222 KB 11/424 KB 100/222 KB 11/424 KB 100/222 KB 13/424 KB 104/222 KB 13/424 KB 108/222 KB 13/424 KB 112/222 KB 13/424 KB 112/222 KB 16/424 KB 112/222 KB 19/424 KB 112/222 KB 21/424 KB 112/222 KB 24/424 KB 116/222 KB 24/424 KB 120/222 KB 24/424 KB 124/222 KB 24/424 KB 124/222 KB 27/424 KB 128/222 KB 27/424 KB 128/222 KB 29/424 KB 128/222 KB 32/424 KB 132/222 KB 32/424 KB 136/222 KB 32/424 KB 140/222 KB 32/424 KB 144/222 KB 32/424 KB 144/222 KB 36/424 KB 144/222 KB 40/424 KB 144/222 KB 44/424 KB 144/222 KB 48/424 KB 148/222 KB 48/424 KB 152/222 KB 48/424 KB 156/222 KB 48/424 KB 160/222 KB 48/424 KB 160/222 KB 52/424 KB 160/222 KB 56/424 KB 160/222 KB 60/424 KB 160/222 KB 64/424 KB 164/222 KB 64/424 KB 168/222 KB 64/424 KB 172/222 KB 64/424 KB 176/222 KB 64/424 KB 176/222 KB 68/424 KB 176/222 KB 72/424 KB 176/222 KB 76/424 KB 176/222 KB 80/424 KB 180/222 KB 80/424 KB 184/222 KB 80/424 KB 188/222 KB 80/424 KB 192/222 KB 80/424 KB 192/222 KB 84/424 KB 192/222 KB 88/424 KB 192/222 KB 92/424 KB 192/222 KB 96/424 KB 196/222 KB 96/424 KB 200/222 KB 96/424 KB 204/222 KB 96/424 KB 208/222 KB 96/424 KB 208/222 KB 100/424 KB 208/222 KB 104/424 KB 208/222 KB 108/424 KB 208/222 KB 112/424 KB 212/222 KB 112/424 KB 216/222 KB 112/424 KB 220/222 KB 112/424 KB 222/222 KB 112/424 KB 222/222 KB 116/424 KB 222/222 KB 120/424 KB 222/222 KB 124/424 KB 222/222 KB 128/424 KB 222/222 KB 132/424 KB 222/222 KB 136/424 KB 222/222 KB 140/424 KB 222/222 KB 144/424 KB 222/222 KB 148/424 KB 222/222 KB 152/424 KB 222/222 KB 156/424 KB 222/222 KB 160/424 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/httpcomponents/httpcore/4.2.4/httpcore-4.2.4.jar (222 KB at 5161.6 KB/sec) 164/424 KB 168/424 KB 172/424 KB 176/424 KB 180/424 KB 184/424 KB 188/424 KB 192/424 KB 196/424 KB 200/424 KB 204/424 KB 208/424 KB 212/424 KB 216/424 KB 220/424 KB 224/424 KB 228/424 KB 232/424 KB 236/424 KB 240/424 KB 244/424 KB 248/424 KB 252/424 KB 256/424 KB 260/424 KB 264/424 KB 268/424 KB 272/424 KB 276/424 KB 280/424 KB 284/424 KB 288/424 KB 292/424 KB 296/424 KB 300/424 KB 304/424 KB 308/424 KB 312/424 KB 316/424 KB 320/424 KB 324/424 KB 328/424 KB 332/424 KB 336/424 KB 340/424 KB 344/424 KB 348/424 KB 352/424 KB 356/424 KB 360/424 KB 364/424 KB 368/424 KB 372/424 KB 376/424 KB 380/424 KB 384/424 KB 388/424 KB 392/424 KB 396/424 KB 400/424 KB 404/424 KB 408/424 KB 412/424 KB 416/424 KB 420/424 KB 424/424 KB Downloaded: https://repo.maven.apache.org/maven2/org/apache/httpcomponents/httpclient/4.2.5/httpclient-4.2.5.jar (424 KB at 5960.7 KB/sec) [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core --- [INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-core --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-core >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-core <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) class AlignmentRecordMaterialization(@transient sc: SparkContext, ^ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) class FeatureMaterialization(@transient sc: SparkContext, ^ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) @transient sc: SparkContext, ^ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) class VariantContextMaterialization(@transient sc: SparkContext, ^ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled. try { ^ warning: there were four feature warnings; re-run with -feature for details model contains 42 documentable templates /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/RefSeq.scala:29: warning: Variable GENOME undefined in comment for object RefSeqFile in object RefSeqFile * Processes refSeq file, downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz ^ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes ^ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes ^ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:51: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz ^ /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:52: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig * - refSeq.txt file: downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz ^ 11 warnings found [INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango: CLI 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml 741/741 B Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml (741 B at 65.8 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-cli --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2854 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- exec-maven-plugin:1.6.0:exec (Run `npm install`) @ mango-cli --- npm WARN mango-cli@0.0.2 No repository field. [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-cli --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli --- [INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-cli --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-cli --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-cli --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-cli --- [INFO] Tests are skipped. [INFO] [INFO] --- sass-maven-plugin:3.7.1:update-stylesheets (default) @ mango-cli --- [INFO] Checked 0 files for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/sass [INFO] Checked 0 filtered (**/*.css) files for /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT/css [INFO] Compiling Sass templates [INFO] Queueing Sass template for compile: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets => /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets Ignoring eventmachine-1.2.7 because its extensions are not built. Try: gem pristine eventmachine --version 1.2.7 Ignoring ffi-1.9.23 because its extensions are not built. Try: gem pristine ffi --version 1.9.23 Ignoring http_parser.rb-0.6.0 because its extensions are not built. Try: gem pristine http_parser.rb --version 0.6.0 [INFO] >> /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.scss => /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/../src/main/webapp/stylesheets/main.css [INFO] [INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-cli --- [INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT.jar [INFO] [INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-cli --- [INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar. [INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar. [INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar. [INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar. [INFO] Including com.google.code.gson:gson:jar:2.2.4 in the shaded jar. [INFO] Including org.apache.curator:curator-client:jar:2.7.1 in the shaded jar. [INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar. [INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar. [INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar. [INFO] Including it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar. [INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar. [INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar. [INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar. [INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar. [INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar. [INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar. [INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar. [INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar. [INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar. [INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar. [INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar. [INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar. [INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar. [INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar. [INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar. [INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar. [INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar. [INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar. [INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar. [INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar. [INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar. [INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar. [INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar. [INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar. [INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar. [INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar. [INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar. [INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar. [INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar. [INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar. [INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar. [INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar. [INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar. [INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar. [INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar. [INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar. [INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar. [INFO] Including oro:oro:jar:2.0.8 in the shaded jar. [INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar. [INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar. [INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar. [INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar. [INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar. [INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar. [INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar. [INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar. [INFO] Including org.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:2.16.1 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 org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar. [INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar. [INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar. [INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar. [INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar. [INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar. [INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar. [INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.2 in the shaded jar. [INFO] Including org.scalatra:scalatra_2.11:jar:2.4.1 in the shaded jar. [INFO] Including org.scalatra:scalatra-common_2.11:jar:2.4.1 in the shaded jar. [INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.0.2 in the shaded jar. [INFO] Including org.scalatra.rl:rl_2.11:jar:0.4.10 in the shaded jar. [INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar. [INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar. [INFO] Including joda-time:joda-time:jar:2.9.1 in the shaded jar. [INFO] Including org.joda:joda-convert:jar:1.8.1 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar. [INFO] Including org.scalatra.scalate:scalate-core_2.11:jar:1.9.1 in the shaded jar. [INFO] Including org.scala-lang:scala-compiler:jar:2.11.12 in the shaded jar. [INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.9.1 in the shaded jar. [INFO] Including org.bdgenomics.mango:mango-core:jar:0.0.3-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar. [WARNING] mango-core-0.0.3-SNAPSHOT.jar, java-xmlbuilder-1.1.jar define 5 overlapping classes: [WARNING] - com.jamesmurty.utils.NamespaceContextImpl [WARNING] - com.jamesmurty.utils.BaseXMLBuilder [WARNING] - com.jamesmurty.utils.XMLBuilder [WARNING] - com.jamesmurty.utils.XMLBuilder2 [WARNING] - com.jamesmurty.utils.XMLBuilderRuntimeException [WARNING] ngs-java-2.9.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 73 overlapping classes: [WARNING] - ngs.itf.ReadItf [WARNING] - gov.nih.nlm.ncbi.ngs.error.cause.JvmErrorCause [WARNING] - ngs.ReferenceIterator [WARNING] - gov.nih.nlm.ncbi.ngs.Manager$1 [WARNING] - gov.nih.nlm.ncbi.ngs.LMProperties [WARNING] - gov.nih.nlm.ncbi.ngs.error.LibraryLoadError [WARNING] - gov.nih.nlm.ncbi.ngs.LibDependencies [WARNING] - gov.nih.nlm.ncbi.ngs.error.cause.ConnectionProblemCause [WARNING] - ngs.itf.PileupEventItf [WARNING] - gov.nih.nlm.ncbi.ngs.LibManager$Location [WARNING] - 63 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, args4j-2.0.31.jar define 71 overlapping classes: [WARNING] - org.kohsuke.args4j.spi.DoubleOptionHandler [WARNING] - org.kohsuke.args4j.spi.MethodSetter [WARNING] - org.kohsuke.args4j.spi.StringArrayOptionHandler [WARNING] - org.kohsuke.args4j.spi.MacAddressOptionHandler [WARNING] - org.kohsuke.args4j.spi.SubCommand [WARNING] - org.kohsuke.args4j.spi.PatternOptionHandler [WARNING] - org.kohsuke.args4j.ParserProperties$1 [WARNING] - org.kohsuke.args4j.OptionHandlerFilter$2 [WARNING] - org.kohsuke.args4j.spi.MultiFileOptionHandler [WARNING] - org.kohsuke.args4j.Localizable [WARNING] - 61 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jets3t-0.9.4.jar define 616 overlapping classes: [WARNING] - org.jets3t.service.acl.GroupGrantee [WARNING] - org.jets3t.service.multithread.CreateObjectsEvent [WARNING] - org.jets3t.service.model.S3BucketLoggingStatus [WARNING] - contribs.com.centerkey.utils.BareBonesBrowserLaunch [WARNING] - org.jets3t.service.impl.rest.CloudFrontXmlResponsesSaxParser$CacheBehaviorHandler [WARNING] - org.jets3t.apps.uploader.XmlGenerator$ObjectAndSignatureRequestDetails [WARNING] - org.jets3t.service.MultipartUploadChunk [WARNING] - org.jets3t.apps.cockpit.Cockpit$27 [WARNING] - org.jets3t.service.model.S3DeleteMarker [WARNING] - org.jets3t.gui.TableSorter$Row [WARNING] - 606 more... [WARNING] javax.inject-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar, javax.inject-1.jar define 6 overlapping classes: [WARNING] - javax.inject.Inject [WARNING] - javax.inject.Singleton [WARNING] - javax.inject.Named [WARNING] - javax.inject.Scope [WARNING] - javax.inject.Provider [WARNING] - javax.inject.Qualifier [WARNING] mango-core-0.0.3-SNAPSHOT.jar, parquet-scala_2.10-1.8.3.jar define 19 overlapping classes: [WARNING] - org.apache.parquet.filter2.dsl.Dsl$SupportsEqNotEq [WARNING] - org.apache.parquet.filter2.dsl.Dsl$FloatColumn$ [WARNING] - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$Column$class [WARNING] - org.apache.parquet.filter2.dsl.Dsl [WARNING] - org.apache.parquet.filter2.dsl.Dsl$FloatColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$LongColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$BinaryColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$IntColumn$ [WARNING] - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn$ [WARNING] - 9 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-net-2.2.jar define 137 overlapping classes: [WARNING] - org.apache.commons.net.telnet.SimpleOptionHandler [WARNING] - org.apache.commons.net.ftp.parser.FTPFileEntryParserFactory [WARNING] - org.apache.commons.net.DefaultDatagramSocketFactory [WARNING] - org.apache.commons.net.ftp.parser.ConfigurableFTPFileEntryParserImpl [WARNING] - org.apache.commons.net.ntp.NTPUDPClient [WARNING] - org.apache.commons.net.util.SubnetUtils$1 [WARNING] - org.apache.commons.net.tftp.TFTP [WARNING] - org.apache.commons.net.ftp.FTPClient [WARNING] - org.apache.commons.net.echo.EchoTCPClient [WARNING] - org.apache.commons.net.telnet.Telnet [WARNING] - 127 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, ivy-2.4.0.jar define 744 overlapping classes: [WARNING] - org.apache.ivy.ant.IvyDeliver [WARNING] - org.apache.ivy.plugins.resolver.util.ApacheHttpURLLister [WARNING] - org.apache.ivy.ant.BuildOBRTask [WARNING] - org.apache.ivy.osgi.p2.P2MetadataParser$UnitsHandler$1 [WARNING] - org.apache.ivy.core.cache.ResolutionCacheManager [WARNING] - org.apache.ivy.osgi.repo.EditableRepoDescriptor [WARNING] - org.apache.ivy.plugins.parser.AbstractModuleDescriptorParser$AbstractParser [WARNING] - org.apache.ivy.plugins.latest.LatestLexicographicStrategy$1 [WARNING] - org.apache.ivy.osgi.repo.FSManifestIterable$3 [WARNING] - org.apache.ivy.util.url.HttpClientHandler [WARNING] - 734 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, javax.ws.rs-api-2.0.1.jar define 125 overlapping classes: [WARNING] - javax.ws.rs.ext.RuntimeDelegate$HeaderDelegate [WARNING] - javax.ws.rs.DefaultValue [WARNING] - javax.ws.rs.core.StreamingOutput [WARNING] - javax.ws.rs.HEAD [WARNING] - javax.ws.rs.ext.WriterInterceptor [WARNING] - javax.ws.rs.core.Request [WARNING] - javax.ws.rs.ext.Providers [WARNING] - javax.ws.rs.container.Suspended [WARNING] - javax.ws.rs.container.ConnectionCallback [WARNING] - javax.ws.rs.client.FactoryFinder [WARNING] - 115 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-network-common_2.11-2.3.3.jar define 1697 overlapping classes: [WARNING] - org.spark_project.guava.annotations.Beta [WARNING] - org.spark_project.guava.util.concurrent.UncaughtExceptionHandlers$Exiter [WARNING] - org.spark_project.guava.eventbus.Subscribe [WARNING] - org.spark_project.guava.collect.TreeRangeMap [WARNING] - org.spark_project.guava.collect.ImmutableList$SubList [WARNING] - org.spark_project.guava.cache.RemovalCause$1 [WARNING] - org.spark_project.guava.collect.ForwardingMultimap [WARNING] - org.spark_project.guava.io.LimitInputStream [WARNING] - org.spark_project.guava.math.BigIntegerMath [WARNING] - org.spark_project.guava.collect.Tables [WARNING] - 1687 more... [WARNING] error_prone_annotations-2.2.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 22 overlapping classes: [WARNING] - com.google.errorprone.annotations.NoAllocation [WARNING] - com.google.errorprone.annotations.Var [WARNING] - com.google.errorprone.annotations.IncompatibleModifiers [WARNING] - com.google.errorprone.annotations.CompatibleWith [WARNING] - com.google.errorprone.annotations.concurrent.LockMethod [WARNING] - com.google.errorprone.annotations.FormatString [WARNING] - com.google.errorprone.annotations.DoNotCall [WARNING] - com.google.errorprone.annotations.Immutable [WARNING] - com.google.errorprone.annotations.RestrictedApi [WARNING] - com.google.errorprone.annotations.CompileTimeConstant [WARNING] - 12 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-server-2.22.2.jar define 665 overlapping classes: [WARNING] - org.glassfish.jersey.server.internal.inject.ParamConverters$TypeFromString [WARNING] - org.glassfish.jersey.server.internal.inject.QueryParamValueFactoryProvider [WARNING] - org.glassfish.jersey.server.internal.inject.ParamInjectionResolver [WARNING] - org.glassfish.jersey.server.internal.InternalServerProperties [WARNING] - org.glassfish.jersey.server.internal.inject.ParameterInjectionBinder$5 [WARNING] - jersey.repackaged.org.objectweb.asm.FieldWriter [WARNING] - org.glassfish.jersey.server.internal.RuntimeDelegateImpl [WARNING] - org.glassfish.jersey.server.internal.inject.ParamConverterFactory [WARNING] - org.glassfish.jersey.server.internal.monitoring.RequestEventImpl$Builder [WARNING] - org.glassfish.jersey.server.ContainerRequest [WARNING] - 655 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jsr305-1.3.9.jar define 35 overlapping classes: [WARNING] - javax.annotation.RegEx [WARNING] - javax.annotation.concurrent.Immutable [WARNING] - javax.annotation.meta.TypeQualifierDefault [WARNING] - javax.annotation.meta.TypeQualifier [WARNING] - javax.annotation.Syntax [WARNING] - javax.annotation.CheckReturnValue [WARNING] - javax.annotation.CheckForNull [WARNING] - javax.annotation.Nonnull [WARNING] - javax.annotation.meta.TypeQualifierNickname [WARNING] - javax.annotation.MatchesPattern [WARNING] - 25 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, gson-2.2.4.jar define 153 overlapping classes: [WARNING] - com.google.gson.internal.bind.JsonTreeWriter [WARNING] - com.google.gson.internal.Excluder [WARNING] - com.google.gson.JsonDeserializationContext [WARNING] - com.google.gson.FieldNamingPolicy$5 [WARNING] - com.google.gson.internal.LinkedTreeMap$KeySet [WARNING] - com.google.gson.internal.$Gson$Types [WARNING] - com.google.gson.internal.UnsafeAllocator$2 [WARNING] - com.google.gson.internal.bind.SqlDateTypeAdapter$1 [WARNING] - com.google.gson.FieldAttributes [WARNING] - com.google.gson.internal.$Gson$Types$ParameterizedTypeImpl [WARNING] - 143 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, hk2-api-2.4.0-b34.jar define 165 overlapping classes: [WARNING] - org.glassfish.hk2.api.ActiveDescriptor [WARNING] - org.glassfish.hk2.api.Proxiable [WARNING] - org.glassfish.hk2.utilities.InjecteeImpl [WARNING] - org.glassfish.hk2.api.ProxyCtl [WARNING] - org.glassfish.hk2.api.DynamicConfiguration [WARNING] - org.glassfish.hk2.internal.ImmediateHelper$1 [WARNING] - org.glassfish.hk2.api.InjectionResolver [WARNING] - org.glassfish.hk2.utilities.ServiceLocatorUtilities$3 [WARNING] - org.glassfish.hk2.api.Validator [WARNING] - org.glassfish.hk2.api.PopulatorPostProcessor [WARNING] - 155 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jul-to-slf4j-1.7.16.jar define 1 overlapping classes: [WARNING] - org.slf4j.bridge.SLF4JBridgeHandler [WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-xml_2.11-1.0.2.jar define 421 overlapping classes: [WARNING] - scala.xml.PrettyPrinter$Para [WARNING] - scala.xml.Group$ [WARNING] - scala.xml.PrettyPrinter$$anonfun$traverse$1 [WARNING] - scala.xml.MetaData [WARNING] - scala.xml.MalformedAttributeException [WARNING] - scala.xml.pull.EvComment [WARNING] - scala.xml.parsing.TokenTests$$anonfun$isSpace$1 [WARNING] - scala.xml.Properties [WARNING] - scala.xml.parsing.MarkupParser$$anonfun$1 [WARNING] - scala.xml.pull.EvEntityRef$ [WARNING] - 411 more... [WARNING] avro-1.8.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 1172 overlapping classes: [WARNING] - org.apache.avro.message.SchemaStore [WARNING] - avro.shaded.com.google.common.collect.SingletonImmutableList [WARNING] - org.apache.avro.io.EncoderFactory$DefaultEncoderFactory [WARNING] - avro.shaded.com.google.common.collect.Iterables$15 [WARNING] - org.apache.avro.GuavaClasses [WARNING] - avro.shaded.com.google.common.collect.Sets$PowerSet$1$1 [WARNING] - avro.shaded.com.google.common.collect.RegularImmutableMap [WARNING] - org.apache.avro.generic.GenericDatumReader$2 [WARNING] - avro.shaded.com.google.common.collect.Synchronized$SynchronizedSortedSet [WARNING] - org.apache.avro.file.BZip2Codec [WARNING] - 1162 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, aopalliance-repackaged-2.4.0-b34.jar define 17 overlapping classes: [WARNING] - org.aopalliance.reflect.ClassLocator [WARNING] - org.aopalliance.reflect.Metadata [WARNING] - org.aopalliance.instrument.Instrumentation [WARNING] - org.aopalliance.reflect.Field [WARNING] - org.aopalliance.intercept.FieldInterceptor [WARNING] - org.aopalliance.reflect.Method [WARNING] - org.aopalliance.reflect.CodeLocator [WARNING] - org.aopalliance.intercept.FieldAccess [WARNING] - org.aopalliance.reflect.ProgramUnit [WARNING] - org.aopalliance.instrument.UndoNotSupportedException [WARNING] - 7 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, convert-0.6.0.jar define 23 overlapping classes: [WARNING] - org.bdgenomics.convert.bdgenomics.SliceToRead [WARNING] - org.bdgenomics.convert.bdgenomics.SliceToSequence [WARNING] - org.bdgenomics.convert.bdgenomics.BdgenomicsModule [WARNING] - org.bdgenomics.convert.ConversionException [WARNING] - org.bdgenomics.convert.bdgenomics.OntologyTermToString [WARNING] - org.bdgenomics.convert.bdgenomics.StringToVariantAnnotationMessage [WARNING] - org.bdgenomics.convert.ConversionStringency [WARNING] - org.bdgenomics.convert.bdgenomics.ReadToSlice [WARNING] - org.bdgenomics.convert.Converter [WARNING] - org.bdgenomics.convert.bdgenomics.ReadToSequence [WARNING] - 13 more... [WARNING] spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 18 overlapping classes: [WARNING] - org.apache.spark.unsafe.types.UTF8String [WARNING] - org.apache.spark.unsafe.memory.HeapMemoryAllocator [WARNING] - org.apache.spark.unsafe.array.LongArray [WARNING] - org.apache.spark.unsafe.types.UTF8String$LongWrapper [WARNING] - org.apache.spark.unsafe.bitset.BitSetMethods [WARNING] - org.apache.spark.unsafe.memory.UnsafeMemoryAllocator [WARNING] - org.apache.spark.sql.catalyst.expressions.HiveHasher [WARNING] - org.apache.spark.unsafe.KVIterator [WARNING] - org.apache.spark.unsafe.types.CalendarInterval [WARNING] - org.apache.spark.unsafe.memory.MemoryBlock [WARNING] - 8 more... [WARNING] lz4-java-1.4.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 77 overlapping classes: [WARNING] - net.jpountz.xxhash.AbstractStreamingXXHash32Java [WARNING] - net.jpountz.lz4.LZ4BlockInputStream [WARNING] - net.jpountz.lz4.LZ4FrameOutputStream [WARNING] - net.jpountz.xxhash.XXHash32JNI [WARNING] - net.jpountz.lz4.LZ4BlockOutputStream [WARNING] - net.jpountz.lz4.LZ4JNI [WARNING] - net.jpountz.lz4.LZ4JavaUnsafeFastDecompressor [WARNING] - net.jpountz.lz4.LZ4SafeUtils [WARNING] - net.jpountz.xxhash.StreamingXXHash32JNI$Factory [WARNING] - net.jpountz.util.UnsafeUtils [WARNING] - 67 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, curator-recipes-2.6.0.jar define 190 overlapping classes: [WARNING] - org.apache.curator.framework.recipes.atomic.DistributedAtomicNumber [WARNING] - org.apache.curator.framework.recipes.locks.Reaper$State [WARNING] - org.apache.curator.framework.recipes.locks.InterProcessReadWriteLock [WARNING] - org.apache.curator.framework.recipes.queue.QueueBase [WARNING] - org.apache.curator.framework.recipes.locks.ChildReaper$1 [WARNING] - org.apache.curator.framework.recipes.cache.Operation [WARNING] - org.apache.curator.framework.recipes.shared.SharedValue$1 [WARNING] - org.apache.curator.framework.recipes.locks.Revoker [WARNING] - org.apache.curator.framework.recipes.queue.QueueSharderPolicies [WARNING] - org.apache.curator.framework.recipes.locks.StandardLockInternalsDriver [WARNING] - 180 more... [WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar define 1955 overlapping classes: [WARNING] - com.google.common.collect.CompactHashMap$Itr [WARNING] - com.google.common.collect.ImmutableMapValues$1 [WARNING] - com.google.common.util.concurrent.AbstractService$5 [WARNING] - com.google.common.io.LineProcessor [WARNING] - com.google.common.io.BaseEncoding$StandardBaseEncoding$2 [WARNING] - com.google.common.io.ByteProcessor [WARNING] - com.google.common.math.package-info [WARNING] - com.google.common.util.concurrent.SimpleTimeLimiter [WARNING] - com.google.common.cache.AbstractCache$StatsCounter [WARNING] - com.google.common.util.concurrent.CycleDetectingLockFactory$Policies [WARNING] - 1945 more... [WARNING] commons-math3-3.4.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 1215 overlapping classes: [WARNING] - org.apache.commons.math3.optim.linear.LinearOptimizer [WARNING] - org.apache.commons.math3.linear.LUDecomposition$Solver [WARNING] - org.apache.commons.math3.analysis.function.Gaussian$Parametric [WARNING] - org.apache.commons.math3.stat.descriptive.WeightedEvaluation [WARNING] - org.apache.commons.math3.analysis.FunctionUtils$3 [WARNING] - org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic [WARNING] - org.apache.commons.math3.ml.clustering.FuzzyKMeansClusterer [WARNING] - org.apache.commons.math3.analysis.FunctionUtils$3$1 [WARNING] - org.apache.commons.math3.ode.nonstiff.MidpointStepInterpolator [WARNING] - org.apache.commons.math3.ode.ParameterConfiguration [WARNING] - 1205 more... [WARNING] commons-compress-1.8.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 127 overlapping classes: [WARNING] - org.apache.commons.compress.archivers.dump.ShortFileException [WARNING] - org.apache.commons.compress.utils.CountingInputStream [WARNING] - org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream [WARNING] - org.apache.commons.compress.compressors.bzip2.CRC [WARNING] - org.apache.commons.compress.archivers.dump.DumpArchiveEntry [WARNING] - org.apache.commons.compress.compressors.bzip2.BlockSort [WARNING] - org.apache.commons.compress.archivers.tar.TarArchiveEntry [WARNING] - org.apache.commons.compress.archivers.dump.UnsupportedCompressionAlgorithmException [WARNING] - org.apache.commons.compress.archivers.zip.AbstractUnicodeExtraField [WARNING] - org.apache.commons.compress.archivers.dump.InvalidFormatException [WARNING] - 117 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, kryo-shaded-3.0.3.jar define 14 overlapping classes: [WARNING] - com.esotericsoftware.kryo.serializers.VersionFieldSerializer [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Context [WARNING] - com.esotericsoftware.kryo.serializers.EnumNameSerializer [WARNING] - com.esotericsoftware.kryo.serializers.ClosureSerializer [WARNING] - com.esotericsoftware.kryo.pool.KryoPool [WARNING] - com.esotericsoftware.kryo.pool.SoftReferenceQueue [WARNING] - com.esotericsoftware.kryo.pool.KryoCallback [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.TypePath [WARNING] - com.esotericsoftware.reflectasm.PublicConstructorAccess [WARNING] - com.esotericsoftware.kryo.pool.KryoPoolQueueImpl [WARNING] - 4 more... [WARNING] jersey-media-jaxb-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 47 overlapping classes: [WARNING] - org.glassfish.jersey.jaxb.internal.XmlRootElementJaxbProvider$App [WARNING] - org.glassfish.jersey.jaxb.internal.XmlJaxbElementProvider$General [WARNING] - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider$General [WARNING] - org.glassfish.jersey.jaxb.internal.JaxbStringReaderProvider$1 [WARNING] - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider [WARNING] - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$4 [WARNING] - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$General [WARNING] - org.glassfish.jersey.jaxb.internal.JaxbMessagingBinder [WARNING] - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$2 [WARNING] - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$Text [WARNING] - 37 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, paranamer-2.8.jar define 21 overlapping classes: [WARNING] - com.thoughtworks.paranamer.PositionalParanamer [WARNING] - com.thoughtworks.paranamer.JavadocParanamer [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer$Type [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer$1 [WARNING] - com.thoughtworks.paranamer.JavadocParanamer$DirJavadocProvider [WARNING] - com.thoughtworks.paranamer.AnnotationParanamer$Jsr330Helper [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer$TypeCollector [WARNING] - com.thoughtworks.paranamer.AnnotationParanamer [WARNING] - com.thoughtworks.paranamer.NullParanamer [WARNING] - 11 more... [WARNING] chill_2.11-0.8.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 150 overlapping classes: [WARNING] - com.twitter.chill.Tuple11Serializer [WARNING] - com.twitter.chill.InnerClosureFinder [WARNING] - com.twitter.chill.Instantiators$$anonfun$reflectAsm$1 [WARNING] - com.twitter.chill.RichKryo$$anonfun$fromInputStream$1 [WARNING] - com.twitter.chill.package$$anon$3 [WARNING] - com.twitter.chill.JavaIterableWrapperSerializer [WARNING] - com.twitter.chill.Instantiators$$anonfun$newOrElse$1 [WARNING] - com.twitter.chill.SortedMapSerializer$$anonfun$write$1 [WARNING] - com.twitter.chill.package$$anon$5$$anonfun$apply$2 [WARNING] - com.twitter.chill.Tuple8Serializer [WARNING] - 140 more... [WARNING] parquet-encoding-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 184 overlapping classes: [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer14 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer24 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer10 [WARNING] - org.apache.parquet.column.values.bitpacking.LemireBitPackingBE$Packer7 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer20 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer7 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer30 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer13 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer23 [WARNING] - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$Packer19 [WARNING] - 174 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, objenesis-2.1.jar define 37 overlapping classes: [WARNING] - org.objenesis.ObjenesisBase [WARNING] - org.objenesis.instantiator.gcj.GCJInstantiator [WARNING] - org.objenesis.strategy.SingleInstantiatorStrategy [WARNING] - org.objenesis.instantiator.sun.SunReflectionFactoryHelper [WARNING] - org.objenesis.ObjenesisHelper [WARNING] - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator [WARNING] - org.objenesis.instantiator.sun.SunReflectionFactoryInstantiator [WARNING] - org.objenesis.instantiator.basic.NullInstantiator [WARNING] - org.objenesis.instantiator.android.Android17Instantiator [WARNING] - org.objenesis.instantiator.ObjectInstantiator [WARNING] - 27 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, ga4gh-schemas-0.6.0a10.jar define 541 overlapping classes: [WARNING] - ga4gh.AlleleAnnotations$TranscriptEffectOrBuilder [WARNING] - ga4gh.PeerServiceOuterClass$GetInfoResponse$1 [WARNING] - ga4gh.MetadataServiceOuterClass$GetDatasetRequestOrBuilder [WARNING] - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest [WARNING] - ga4gh.RnaQuantificationServiceOuterClass$SearchExpressionLevelsRequest$Builder [WARNING] - ga4gh.GenotypePhenotypeServiceOuterClass$EvidenceQuery$1 [WARNING] - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest$1 [WARNING] - ga4gh.ReferenceServiceOuterClass$ListReferenceBasesResponseOrBuilder [WARNING] - ga4gh.VariantServiceOuterClass$SearchCallSetsRequest [WARNING] - ga4gh.RnaQuantificationServiceOuterClass$GetExpressionLevelRequest [WARNING] - 531 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-io-spark2_2.11-0.2.13.jar define 23 overlapping classes: [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$3 [WARNING] - org.bdgenomics.utils.io.FileLocator [WARNING] - org.bdgenomics.utils.io.ByteAccess [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$readByteStream$1 [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$1 [WARNING] - org.bdgenomics.utils.io.ByteAccess$$anonfun$readFully$2 [WARNING] - org.bdgenomics.utils.io.LocalFileByteAccess [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$2 [WARNING] - org.bdgenomics.utils.io.HTTPFileLocator$ [WARNING] - 13 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, json4s-ast_2.11-3.2.11.jar define 68 overlapping classes: [WARNING] - org.json4s.Merge$Mergeable [WARNING] - org.json4s.Merge$Mergeable$MergeSyntax [WARNING] - org.json4s.Merge$$anonfun$mergeRec$2$1 [WARNING] - org.json4s.BigDecimalMode$class [WARNING] - org.json4s.JsonAST$JBool$ [WARNING] - org.json4s.JsonAST$JField$ [WARNING] - org.json4s.DoubleMode$class [WARNING] - org.json4s.JsonAST$JString [WARNING] - org.json4s.LowPriorityMergeDep$class [WARNING] - org.json4s.JsonAST [WARNING] - 58 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, slf4j-log4j12-1.7.16.jar define 6 overlapping classes: [WARNING] - org.slf4j.impl.Log4jLoggerAdapter [WARNING] - org.slf4j.impl.Log4jMDCAdapter [WARNING] - org.slf4j.impl.StaticMarkerBinder [WARNING] - org.slf4j.impl.Log4jLoggerFactory [WARNING] - org.slf4j.impl.StaticLoggerBinder [WARNING] - org.slf4j.impl.StaticMDCBinder [WARNING] mango-core-0.0.3-SNAPSHOT.jar, minlog-1.3.0.jar, minlog-1.2.jar define 2 overlapping classes: [WARNING] - com.esotericsoftware.minlog.Log [WARNING] - com.esotericsoftware.minlog.Log$Logger [WARNING] mango-core-0.0.3-SNAPSHOT.jar, kryo-shaded-3.0.3.jar, kryo-2.24.0.jar define 193 overlapping classes: [WARNING] - com.esotericsoftware.kryo.serializers.BeanSerializer$1 [WARNING] - com.esotericsoftware.kryo.Registration [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor [WARNING] - com.esotericsoftware.kryo.util.IntMap$Values [WARNING] - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer [WARNING] - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl [WARNING] - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField [WARNING] - com.esotericsoftware.kryo.serializers.JavaSerializer [WARNING] - 183 more... [WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, spark-tags_2.11-2.3.3.jar, spark-launcher_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, spark-kvstore_2.11-2.3.3.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: [WARNING] - org.apache.spark.unused.UnusedStubClass [WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-parser-combinators_2.11-1.0.4.jar define 352 overlapping classes: [WARNING] - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$whitespace$1$$anonfun$apply$20$$anonfun$apply$21 [WARNING] - scala.util.parsing.combinator.ImplicitConversions$$anonfun$flatten5$1 [WARNING] - scala.util.parsing.combinator.Parsers$$anonfun$rep$1 [WARNING] - scala.util.parsing.json.Lexer$$anonfun$number$1$$anonfun$apply$16 [WARNING] - scala.util.parsing.combinator.Parsers$NoSuccess$$anonfun$1 [WARNING] - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$3$$anonfun$apply$3$$anonfun$apply$4 [WARNING] - scala.util.parsing.combinator.token.StdTokens$class [WARNING] - scala.util.parsing.json.Lexer$$anonfun$charSeq$10 [WARNING] - scala.util.parsing.combinator.Parsers$Parser$$anonfun$$tilde$greater$1 [WARNING] - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$5 [WARNING] - 342 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-common-2.22.2.jar define 474 overlapping classes: [WARNING] - org.glassfish.jersey.internal.inject.ContextInjectionResolver$Binder [WARNING] - org.glassfish.jersey.internal.ServiceFinder$ServiceIteratorProvider [WARNING] - org.glassfish.jersey.message.internal.HttpHeaderReader$1 [WARNING] - org.glassfish.jersey.internal.util.collection.KeyComparatorHashMap$1 [WARNING] - org.glassfish.jersey.uri.UriTemplate$1ValuesFromArrayStrategy [WARNING] - org.glassfish.jersey.message.internal.TracingLogger$Level [WARNING] - org.glassfish.jersey.internal.util.PropertyAlias [WARNING] - org.glassfish.jersey.uri.UriTemplate$3 [WARNING] - org.glassfish.jersey.model.internal.ComponentBag$7 [WARNING] - org.glassfish.jersey.spi.AbstractThreadPoolProvider [WARNING] - 464 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, parquet-column-1.8.3.jar define 731 overlapping classes: [WARNING] - org.apache.parquet.it.unimi.dsi.fastutil.longs.LongComparator [WARNING] - org.apache.parquet.filter2.recordlevel.IncrementallyUpdatedFilterPredicateBuilder$25 [WARNING] - org.apache.parquet.column.values.dictionary.DictionaryValuesWriter$PlainIntegerDictionaryValuesWriter [WARNING] - org.apache.parquet.it.unimi.dsi.fastutil.ints.Int2IntLinkedOpenHashMap$MapEntry [WARNING] - org.apache.parquet.io.PrimitiveColumnIO [WARNING] - org.apache.parquet.io.api.Binary$ByteBufferBackedBinary [WARNING] - org.apache.parquet.column.statistics.BooleanStatistics [WARNING] - org.apache.parquet.column.values.boundedint.BoundedIntValuesReader [WARNING] - org.apache.parquet.schema.PrimitiveType$PrimitiveTypeName$3 [WARNING] - org.apache.parquet.it.unimi.dsi.fastutil.doubles.DoubleSortedSet [WARNING] - 721 more... [WARNING] log4j-1.2.17.jar, mango-core-0.0.3-SNAPSHOT.jar define 314 overlapping classes: [WARNING] - org.apache.log4j.or.sax.AttributesRenderer [WARNING] - org.apache.log4j.pattern.MessagePatternConverter [WARNING] - org.apache.log4j.chainsaw.ControlPanel$3 [WARNING] - org.apache.log4j.pattern.NameAbbreviator$DropElementAbbreviator [WARNING] - org.apache.log4j.jmx.MethodUnion [WARNING] - org.apache.log4j.lf5.viewer.LogTable [WARNING] - org.apache.log4j.BasicConfigurator [WARNING] - org.apache.log4j.rewrite.RewriteAppender [WARNING] - org.apache.log4j.lf5.viewer.LogBrokerMonitor$22 [WARNING] - org.apache.log4j.pattern.LoggingEventPatternConverter [WARNING] - 304 more... [WARNING] hk2-utils-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar define 80 overlapping classes: [WARNING] - org.glassfish.hk2.utilities.cache.Cache$1 [WARNING] - org.jvnet.hk2.component.MultiMap$1 [WARNING] - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperImpl$4 [WARNING] - org.glassfish.hk2.utilities.cache.internal.WeakCARCacheImpl$1 [WARNING] - org.glassfish.hk2.utilities.cache.LRUHybridCache [WARNING] - org.glassfish.hk2.utilities.cache.LRUCache [WARNING] - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperUtilities [WARNING] - org.glassfish.hk2.utilities.reflection.ClassReflectionHelper [WARNING] - org.glassfish.hk2.utilities.cache.CacheEntry [WARNING] - org.glassfish.hk2.utilities.reflection.ReflectionHelper [WARNING] - 70 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, base64-2.3.8.jar define 4 overlapping classes: [WARNING] - net.iharder.Base64$InputStream [WARNING] - net.iharder.Base64$OutputStream [WARNING] - net.iharder.Base64$1 [WARNING] - net.iharder.Base64 [WARNING] adam-cli-spark2_2.11-0.26.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 3 overlapping classes: [WARNING] - org.bdgenomics.adam.cli.CommandGroup [WARNING] - org.bdgenomics.adam.cli.InitArgs [WARNING] - org.bdgenomics.adam.cli.CommandGroup$ [WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-misc-spark2_2.11-0.2.13.jar define 11 overlapping classes: [WARNING] - org.bdgenomics.utils.misc.MathUtils [WARNING] - org.bdgenomics.utils.misc.Logging$ [WARNING] - org.bdgenomics.utils.misc.MathUtils$$anonfun$scalarArrayMultiply$1 [WARNING] - org.bdgenomics.utils.misc.Logging$class [WARNING] - org.bdgenomics.utils.misc.Logging$$anonfun$getContextOrClassLoader$1 [WARNING] - org.bdgenomics.utils.misc.MathUtils$$anonfun$aggregateArray$1 [WARNING] - org.bdgenomics.utils.misc.Logging [WARNING] - org.bdgenomics.utils.misc.HadoopUtil$ [WARNING] - org.bdgenomics.utils.misc.MathUtils$$anonfun$softmax$1 [WARNING] - org.bdgenomics.utils.misc.MathUtils$ [WARNING] - 1 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, pyrolite-4.13.jar define 54 overlapping classes: [WARNING] - net.razorvine.pickle.objects.ByteArrayConstructor [WARNING] - net.razorvine.pyro.NameServerProxy [WARNING] - net.razorvine.pyro.serializer.PyroSerializer [WARNING] - net.razorvine.pickle.objects.DateTimeConstructor [WARNING] - net.razorvine.pickle.IObjectConstructor [WARNING] - net.razorvine.pickle.objects.ClassDictConstructor [WARNING] - net.razorvine.pyro.serializer.PyroUriSerpent [WARNING] - net.razorvine.pickle.objects.OperatorAttrGetterForCalendarTz$CalendarLocalizer [WARNING] - net.razorvine.pickle.objects.TimeZoneConstructor [WARNING] - net.razorvine.pyro.Config [WARNING] - 44 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-core_2.11-2.3.3.jar define 8350 overlapping classes: [WARNING] - org.apache.spark.shuffle.BaseShuffleHandle [WARNING] - org.apache.spark.SparkContext$$anonfun$11 [WARNING] - org.spark_project.jetty.client.util.MultiPartContentProvider$1 [WARNING] - org.apache.spark.TaskContextImpl$$anonfun$markTaskFailed$1 [WARNING] - org.apache.spark.util.collection.PrimitiveVector$mcI$sp [WARNING] - org.spark_project.jetty.servlets.PushCacheFilter [WARNING] - org.apache.spark.util.Utils$$anonfun$downloadFile$1 [WARNING] - org.apache.spark.util.JsonProtocol$$anonfun$52 [WARNING] - org.apache.spark.ExecutorAllocationManager$$anonfun$org$apache$spark$ExecutorAllocationManager$$onExecutorAdded$2 [WARNING] - org.apache.spark.rdd.util.PeriodicRDDCheckpointer [WARNING] - 8340 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, adam-codegen-spark2_2.11-0.26.0.jar define 18 overlapping classes: [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$ [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$getters$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$setters$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$apply$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$ [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$fields$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$$anonfun$fields$1 [WARNING] - 8 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, httpclient-4.5.2.jar define 463 overlapping classes: [WARNING] - org.apache.http.impl.cookie.RFC2109Spec [WARNING] - org.apache.http.impl.execchain.MainClientExec [WARNING] - org.apache.http.conn.routing.RouteInfo$TunnelType [WARNING] - org.apache.http.client.methods.HttpGet [WARNING] - org.apache.http.impl.cookie.BrowserCompatSpecFactory [WARNING] - org.apache.http.impl.client.HttpAuthenticator [WARNING] - org.apache.http.conn.ManagedClientConnection [WARNING] - org.apache.http.client.protocol.RequestAuthCache [WARNING] - org.apache.http.conn.params.ConnConnectionParamBean [WARNING] - org.apache.http.impl.client.IdleConnectionEvictor [WARNING] - 453 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-kvstore_2.11-2.3.3.jar define 28 overlapping classes: [WARNING] - org.apache.spark.util.kvstore.LevelDB$TypeAliases [WARNING] - org.apache.spark.util.kvstore.LevelDB$1 [WARNING] - org.apache.spark.util.kvstore.LevelDB$PrefixCache [WARNING] - org.apache.spark.util.kvstore.LevelDBTypeInfo$Index [WARNING] - org.apache.spark.util.kvstore.KVStore [WARNING] - org.apache.spark.util.kvstore.KVTypeInfo [WARNING] - org.apache.spark.util.kvstore.KVIndex [WARNING] - org.apache.spark.util.kvstore.KVStoreIterator [WARNING] - org.apache.spark.util.kvstore.InMemoryStore$InMemoryView [WARNING] - org.apache.spark.util.kvstore.InMemoryStore$1 [WARNING] - 18 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-metrics-spark2_2.11-0.2.13.jar define 407 overlapping classes: [WARNING] - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$reduceByKey$2$$anonfun$apply$33 [WARNING] - org.bdgenomics.utils.instrumentation.SimpleMonitorValueExtractor [WARNING] - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$fullOuterJoin$2 [WARNING] - org.bdgenomics.utils.instrumentation.MetricsListener$$anonfun$onTaskEnd$2 [WARNING] - org.bdgenomics.utils.metrics.Histogram$$anonfun$countSubset$1 [WARNING] - org.bdgenomics.utils.instrumentation.Alignment$ [WARNING] - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$saveAsHadoopFile$3 [WARNING] - org.bdgenomics.utils.instrumentation.Metrics$TreeNode$$anonfun$6 [WARNING] - org.apache.spark.rdd.InstrumentedRDD$$anonfun$reduce$1$$anonfun$apply$35 [WARNING] - org.apache.spark.rdd.InstrumentedRDD$$anonfun$aggregate$1$$anonfun$apply$39$$anonfun$apply$40 [WARNING] - 397 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-launcher_2.11-2.3.3.jar define 34 overlapping classes: [WARNING] - org.apache.spark.launcher.AbstractAppHandle [WARNING] - org.apache.spark.launcher.SparkAppHandle$State [WARNING] - org.apache.spark.launcher.SparkAppHandle$Listener [WARNING] - org.apache.spark.launcher.ChildProcAppHandle [WARNING] - org.apache.spark.launcher.LauncherProtocol [WARNING] - org.apache.spark.launcher.LauncherProtocol$Stop [WARNING] - org.apache.spark.launcher.SparkSubmitOptionParser [WARNING] - org.apache.spark.launcher.LauncherProtocol$Message [WARNING] - org.apache.spark.launcher.CommandBuilderUtils [WARNING] - org.apache.spark.launcher.SparkSubmitCommandBuilder$OptionParser [WARNING] - 24 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, avro-mapred-1.7.7-hadoop2.jar define 126 overlapping classes: [WARNING] - org.apache.avro.mapreduce.AvroMultipleOutputs [WARNING] - org.apache.avro.mapreduce.AvroKeyValueOutputFormat [WARNING] - org.apache.avro.mapred.SequenceFileReader$8 [WARNING] - org.apache.avro.hadoop.file.HadoopCodecFactory [WARNING] - org.apache.avro.mapred.Pair [WARNING] - org.apache.avro.mapred.AvroMultipleOutputs [WARNING] - org.apache.avro.mapred.FsInput [WARNING] - org.apache.avro.mapred.tether.InputProtocol$Callback [WARNING] - org.apache.avro.mapred.AvroOutputFormat$1 [WARNING] - org.apache.avro.hadoop.file.SortedKeyValueFile$Reader$Options [WARNING] - 116 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-logging-1.1.3.jar define 22 overlapping classes: [WARNING] - org.apache.commons.logging.LogSource [WARNING] - org.apache.commons.logging.impl.ServletContextCleaner [WARNING] - org.apache.commons.logging.LogFactory$4 [WARNING] - org.apache.commons.logging.impl.WeakHashtable$1 [WARNING] - org.apache.commons.logging.LogFactory$3 [WARNING] - org.apache.commons.logging.LogFactory$2 [WARNING] - org.apache.commons.logging.impl.LogFactoryImpl$2 [WARNING] - org.apache.commons.logging.impl.LogKitLogger [WARNING] - org.apache.commons.logging.impl.LogFactoryImpl$3 [WARNING] - org.apache.commons.logging.impl.WeakHashtable$Entry [WARNING] - 12 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, htsjdk-2.16.1.jar define 983 overlapping classes: [WARNING] - htsjdk.samtools.cram.ref.ReferenceSource [WARNING] - htsjdk.samtools.HighAccuracyDownsamplingIterator [WARNING] - htsjdk.samtools.util.zip.DeflaterFactory [WARNING] - htsjdk.samtools.filter.DuplicateReadFilter [WARNING] - htsjdk.variant.vcf.VCFEncoder [WARNING] - htsjdk.samtools.util.CloserUtil [WARNING] - htsjdk.tribble.TribbleException$FeatureFileDoesntExist [WARNING] - htsjdk.tribble.index.tabix.TabixIndex [WARNING] - htsjdk.samtools.AbstractBAMFileIndex [WARNING] - htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder$1 [WARNING] - 973 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-intervalrdd-spark2_2.11-0.2.13.jar define 51 overlapping classes: [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$ [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$collect$2 [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$4 [WARNING] - org.bdgenomics.utils.interval.array.Interval$class [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$get$1 [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$4 [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$1 [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$ [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$filter$1 [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$mapValues$1 [WARNING] - 41 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-library-2.11.11.jar define 3828 overlapping classes: [WARNING] - scala.collection.mutable.SortedSet$class [WARNING] - scala.collection.immutable.IndexedSeq [WARNING] - scala.collection.SeqLike$$anonfun$reverseMap$2 [WARNING] - scala.Function2$mcDID$sp [WARNING] - scala.collection.immutable.IntMapValueIterator [WARNING] - scala.collection.MapLike$DefaultKeySet [WARNING] - scala.collection.parallel.FactoryOps$Otherwise [WARNING] - scala.math.Ordering$String$ [WARNING] - scala.util.Either$ [WARNING] - scala.collection.mutable.SetProxy [WARNING] - 3818 more... [WARNING] RoaringBitmap-0.5.11.jar, mango-core-0.0.3-SNAPSHOT.jar define 69 overlapping classes: [WARNING] - org.roaringbitmap.ReverseRunContainerShortIterator [WARNING] - org.roaringbitmap.ShortIterator [WARNING] - org.roaringbitmap.Util [WARNING] - org.roaringbitmap.buffer.RawMappeableRunContainerShortIterator [WARNING] - org.roaringbitmap.buffer.MappeableBitmapContainer [WARNING] - org.roaringbitmap.buffer.BufferFastAggregation$2 [WARNING] - org.roaringbitmap.buffer.MappeableBitmapContainerShortIterator [WARNING] - org.roaringbitmap.RunContainerShortIterator [WARNING] - org.roaringbitmap.buffer.ReverseMappeableArrayContainerShortIterator [WARNING] - org.roaringbitmap.buffer.MappeableContainerPointer [WARNING] - 59 more... [WARNING] jackson-module-scala_2.11-2.6.7.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 403 overlapping classes: [WARNING] - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializer$$anonfun$2 [WARNING] - com.fasterxml.jackson.module.scala.deser.UnsortedSetDeserializerModule [WARNING] - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializerModule$class [WARNING] - com.fasterxml.jackson.module.scala.JacksonModule$$anonfun$1 [WARNING] - com.fasterxml.jackson.module.scala.deser.SortedSetDeserializer$$anonfun$4 [WARNING] - com.fasterxml.jackson.module.scala.util.Options$class [WARNING] - com.fasterxml.jackson.module.scala.util.EnumResolver$ [WARNING] - com.fasterxml.jackson.module.scala.ser.OptionSerializer$$anonfun$serialize$1 [WARNING] - com.fasterxml.jackson.module.scala.ser.OptionSerializerModule [WARNING] - com.fasterxml.jackson.module.scala.modifiers.CollectionLikeTypeModifier$$anonfun$modifyType$3 [WARNING] - 393 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, fastutil-6.5.7.jar define 10653 overlapping classes: [WARNING] - it.unimi.dsi.fastutil.doubles.Double2IntRBTreeMap$Submap$KeySet [WARNING] - it.unimi.dsi.fastutil.longs.Long2CharAVLTreeMap$2$1 [WARNING] - it.unimi.dsi.fastutil.bytes.Byte2ObjectLinkedOpenHashMap$EntryIterator [WARNING] - it.unimi.dsi.fastutil.shorts.Short2FloatOpenCustomHashMap$KeySet [WARNING] - it.unimi.dsi.fastutil.ints.Int2ReferenceRBTreeMap$Submap [WARNING] - it.unimi.dsi.fastutil.bytes.Byte2BooleanRBTreeMap$Submap$1 [WARNING] - it.unimi.dsi.fastutil.floats.AbstractFloat2ShortSortedMap$ValuesCollection [WARNING] - it.unimi.dsi.fastutil.longs.Long2ReferenceRBTreeMap$Submap$2 [WARNING] - it.unimi.dsi.fastutil.chars.AbstractChar2LongSortedMap$ValuesIterator [WARNING] - it.unimi.dsi.fastutil.doubles.DoubleHeaps [WARNING] - 10643 more... [WARNING] curator-client-2.7.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 56 overlapping classes: [WARNING] - org.apache.curator.HandleHolder$Helper [WARNING] - org.apache.curator.utils.PathUtils [WARNING] - org.apache.curator.ensemble.exhibitor.ExhibitorEnsembleProvider$1 [WARNING] - org.apache.curator.utils.CloseableScheduledExecutorService [WARNING] - org.apache.curator.utils.EnsurePath$InitialHelper$1 [WARNING] - org.apache.curator.SessionFailRetryLoop$2 [WARNING] - org.apache.curator.utils.ZKPaths$PathAndNode [WARNING] - org.apache.curator.ensemble.exhibitor.DefaultExhibitorRestClient [WARNING] - org.apache.curator.TimeTrace [WARNING] - org.apache.curator.HandleHolder$1$1 [WARNING] - 46 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, servo-core-0.12.12.jar define 162 overlapping classes: [WARNING] - com.netflix.servo.util.Objects [WARNING] - com.netflix.servo.util.Clock [WARNING] - com.netflix.servo.monitor.MaxGauge [WARNING] - com.netflix.servo.publish.LocalJmxConnector [WARNING] - com.netflix.servo.publish.MonitorRegistryMetricPoller$MonitorValueCallable [WARNING] - com.netflix.servo.util.ExpiringCache$Entry [WARNING] - com.netflix.servo.util.ThreadCpuStats$CpuUsage [WARNING] - com.netflix.servo.tag.SmallTagMap$Builder [WARNING] - com.netflix.servo.stats.StatsConfig [WARNING] - com.netflix.servo.monitor.Monitors$CounterFactory [WARNING] - 152 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-core-2.6.7.jar define 93 overlapping classes: [WARNING] - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer$Bucket [WARNING] - com.fasterxml.jackson.core.FormatSchema [WARNING] - com.fasterxml.jackson.core.io.InputDecorator [WARNING] - com.fasterxml.jackson.core.JsonGenerator$Feature [WARNING] - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer [WARNING] - com.fasterxml.jackson.core.type.ResolvedType [WARNING] - com.fasterxml.jackson.core.io.SegmentedStringWriter [WARNING] - com.fasterxml.jackson.core.TreeNode [WARNING] - com.fasterxml.jackson.core.sym.Name [WARNING] - com.fasterxml.jackson.core.util.JsonGeneratorDelegate [WARNING] - 83 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-io-2.6.jar define 127 overlapping classes: [WARNING] - org.apache.commons.io.FileCleaningTracker [WARNING] - org.apache.commons.io.comparator.SizeFileComparator [WARNING] - org.apache.commons.io.input.CloseShieldInputStream [WARNING] - org.apache.commons.io.ByteOrderParser [WARNING] - org.apache.commons.io.filefilter.EmptyFileFilter [WARNING] - org.apache.commons.io.monitor.FileEntry [WARNING] - org.apache.commons.io.output.ThresholdingOutputStream [WARNING] - org.apache.commons.io.input.TailerListener [WARNING] - org.apache.commons.io.IOExceptionWithCause [WARNING] - org.apache.commons.io.filefilter.NotFileFilter [WARNING] - 117 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, guice-4.2.0.jar define 572 overlapping classes: [WARNING] - com.google.inject.Scope [WARNING] - com.google.inject.Binding [WARNING] - com.google.inject.internal.cglib.core.$EmitUtils$3 [WARNING] - com.google.inject.spi.TypeConverter [WARNING] - com.google.inject.internal.ConstructionProxy [WARNING] - com.google.inject.spi.InjectionPoint [WARNING] - com.google.inject.spi.StaticInjectionRequest [WARNING] - com.google.inject.internal.cglib.proxy.$FixedValueGenerator [WARNING] - com.google.inject.internal.cglib.proxy.$DispatcherGenerator [WARNING] - com.google.inject.spi.Elements$ElementsAsModule [WARNING] - 562 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-cli-spark2_2.11-0.2.13.jar define 23 overlapping classes: [WARNING] - org.bdgenomics.utils.cli.Args4j [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$4 [WARNING] - org.bdgenomics.utils.cli.ParquetArgs [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$3 [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$class [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$2 [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$run$1 [WARNING] - org.bdgenomics.utils.cli.ParquetArgs$class [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$1 [WARNING] - org.bdgenomics.utils.cli.SaveArgs [WARNING] - 13 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, activation-1.1.1.jar define 38 overlapping classes: [WARNING] - javax.activation.DataContentHandlerFactory [WARNING] - javax.activation.ObjectDataContentHandler [WARNING] - javax.activation.DataContentHandler [WARNING] - com.sun.activation.registries.MimeTypeEntry [WARNING] - com.sun.activation.viewers.TextViewer [WARNING] - com.sun.activation.registries.LogSupport [WARNING] - javax.activation.CommandObject [WARNING] - javax.activation.SecuritySupport$2 [WARNING] - com.sun.activation.viewers.TextEditor [WARNING] - com.sun.activation.viewers.ImageViewerCanvas [WARNING] - 28 more... [WARNING] bcprov-jdk15on-1.52.jar, mango-core-0.0.3-SNAPSHOT.jar define 2430 overlapping classes: [WARNING] - org.bouncycastle.crypto.modes.gcm.Tables8kGCMMultiplier [WARNING] - org.bouncycastle.crypto.tls.HeartbeatMode [WARNING] - org.bouncycastle.pqc.math.linearalgebra.GF2nPolynomialElement [WARNING] - org.bouncycastle.jcajce.provider.asymmetric.ecgost.KeyFactorySpi [WARNING] - org.bouncycastle.jcajce.provider.symmetric.AES$AlgParamsCCM [WARNING] - org.bouncycastle.asn1.tsp.TimeStampResp [WARNING] - org.bouncycastle.jcajce.provider.digest.SHA384$Mappings [WARNING] - org.bouncycastle.jcajce.provider.asymmetric.elgamal.AlgorithmParameterGeneratorSpi [WARNING] - org.bouncycastle.asn1.x509.CRLNumber [WARNING] - org.bouncycastle.jcajce.provider.digest.SM3 [WARNING] - 2420 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-databind-2.6.7.1.jar define 563 overlapping classes: [WARNING] - com.fasterxml.jackson.databind.BeanDescription [WARNING] - com.fasterxml.jackson.databind.deser.impl.BeanAsArrayBuilderDeserializer [WARNING] - com.fasterxml.jackson.databind.SerializerProvider [WARNING] - com.fasterxml.jackson.databind.introspect.AnnotatedMethodMap [WARNING] - com.fasterxml.jackson.databind.ser.std.StaticListSerializerBase [WARNING] - com.fasterxml.jackson.databind.ser.std.NumberSerializers$ShortSerializer [WARNING] - com.fasterxml.jackson.databind.ser.BeanSerializerFactory [WARNING] - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonMapFormatVisitor [WARNING] - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatTypes [WARNING] - com.fasterxml.jackson.databind.deser.impl.MethodProperty [WARNING] - 553 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, hadoop-bam-7.9.2.jar define 115 overlapping classes: [WARNING] - org.seqdoop.hadoop_bam.BAMSplitGuesser [WARNING] - org.seqdoop.hadoop_bam.util.SAMHeaderReader [WARNING] - org.seqdoop.hadoop_bam.QseqInputFormat [WARNING] - org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter [WARNING] - org.seqdoop.hadoop_bam.FastaInputFormat$1 [WARNING] - org.seqdoop.hadoop_bam.util.SAMOutputPreparer$1 [WARNING] - org.seqdoop.hadoop_bam.QseqOutputFormat$QseqRecordWriter [WARNING] - org.seqdoop.hadoop_bam.FastaInputFormat [WARNING] - org.seqdoop.hadoop_bam.LineReader [WARNING] - org.seqdoop.hadoop_bam.util.BGZFCodec [WARNING] - 105 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, snappy-java-1.0.5.jar define 12 overlapping classes: [WARNING] - org.xerial.snappy.SnappyLoader [WARNING] - org.xerial.snappy.SnappyOutputStream [WARNING] - org.xerial.snappy.SnappyErrorCode [WARNING] - org.xerial.snappy.SnappyBundleActivator [WARNING] - org.xerial.snappy.SnappyError [WARNING] - org.xerial.snappy.SnappyNativeAPI [WARNING] - org.xerial.snappy.SnappyException [WARNING] - org.xerial.snappy.Snappy [WARNING] - org.xerial.snappy.SnappyNative [WARNING] - org.xerial.snappy.OSInfo [WARNING] - 2 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar define 3 overlapping classes: [WARNING] - org.apache.commons.logging.impl.SLF4JLogFactory [WARNING] - org.apache.commons.logging.impl.SLF4JLocationAwareLog [WARNING] - org.apache.commons.logging.impl.SLF4JLog [WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-json-3.1.5.jar define 11 overlapping classes: [WARNING] - com.codahale.metrics.json.MetricsModule$MetricRegistrySerializer [WARNING] - com.codahale.metrics.json.HealthCheckModule$HealthCheckResultSerializer [WARNING] - com.codahale.metrics.json.HealthCheckModule [WARNING] - com.codahale.metrics.json.MetricsModule$TimerSerializer [WARNING] - com.codahale.metrics.json.MetricsModule$GaugeSerializer [WARNING] - com.codahale.metrics.json.MetricsModule$1 [WARNING] - com.codahale.metrics.json.MetricsModule$MeterSerializer [WARNING] - com.codahale.metrics.json.MetricsModule [WARNING] - com.codahale.metrics.json.MetricsModule$HistogramSerializer [WARNING] - com.codahale.metrics.json.MetricsModule$CounterSerializer [WARNING] - 1 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, checker-qual-2.5.2.jar define 302 overlapping classes: [WARNING] - org.checkerframework.checker.formatter.FormatUtil [WARNING] - org.checkerframework.checker.units.qual.MixedUnits [WARNING] - org.checkerframework.checker.units.qual.PolyUnit [WARNING] - org.checkerframework.checker.regex.qual.PolyRegex [WARNING] - org.checkerframework.checker.units.qual.C [WARNING] - org.checkerframework.checker.formatter.FormatUtil$IllegalFormatConversionCategoryException [WARNING] - org.checkerframework.framework.qual.Unqualified [WARNING] - org.checkerframework.common.reflection.qual.UnknownMethod [WARNING] - org.checkerframework.framework.qual.EnsuresQualifierIf [WARNING] - org.checkerframework.checker.signedness.SignednessUtil [WARNING] - 292 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-tags_2.11-2.3.3.jar define 11 overlapping classes: [WARNING] - org.apache.spark.annotation.Since [WARNING] - org.apache.spark.annotation.InterfaceStability$Stable [WARNING] - org.apache.spark.annotation.package [WARNING] - org.apache.spark.annotation.DeveloperApi [WARNING] - org.apache.spark.annotation.InterfaceStability$Evolving [WARNING] - org.apache.spark.annotation.package$ [WARNING] - org.apache.spark.annotation.Experimental [WARNING] - org.apache.spark.annotation.AlphaComponent [WARNING] - org.apache.spark.annotation.Private [WARNING] - org.apache.spark.annotation.InterfaceStability [WARNING] - 1 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-codec-1.10.jar define 92 overlapping classes: [WARNING] - org.apache.commons.codec.language.Nysiis [WARNING] - org.apache.commons.codec.language.bm.Rule$1 [WARNING] - org.apache.commons.codec.language.bm.Rule$RPattern [WARNING] - org.apache.commons.codec.language.ColognePhonetic$CologneInputBuffer [WARNING] - org.apache.commons.codec.digest.HmacUtils [WARNING] - org.apache.commons.codec.language.bm.BeiderMorseEncoder [WARNING] - org.apache.commons.codec.digest.UnixCrypt [WARNING] - org.apache.commons.codec.language.Soundex [WARNING] - org.apache.commons.codec.binary.BinaryCodec [WARNING] - org.apache.commons.codec.language.bm.Languages$1 [WARNING] - 82 more... [WARNING] jackson-core-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 121 overlapping classes: [WARNING] - org.codehaus.jackson.annotate.JsonManagedReference [WARNING] - org.codehaus.jackson.util.DefaultPrettyPrinter$FixedSpaceIndenter [WARNING] - org.codehaus.jackson.JsonGenerationException [WARNING] - org.codehaus.jackson.util.BufferRecycler$CharBufferType [WARNING] - org.codehaus.jackson.io.UTF32Reader [WARNING] - org.codehaus.jackson.sym.Name1 [WARNING] - org.codehaus.jackson.util.MinimalPrettyPrinter [WARNING] - org.codehaus.jackson.impl.JsonParserBase [WARNING] - org.codehaus.jackson.annotate.JsonValue [WARNING] - org.codehaus.jackson.sym.CharsToNameCanonicalizer$Bucket [WARNING] - 111 more... [WARNING] json4s-jackson_2.11-3.2.11.jar, mango-core-0.0.3-SNAPSHOT.jar define 27 overlapping classes: [WARNING] - org.json4s.jackson.JsonMethods$class [WARNING] - org.json4s.jackson.Json [WARNING] - org.json4s.jackson.Json$ [WARNING] - org.json4s.jackson.JValueSerializerResolver$ [WARNING] - org.json4s.jackson.Json4sModule$ [WARNING] - org.json4s.jackson.JsonMethods$$anonfun$parseOpt$1 [WARNING] - org.json4s.jackson.JValueDeserializerResolver$ [WARNING] - org.json4s.jackson.package [WARNING] - org.json4s.jackson.package$ [WARNING] - org.json4s.jackson.Json4sScalaModule$ [WARNING] - 17 more... [WARNING] parquet-common-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 32 overlapping classes: [WARNING] - org.apache.parquet.SemanticVersion$SemanticVersionParseException [WARNING] - org.apache.parquet.glob.GlobNode$GlobNodeSequence [WARNING] - org.apache.parquet.Ints [WARNING] - org.apache.parquet.Version [WARNING] - org.apache.parquet.glob.GlobNode$Atom [WARNING] - org.apache.parquet.SemanticVersion$NumberOrString [WARNING] - org.apache.parquet.Files [WARNING] - org.apache.parquet.ParquetRuntimeException [WARNING] - org.apache.parquet.glob.GlobNode [WARNING] - org.apache.parquet.io.InputFile [WARNING] - 22 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar, commons-logging-1.1.3.jar define 6 overlapping classes: [WARNING] - org.apache.commons.logging.impl.SimpleLog$1 [WARNING] - org.apache.commons.logging.Log [WARNING] - org.apache.commons.logging.impl.SimpleLog [WARNING] - org.apache.commons.logging.LogConfigurationException [WARNING] - org.apache.commons.logging.impl.NoOpLog [WARNING] - org.apache.commons.logging.LogFactory [WARNING] mango-core-0.0.3-SNAPSHOT.jar, xbean-asm5-shaded-4.4.jar define 81 overlapping classes: [WARNING] - org.apache.xbean.asm5.FieldWriter [WARNING] - org.apache.xbean.asm5.commons.GeneratorAdapter [WARNING] - org.apache.xbean.asm5.AnnotationWriter [WARNING] - org.apache.xbean.asm5.tree.IntInsnNode [WARNING] - org.apache.xbean.asm5.Type [WARNING] - org.apache.xbean.asm5.commons.RemappingClassAdapter [WARNING] - org.apache.xbean.asm5.tree.FieldInsnNode [WARNING] - org.apache.xbean.asm5.tree.MultiANewArrayInsnNode [WARNING] - org.apache.xbean.asm5.tree.IincInsnNode [WARNING] - org.apache.xbean.asm5.tree.InsnList$InsnListIterator [WARNING] - 71 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, lift-json_2.11-3.3.0.jar define 390 overlapping classes: [WARNING] - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$deserialize$2 [WARNING] - net.liftweb.json.TypeInfo$ [WARNING] - net.liftweb.json.JsonAST$JString$ [WARNING] - net.liftweb.json.JsonAST$RenderSettings$ [WARNING] - net.liftweb.json.JsonAST$JDouble$ [WARNING] - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$classFor$2 [WARNING] - net.liftweb.json.JsonAST$RenderSpecialDoubleValuesAsIs$ [WARNING] - net.liftweb.json.Meta$$anonfun$net$liftweb$json$Meta$$fieldMapping$1$4 [WARNING] - net.liftweb.json.Meta$DeclaredConstructor [WARNING] - net.liftweb.json.Formats$$anonfun$customSerializer$1 [WARNING] - 380 more... [WARNING] httpcore-4.4.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 254 overlapping classes: [WARNING] - org.apache.http.protocol.HttpRequestHandler [WARNING] - org.apache.http.impl.io.ChunkedOutputStream [WARNING] - org.apache.http.protocol.ChainBuilder [WARNING] - org.apache.http.impl.entity.DisallowIdentityContentLengthStrategy [WARNING] - org.apache.http.impl.ConnSupport [WARNING] - org.apache.http.impl.io.DefaultHttpResponseParserFactory [WARNING] - org.apache.http.HttpClientConnection [WARNING] - org.apache.http.NameValuePair [WARNING] - org.apache.http.protocol.HttpExpectationVerifier [WARNING] - org.apache.http.protocol.UriPatternMatcher [WARNING] - 244 more... [WARNING] jackson-mapper-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 502 overlapping classes: [WARNING] - org.codehaus.jackson.map.ext.DOMSerializer [WARNING] - org.codehaus.jackson.node.POJONode [WARNING] - org.codehaus.jackson.map.ext.JodaDeserializers$LocalDateDeserializer [WARNING] - org.codehaus.jackson.map.ser.StdSerializers$UtilDateSerializer [WARNING] - org.codehaus.jackson.map.deser.std.JsonNodeDeserializer$ArrayDeserializer [WARNING] - org.codehaus.jackson.map.deser.std.PrimitiveArrayDeserializers$StringDeser [WARNING] - org.codehaus.jackson.map.util.Comparators$1 [WARNING] - org.codehaus.jackson.map.util.StdDateFormat [WARNING] - org.codehaus.jackson.map.KeyDeserializer [WARNING] - org.codehaus.jackson.map.MapperConfig$Impl [WARNING] - 492 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-module-paranamer-2.7.9.jar define 26 overlapping classes: [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.NullParanamer [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.ParameterNamesNotFoundException [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$1 [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$MethodCollector [WARNING] - com.fasterxml.jackson.module.paranamer.SerializableParanamer [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.JavadocParanamer$DirJavadocProvider [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$Type [WARNING] - com.fasterxml.jackson.module.paranamer.ParanamerAnnotationIntrospector [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.CachingParanamer$WithoutWeakReferences [WARNING] - com.fasterxml.jackson.module.paranamer.ParanamerOnJacksonAnnotationIntrospector [WARNING] - 16 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-compiler-2.11.12.jar define 9084 overlapping classes: [WARNING] - scala.tools.nsc.doc.base.CommentFactoryBase$SimpleTagKey [WARNING] - scala.tools.jline_embedded.Terminal [WARNING] - scala.tools.nsc.Global$$anonfun$scala$tools$nsc$Global$$writeICode$1 [WARNING] - scala.tools.nsc.backend.opt.ClosureElimination$ClosureElim$$anonfun$analyzeMethod$1$$anonfun$apply$2 [WARNING] - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$typedCase$2$$anonfun$apply$27 [WARNING] - scala.tools.nsc.backend.icode.analysis.TypeFlowAnalysis$MTFAGrowable$$anonfun$scala$tools$nsc$backend$icode$analysis$TypeFlowAnalysis$MTFAGrowable$$putOnRadar$1$$anonfun$3 [WARNING] - scala.tools.nsc.interpreter.ILoop$$anonfun$standardCommands$3 [WARNING] - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$isReferencedFrom$1 [WARNING] - scala.tools.nsc.typechecker.Typers$Typer$dyna$ [WARNING] - scala.tools.nsc.transform.patmat.MatchAnalysis$MatchAnalyzer$NegativeExample$$anonfun$23 [WARNING] - 9074 more... [WARNING] scala-reflect-2.11.7.jar, mango-core-0.0.3-SNAPSHOT.jar define 2793 overlapping classes: [WARNING] - scala.reflect.runtime.ReflectionUtils [WARNING] - scala.reflect.internal.Types$LazyType [WARNING] - scala.reflect.internal.Scopes$LookupInaccessible$ [WARNING] - scala.reflect.internal.Definitions$DefinitionsClass$$anonfun$newT1NullaryMethod$1 [WARNING] - scala.reflect.internal.SymbolPairs$Cursor [WARNING] - scala.reflect.internal.Types$StaticallyAnnotatedType$ [WARNING] - scala.reflect.runtime.SynchronizedOps$SynchronizedScope$$anonfun$isEmpty$1 [WARNING] - scala.reflect.internal.Kinds$TypeConKind$$anonfun$buildState$3 [WARNING] - scala.reflect.api.StandardLiftables$StandardUnliftableInstances$$anonfun$unliftTuple18$1 [WARNING] - scala.reflect.runtime.SynchronizedSymbols$SynchronizedClassSymbol [WARNING] - 2783 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, adam-core-spark2_2.11-0.26.0.jar define 2708 overlapping classes: [WARNING] - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$74$$anonfun$apply$77 [WARNING] - org.bdgenomics.adam.rdd.feature.FeatureDataset$$anonfun$filterToTranscript$2$$anonfun$apply$9$$anonfun$apply$10 [WARNING] - org.bdgenomics.adam.rdd.read.AlignmentRecordDataset$$typecreator9$1 [WARNING] - org.bdgenomics.adam.sql.VariantCallingAnnotations$$anonfun$toAvro$58 [WARNING] - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$63 [WARNING] - org.bdgenomics.adam.rdd.feature.DatasetBoundFeatureDataset$$anonfun$filterByAttribute$1 [WARNING] - org.bdgenomics.adam.io.InterleavedFastqInputFormat [WARNING] - org.bdgenomics.adam.util.FileMerger$$anonfun$mergeFilesAcrossFilesystems$4 [WARNING] - org.bdgenomics.adam.rdd.fragment.DatasetBoundFragmentDataset [WARNING] - org.bdgenomics.adam.sql.VariantAnnotation$$anonfun$fromAvro$80 [WARNING] - 2698 more... [WARNING] commons-lang3-3.5.jar, mango-core-0.0.3-SNAPSHOT.jar define 260 overlapping classes: [WARNING] - org.apache.commons.lang3.time.StopWatch$State$1 [WARNING] - org.apache.commons.lang3.ThreadUtils$1 [WARNING] - org.apache.commons.lang3.ThreadUtils$ThreadGroupPredicate [WARNING] - org.apache.commons.lang3.builder.MultilineRecursiveToStringStyle [WARNING] - org.apache.commons.lang3.concurrent.AbstractCircuitBreaker [WARNING] - org.apache.commons.lang3.SerializationUtils [WARNING] - org.apache.commons.lang3.time.FastDatePrinter$TwentyFourHourField [WARNING] - org.apache.commons.lang3.LocaleUtils [WARNING] - org.apache.commons.lang3.concurrent.ConcurrentException [WARNING] - org.apache.commons.lang3.CharRange [WARNING] - 250 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, animal-sniffer-annotations-1.17.jar define 1 overlapping classes: [WARNING] - org.codehaus.mojo.animal_sniffer.IgnoreJRERequirement [WARNING] mango-core-0.0.3-SNAPSHOT.jar, leveldbjni-all-1.8.jar define 75 overlapping classes: [WARNING] - org.fusesource.leveldbjni.internal.NativeObject [WARNING] - org.fusesource.leveldbjni.internal.NativeDB$DBJNI [WARNING] - org.fusesource.leveldbjni.internal.NativeCache [WARNING] - org.fusesource.leveldbjni.internal.NativeComparator$ComparatorJNI [WARNING] - org.fusesource.leveldbjni.internal.NativeIterator [WARNING] - org.iq80.leveldb.WriteBatch [WARNING] - org.fusesource.hawtjni.runtime.ClassFlag [WARNING] - org.fusesource.leveldbjni.internal.NativeBuffer$1 [WARNING] - org.iq80.leveldb.DBComparator [WARNING] - org.fusesource.leveldbjni.internal.NativeBuffer$Pool [WARNING] - 65 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, py4j-0.10.7.jar define 67 overlapping classes: [WARNING] - py4j.reflection.TypeConverter [WARNING] - py4j.Py4JJavaServer [WARNING] - py4j.Py4JNetworkException [WARNING] - py4j.reflection.PythonProxyHandler [WARNING] - py4j.reflection.MethodInvoker$1 [WARNING] - py4j.commands.JVMViewCommand [WARNING] - py4j.Py4JClientConnection [WARNING] - py4j.model.Py4JClass [WARNING] - py4j.commands.ReflectionCommand [WARNING] - py4j.commands.MemoryCommand [WARNING] - 57 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, slf4j-api-1.7.7.jar define 24 overlapping classes: [WARNING] - org.slf4j.helpers.SubstituteLogger [WARNING] - org.slf4j.ILoggerFactory [WARNING] - org.slf4j.MDC [WARNING] - org.slf4j.helpers.BasicMDCAdapter [WARNING] - org.slf4j.spi.MDCAdapter [WARNING] - org.slf4j.LoggerFactory [WARNING] - org.slf4j.helpers.Util [WARNING] - org.slf4j.helpers.NOPLogger [WARNING] - org.slf4j.helpers.NOPLoggerFactory [WARNING] - org.slf4j.helpers.SubstituteLoggerFactory [WARNING] - 14 more... [WARNING] jsr203hadoop-1.0.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 27 overlapping classes: [WARNING] - hdfs.jsr203.HadoopDirectoryStream [WARNING] - hdfs.jsr203.HadoopPath [WARNING] - hdfs.jsr203.HadoopFileSystem$1 [WARNING] - hdfs.jsr203.HadoopFileOwnerAttributeView [WARNING] - hdfs.jsr203.HadoopUserPrincipal [WARNING] - hdfs.jsr203.IAttributeReader [WARNING] - hdfs.jsr203.HadoopPath$1 [WARNING] - hdfs.jsr203.HadoopBasicFileAttributes [WARNING] - hdfs.jsr203.HadoopDirectoryStream$1 [WARNING] - hdfs.jsr203.package-info [WARNING] - 17 more... [WARNING] convert-ga4gh-0.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 20 overlapping classes: [WARNING] - org.bdgenomics.convert.ga4gh.CigarOperatorToOperation$1 [WARNING] - org.bdgenomics.convert.ga4gh.BdgenomicsVariantToGa4ghVariant [WARNING] - org.bdgenomics.convert.ga4gh.CigarToCigarUnits [WARNING] - org.bdgenomics.convert.ga4gh.BdgenomicsFeatureToGa4ghFeature [WARNING] - org.bdgenomics.convert.ga4gh.StringToOntologyTerm [WARNING] - org.bdgenomics.convert.ga4gh.ProgramToProcessingStep [WARNING] - org.bdgenomics.convert.ga4gh.Ga4ghReadGroupToBdgenomicsReadGroup [WARNING] - org.bdgenomics.convert.ga4gh.Ga4ghOntologyTermToBdgenomicsOntologyTerm [WARNING] - org.bdgenomics.convert.ga4gh.ProcessingStepToProgram [WARNING] - org.bdgenomics.convert.ga4gh.BdgenomicsStrandToGa4ghStrand [WARNING] - 10 more... [WARNING] stream-2.7.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 78 overlapping classes: [WARNING] - com.clearspring.analytics.stream.cardinality.HyperLogLog [WARNING] - com.clearspring.analytics.stream.membership.DataOutputBuffer [WARNING] - com.clearspring.analytics.stream.quantile.TDigest [WARNING] - com.clearspring.analytics.stream.cardinality.HyperLogLog$SerializationHolder [WARNING] - com.clearspring.analytics.util.ListNode2 [WARNING] - com.clearspring.analytics.stream.frequency.CountMinSketch [WARNING] - com.clearspring.analytics.util.DoublyLinkedList [WARNING] - com.clearspring.analytics.stream.cardinality.CountThenEstimate$CountThenEstimateMergeException [WARNING] - com.clearspring.analytics.stream.quantile.QDigest$1 [WARNING] - com.clearspring.analytics.stream.cardinality.HyperLogLog$HyperLogLogMergeException [WARNING] - 68 more... [WARNING] bdg-formats-0.12.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 61 overlapping classes: [WARNING] - org.bdgenomics.formats.avro.VariantCallingAnnotations$Builder [WARNING] - org.bdgenomics.formats.avro.VariantAnnotation$Builder [WARNING] - org.bdgenomics.formats.avro.Reference$1 [WARNING] - org.bdgenomics.formats.avro.VariantAnnotationMessage [WARNING] - org.bdgenomics.formats.avro.OntologyTerm$1 [WARNING] - org.bdgenomics.formats.avro.Feature$1 [WARNING] - org.bdgenomics.formats.avro.AlignmentRecord [WARNING] - org.bdgenomics.formats.avro.Sequence$1 [WARNING] - org.bdgenomics.formats.avro.ReadGroup$Builder [WARNING] - org.bdgenomics.formats.avro.ReadGroup [WARNING] - 51 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, osgi-resource-locator-1.0.1.jar define 12 overlapping classes: [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$1 [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoader$ProviderFactory [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoader [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$ProvidersPerBundle [WARNING] - org.glassfish.hk2.osgiresourcelocator.ResourceFinderImpl [WARNING] - org.glassfish.hk2.osgiresourcelocator.ResourceFinder [WARNING] - org.glassfish.hk2.osgiresourcelocator.Activator [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$DefaultFactory [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$BundleTracker [WARNING] - 2 more... [WARNING] javax.servlet-api-3.1.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 79 overlapping classes: [WARNING] - javax.servlet.http.Cookie [WARNING] - javax.servlet.ServletContext [WARNING] - javax.servlet.Registration [WARNING] - javax.servlet.http.HttpSessionListener [WARNING] - javax.servlet.http.HttpSessionContext [WARNING] - javax.servlet.FilterChain [WARNING] - javax.servlet.http.WebConnection [WARNING] - javax.servlet.http.HttpServletRequestWrapper [WARNING] - javax.servlet.http.HttpSessionAttributeListener [WARNING] - javax.servlet.annotation.HandlesTypes [WARNING] - 69 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, curator-framework-2.6.0.jar define 167 overlapping classes: [WARNING] - org.apache.curator.framework.imps.TempGetDataBuilderImpl [WARNING] - org.apache.curator.framework.imps.GetDataBuilderImpl$2 [WARNING] - org.apache.curator.framework.imps.CuratorFrameworkImpl$4 [WARNING] - org.apache.curator.framework.state.ConnectionState [WARNING] - org.apache.curator.framework.api.CreateModable [WARNING] - org.apache.curator.framework.imps.SetDataBuilderImpl$4 [WARNING] - org.apache.curator.framework.imps.PathAndBytes [WARNING] - org.apache.curator.framework.api.ACLVersionBackgroundPathable [WARNING] - org.apache.curator.framework.api.ACLCreateModeBackgroundPathAndBytesable [WARNING] - org.apache.curator.framework.listen.ListenerContainer [WARNING] - 157 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, validation-api-1.1.0.Final.jar define 106 overlapping classes: [WARNING] - javax.validation.ConstraintDeclarationException [WARNING] - javax.validation.GroupDefinitionException [WARNING] - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder$LeafNodeBuilderDefinedContext [WARNING] - javax.validation.metadata.ParameterDescriptor [WARNING] - javax.validation.Validator [WARNING] - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder [WARNING] - javax.validation.constraints.AssertTrue$List [WARNING] - javax.validation.constraints.Past [WARNING] - javax.validation.metadata.GroupConversionDescriptor [WARNING] - javax.validation.constraints.Max [WARNING] - 96 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, parquet-avro-1.8.1.jar define 83 overlapping classes: [WARNING] - org.apache.parquet.avro.AvroRecordConverter$AvroCollectionConverter$1 [WARNING] - org.apache.parquet.avro.AvroParquetInputFormat [WARNING] - org.apache.parquet.avro.AvroRecordConverter$AvroArrayConverter$7 [WARNING] - org.apache.parquet.avro.AvroConverters$AvroPrimitiveConverter [WARNING] - org.apache.parquet.avro.AvroWriteSupport$TwoLevelListWriter [WARNING] - org.apache.parquet.avro.AvroConverters$FieldIntegerConverter [WARNING] - org.apache.parquet.avro.AvroCompatRecordMaterializer [WARNING] - org.apache.parquet.avro.AvroIndexedRecordConverter$AvroArrayConverter$1 [WARNING] - org.apache.parquet.avro.AvroWriteSupport$ListWriter [WARNING] - org.apache.parquet.avro.AvroConverters$FieldByteBufferConverter [WARNING] - 73 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, avro-ipc-1.7.7-tests.jar define 248 overlapping classes: [WARNING] - test.StringablesRecord$Builder [WARNING] - org.apache.avro.specific.TestSpecificRecordBuilder [WARNING] - org.apache.avro.test.TestRecordWithUnion$Builder [WARNING] - org.apache.avro.test.TestError [WARNING] - org.apache.avro.test.Kind [WARNING] - org.apache.avro.io.Perf$IntTest [WARNING] - org.apache.avro.Interop$1 [WARNING] - org.apache.avro.test.TestError$Builder [WARNING] - org.apache.avro.TestProtocolReflect$1 [WARNING] - org.apache.avro.ipc.trace.TestFileSpanStorage [WARNING] - 238 more... [WARNING] javax.annotation-api-1.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 15 overlapping classes: [WARNING] - javax.annotation.ManagedBean [WARNING] - javax.annotation.PreDestroy [WARNING] - javax.annotation.Generated [WARNING] - javax.annotation.Resource$AuthenticationType [WARNING] - javax.annotation.security.DeclareRoles [WARNING] - javax.annotation.Priority [WARNING] - javax.annotation.Resource [WARNING] - javax.annotation.security.DenyAll [WARNING] - javax.annotation.security.RunAs [WARNING] - javax.annotation.sql.DataSourceDefinitions [WARNING] - 5 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, javassist-3.18.1-GA.jar define 390 overlapping classes: [WARNING] - javassist.util.proxy.ProxyFactory$3 [WARNING] - javassist.bytecode.FieldInfo [WARNING] - javassist.DirClassPath [WARNING] - javassist.ClassPool$1 [WARNING] - javassist.expr.Cast$ProceedForCast [WARNING] - javassist.URLClassPath [WARNING] - javassist.CtMethod$LongConstParameter [WARNING] - javassist.compiler.Javac$2 [WARNING] - javassist.bytecode.annotation.ClassMemberValue [WARNING] - javassist.bytecode.stackmap.TypeData$ClassName [WARNING] - 380 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, convert-htsjdk-0.6.0.jar define 3 overlapping classes: [WARNING] - org.bdgenomics.convert.htsjdk.HtsjdkModule [WARNING] - org.bdgenomics.convert.htsjdk.ConversionStringencyToValidationStringency [WARNING] - org.bdgenomics.convert.htsjdk.ValidationStringencyToConversionStringency [WARNING] commons-crypto-1.0.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 46 overlapping classes: [WARNING] - org.apache.commons.crypto.stream.PositionedCryptoInputStream [WARNING] - org.apache.commons.crypto.cipher.OpenSsl [WARNING] - org.apache.commons.crypto.random.CryptoRandomFactory$RandomProvider [WARNING] - org.apache.commons.crypto.cipher.OpenSsl$AlgorithmMode [WARNING] - org.apache.commons.crypto.utils.Utils$DefaultPropertiesHolder [WARNING] - org.apache.commons.crypto.Crypto [WARNING] - org.apache.commons.crypto.cipher.OpenSsl$Transform [WARNING] - org.apache.commons.crypto.OpenSslInfoNative [WARNING] - org.apache.commons.crypto.stream.CtrCryptoOutputStream [WARNING] - org.apache.commons.crypto.jna.OpenSslNativeJna [WARNING] - 36 more... [WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar, failureaccess-1.0.jar define 2 overlapping classes: [WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess [WARNING] - com.google.common.util.concurrent.internal.InternalFutures [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-guava-2.22.2.jar define 753 overlapping classes: [WARNING] - jersey.repackaged.com.google.common.collect.AbstractNavigableMap$DescendingMap [WARNING] - jersey.repackaged.com.google.common.collect.AbstractMultiset$ElementSet [WARNING] - jersey.repackaged.com.google.common.collect.Collections2$OrderedPermutationCollection [WARNING] - jersey.repackaged.com.google.common.collect.StandardTable$TableSet [WARNING] - jersey.repackaged.com.google.common.base.Splitter [WARNING] - jersey.repackaged.com.google.common.util.concurrent.Futures$1$1 [WARNING] - jersey.repackaged.com.google.common.base.CharMatcher$5 [WARNING] - jersey.repackaged.com.google.common.collect.SortedMapDifference [WARNING] - jersey.repackaged.com.google.common.collect.ImmutableListMultimap [WARNING] - jersey.repackaged.com.google.common.cache.LocalCache$AbstractReferenceEntry [WARNING] - 743 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, scalap-2.11.11.jar define 581 overlapping classes: [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigEntryParsers$$anonfun$25$$anonfun$apply$13 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$_pmt$1$1 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigParser$$anonfun$scalaSigFromAnnotation$2 [WARNING] - scala.tools.scalap.scalax.rules.StateRules$$anonfun$anyOf$2 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ConstantType$ [WARNING] - scala.tools.scalap.scalax.rules.scalasig.Symbol$class [WARNING] - scala.tools.scalap.scalax.rules.Rule$$anonfun$flatMap$1 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$printSymbolAttributes$1 [WARNING] - scala.tools.scalap.scalax.rules.InRule$$anonfun$unary_$bang$1$$anonfun$apply$1 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.NoType$ [WARNING] - 571 more... [WARNING] jersey-container-servlet-core-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 51 overlapping classes: [WARNING] - org.glassfish.jersey.servlet.WebComponent$3 [WARNING] - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder [WARNING] - org.glassfish.jersey.servlet.internal.LocalizationMessages [WARNING] - org.glassfish.jersey.servlet.WebConfig [WARNING] - org.glassfish.jersey.servlet.spi.FilterUrlMappingsProvider [WARNING] - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder$3 [WARNING] - org.glassfish.jersey.servlet.ServletPropertiesDelegate [WARNING] - org.glassfish.jersey.servlet.WebComponent$7 [WARNING] - org.glassfish.jersey.servlet.internal.ResponseWriter [WARNING] - org.glassfish.jersey.servlet.WebAppResourcesScanner$1 [WARNING] - 41 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, j2objc-annotations-1.1.jar define 12 overlapping classes: [WARNING] - com.google.j2objc.annotations.Property [WARNING] - com.google.j2objc.annotations.RetainedWith [WARNING] - com.google.j2objc.annotations.RetainedLocalRef [WARNING] - com.google.j2objc.annotations.J2ObjCIncompatible [WARNING] - com.google.j2objc.annotations.AutoreleasePool [WARNING] - com.google.j2objc.annotations.LoopTranslation$LoopStyle [WARNING] - com.google.j2objc.annotations.ReflectionSupport$Level [WARNING] - com.google.j2objc.annotations.ReflectionSupport [WARNING] - com.google.j2objc.annotations.Weak [WARNING] - com.google.j2objc.annotations.WeakOuter [WARNING] - 2 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, netty-all-4.1.17.Final.jar define 2501 overlapping classes: [WARNING] - io.netty.handler.codec.http.multipart.InterfaceHttpData$HttpDataType [WARNING] - io.netty.resolver.dns.InflightNameResolver$1 [WARNING] - io.netty.channel.AbstractChannel$AbstractUnsafe$8 [WARNING] - io.netty.handler.codec.smtp.DefaultSmtpRequest [WARNING] - io.netty.handler.codec.redis.RedisMessage [WARNING] - io.netty.handler.codec.memcache.binary.BinaryMemcacheResponse [WARNING] - io.netty.handler.timeout.IdleStateHandler [WARNING] - io.netty.buffer.FixedCompositeByteBuf$Component [WARNING] - io.netty.handler.codec.http.HttpHeaders [WARNING] - io.netty.handler.codec.http2.Http2ClientUpgradeCodec [WARNING] - 2491 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, hk2-locator-2.4.0-b34.jar define 95 overlapping classes: [WARNING] - org.jvnet.hk2.internal.PerLocatorUtilities$1 [WARNING] - org.jvnet.hk2.internal.Utilities$4 [WARNING] - org.jvnet.hk2.internal.ProxyUtilities$2 [WARNING] - org.jvnet.hk2.internal.ServiceLocatorImpl$12 [WARNING] - org.jvnet.hk2.internal.MethodInterceptorInvocationHandler [WARNING] - org.jvnet.hk2.internal.ClazzCreator [WARNING] - org.jvnet.hk2.internal.ValidationInformationImpl [WARNING] - org.jvnet.hk2.internal.ServiceLocatorImpl$6 [WARNING] - org.jvnet.hk2.internal.ConstructorInterceptorHandler$1 [WARNING] - org.jvnet.hk2.internal.ServiceLocatorImpl$IgdValue [WARNING] - 85 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, json4s-core_2.11-3.2.11.jar define 407 overlapping classes: [WARNING] - org.json4s.CustomSerializer [WARNING] - org.json4s.reflect.Reflector$ClassDescriptorBuilder$$anonfun$constructorsAndCompanion$3$$anonfun$13$$anonfun$apply$3 [WARNING] - org.json4s.reflect.package$$anon$2 [WARNING] - org.json4s.DefaultReaders$JValueReader$ [WARNING] - org.json4s.StreamingJsonWriter$$anonfun$addJValue$1 [WARNING] - org.json4s.ParserUtil$RecycledSegment [WARNING] - org.json4s.package [WARNING] - org.json4s.DefaultReaders$ [WARNING] - org.json4s.Xml$$anonfun$directChildren$1$1 [WARNING] - org.json4s.JDoubleJObjectJsonWriter [WARNING] - 397 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, aopalliance-1.0.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: [WARNING] - org.aopalliance.intercept.ConstructorInterceptor [WARNING] - org.aopalliance.intercept.MethodInvocation [WARNING] - org.aopalliance.intercept.MethodInterceptor [WARNING] - org.aopalliance.intercept.Invocation [WARNING] - org.aopalliance.aop.AspectException [WARNING] - org.aopalliance.intercept.Interceptor [WARNING] - org.aopalliance.intercept.Joinpoint [WARNING] - org.aopalliance.aop.Advice [WARNING] - org.aopalliance.intercept.ConstructorInvocation [WARNING] mango-core-0.0.3-SNAPSHOT.jar, oro-2.0.8.jar define 62 overlapping classes: [WARNING] - org.apache.oro.text.perl.MalformedPerl5PatternException [WARNING] - org.apache.oro.text.regex.Perl5Pattern [WARNING] - org.apache.oro.io.RegexFilenameFilter [WARNING] - org.apache.oro.util.Cache [WARNING] - org.apache.oro.text.GenericPatternCache [WARNING] - org.apache.oro.text.awk.DFAState [WARNING] - org.apache.oro.text.regex.StringSubstitution [WARNING] - org.apache.oro.text.awk.AwkCompiler [WARNING] - org.apache.oro.text.PatternCacheLRU [WARNING] - org.apache.oro.text.regex.Substitution [WARNING] - 52 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, netty-3.9.9.Final.jar define 879 overlapping classes: [WARNING] - org.jboss.netty.handler.traffic.TrafficCounter$TrafficMonitoringTask [WARNING] - org.jboss.netty.handler.codec.spdy.SpdyGoAwayFrame [WARNING] - org.jboss.netty.util.internal.jzlib.Deflate [WARNING] - org.jboss.netty.channel.socket.ServerSocketChannelConfig [WARNING] - org.jboss.netty.util.internal.ConcurrentHashMap$HashIterator [WARNING] - org.jboss.netty.handler.codec.serialization.ObjectDecoder [WARNING] - org.jboss.netty.util.internal.jzlib.Tree [WARNING] - org.jboss.netty.util.internal.ConcurrentIdentityWeakKeyHashMap$Segment [WARNING] - org.jboss.netty.util.internal.ConcurrentIdentityHashMap$ValueIterator [WARNING] - org.jboss.netty.handler.codec.http.multipart.HttpPostRequestEncoder [WARNING] - 869 more... [WARNING] jersey-container-servlet-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 6 overlapping classes: [WARNING] - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl [WARNING] - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$ExtensionImpl [WARNING] - org.glassfish.jersey.servlet.init.JerseyServletContainerInitializer [WARNING] - org.glassfish.jersey.servlet.init.FilterUrlMappingsProviderImpl [WARNING] - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$1 [WARNING] - org.glassfish.jersey.servlet.init.internal.LocalizationMessages [WARNING] avro-ipc-1.7.7.jar, mango-core-0.0.3-SNAPSHOT.jar define 114 overlapping classes: [WARNING] - org.apache.avro.ipc.HandshakeRequest$1 [WARNING] - org.apache.avro.ipc.stats.Histogram [WARNING] - org.apache.avro.ipc.stats.Histogram$Entry [WARNING] - org.apache.avro.ipc.trace.Span$Builder [WARNING] - org.apache.avro.ipc.trace.TraceNode [WARNING] - org.apache.avro.ipc.specific.SpecificRequestor [WARNING] - org.apache.avro.ipc.stats.Histogram$SegmenterException [WARNING] - org.apache.avro.ipc.SaslSocketServer$AnonymousServer [WARNING] - org.apache.avro.ipc.stats.Histogram$Segmenter [WARNING] - org.apache.avro.ipc.SaslSocketServer$2 [WARNING] - 104 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, zookeeper-3.4.6.jar define 440 overlapping classes: [WARNING] - org.apache.zookeeper.server.NettyServerCnxn$DumpCommand [WARNING] - org.apache.zookeeper.proto.GetMaxChildrenRequest [WARNING] - org.apache.jute.XmlInputArchive$XMLParser [WARNING] - org.apache.zookeeper.server.NettyServerCnxn$SendBufferWriter [WARNING] - org.apache.jute.CsvInputArchive$1 [WARNING] - org.apache.zookeeper.KeeperException$CodeDeprecated [WARNING] - org.apache.zookeeper.server.ZooKeeperServerMXBean [WARNING] - org.apache.zookeeper.server.NettyServerCnxn$EnvCommand [WARNING] - org.apache.zookeeper.server.quorum.Learner$PacketInFlight [WARNING] - org.apache.zookeeper.Op$Check [WARNING] - 430 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-jvm-3.1.5.jar define 38 overlapping classes: [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$15 [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$3 [WARNING] - com.codahale.metrics.jvm.CachedThreadStatesGaugeSet [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$8 [WARNING] - com.codahale.metrics.jvm.ClassLoadingGaugeSet$1 [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$5 [WARNING] - com.codahale.metrics.jvm.BufferPoolMetricSet [WARNING] - com.codahale.metrics.jvm.ThreadStatesGaugeSet [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$10 [WARNING] - 28 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-core-3.1.5.jar define 115 overlapping classes: [WARNING] - com.codahale.metrics.JmxReporter$JmxGaugeMBean [WARNING] - com.codahale.metrics.ThreadLocalRandomProxy$InternalProvider [WARNING] - com.codahale.metrics.JmxReporter [WARNING] - com.codahale.metrics.EWMA [WARNING] - com.codahale.metrics.Gauge [WARNING] - com.codahale.metrics.MetricRegistry$MetricBuilder$1 [WARNING] - com.codahale.metrics.MetricFilter$1 [WARNING] - com.codahale.metrics.JmxReporter$JmxCounterMBean [WARNING] - com.codahale.metrics.InstrumentedExecutorService$InstrumentedRunnable [WARNING] - com.codahale.metrics.RatioGauge$Ratio [WARNING] - 105 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, zstd-jni-1.3.2-2.jar define 8 overlapping classes: [WARNING] - com.github.luben.zstd.ZstdDirectBufferDecompressingStream [WARNING] - com.github.luben.zstd.ZstdOutputStream [WARNING] - com.github.luben.zstd.ZstdDictCompress [WARNING] - com.github.luben.zstd.ZstdDictDecompress [WARNING] - com.github.luben.zstd.ZstdInputStream [WARNING] - com.github.luben.zstd.Zstd [WARNING] - com.github.luben.zstd.util.Native [WARNING] - com.github.luben.zstd.ZstdDirectBufferCompressingStream [WARNING] mango-core-0.0.3-SNAPSHOT.jar, xz-1.5.jar define 105 overlapping classes: [WARNING] - org.tukaani.xz.lzma.LZMADecoder$LengthDecoder [WARNING] - org.tukaani.xz.index.IndexDecoder [WARNING] - org.tukaani.xz.lzma.LZMADecoder [WARNING] - org.tukaani.xz.lzma.LZMAEncoderFast [WARNING] - org.tukaani.xz.lzma.LZMAEncoder$LengthEncoder [WARNING] - org.tukaani.xz.BlockOutputStream [WARNING] - org.tukaani.xz.simple.SimpleFilter [WARNING] - org.tukaani.xz.rangecoder.RangeCoder [WARNING] - org.tukaani.xz.XZOutputStream [WARNING] - org.tukaani.xz.UncompressedLZMA2OutputStream [WARNING] - 95 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-graphite-3.1.5.jar define 10 overlapping classes: [WARNING] - com.codahale.metrics.graphite.PickledGraphite$MetricTuple [WARNING] - com.codahale.metrics.graphite.GraphiteReporter$Builder [WARNING] - com.codahale.metrics.graphite.Graphite [WARNING] - com.codahale.metrics.graphite.GraphiteRabbitMQ$1 [WARNING] - com.codahale.metrics.graphite.GraphiteSender [WARNING] - com.codahale.metrics.graphite.PickledGraphite [WARNING] - com.codahale.metrics.graphite.GraphiteUDP [WARNING] - com.codahale.metrics.graphite.GraphiteReporter [WARNING] - com.codahale.metrics.graphite.GraphiteReporter$1 [WARNING] - com.codahale.metrics.graphite.GraphiteRabbitMQ [WARNING] jersey-client-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 111 overlapping classes: [WARNING] - org.glassfish.jersey.client.ChunkParser [WARNING] - org.glassfish.jersey.client.HttpUrlConnectorProvider [WARNING] - org.glassfish.jersey.client.JerseyInvocation$EntityPresence [WARNING] - org.glassfish.jersey.client.ResponseCallback [WARNING] - org.glassfish.jersey.client.authentication.RequestAuthenticationException [WARNING] - org.glassfish.jersey.client.JerseyInvocation$5 [WARNING] - org.glassfish.jersey.client.ClientConfig$State$4 [WARNING] - org.glassfish.jersey.client.ClientResponse$1 [WARNING] - org.glassfish.jersey.client.InboundJaxrsResponse$2 [WARNING] - org.glassfish.jersey.client.internal.HttpUrlConnector$5 [WARNING] - 101 more... [WARNING] spark-network-shuffle_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 41 overlapping classes: [WARNING] - org.apache.spark.network.shuffle.RetryingBlockFetcher$1 [WARNING] - org.apache.spark.network.shuffle.protocol.BlockTransferMessage$Type [WARNING] - org.apache.spark.network.shuffle.ShuffleIndexRecord [WARNING] - org.apache.spark.network.sasl.ShuffleSecretManager [WARNING] - org.apache.spark.network.shuffle.SimpleDownloadFile [WARNING] - org.apache.spark.network.shuffle.OneForOneBlockFetcher [WARNING] - org.apache.spark.network.shuffle.ExternalShuffleBlockResolver$2 [WARNING] - org.apache.spark.network.shuffle.ExternalShuffleBlockHandler$ManagedBufferIterator [WARNING] - org.apache.spark.network.shuffle.DownloadFileManager [WARNING] - org.apache.spark.network.shuffle.protocol.RegisterExecutor [WARNING] - 31 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, chill-java-0.8.4.jar define 54 overlapping classes: [WARNING] - com.twitter.chill.java.ClosureSerializer [WARNING] - com.twitter.chill.config.JavaMapConfig [WARNING] - com.twitter.chill.java.IterableRegistrar [WARNING] - com.twitter.chill.java.SqlTimeSerializer [WARNING] - com.twitter.chill.KryoInstantiator [WARNING] - com.twitter.chill.java.PackageRegistrar [WARNING] - com.twitter.chill.config.ConfiguredInstantiator [WARNING] - com.twitter.chill.java.SimpleDateFormatSerializer [WARNING] - com.twitter.chill.KryoInstantiator$4 [WARNING] - com.twitter.chill.java.UnmodifiableSetSerializer [WARNING] - 44 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-jexl-2.1.1.jar define 178 overlapping classes: [WARNING] - org.apache.commons.jexl2.internal.AbstractExecutor$Get [WARNING] - org.apache.commons.jexl2.introspection.JexlPropertyGet [WARNING] - org.apache.commons.jexl2.parser.StringParser [WARNING] - org.apache.commons.jexl2.parser.ASTBitwiseOrNode [WARNING] - org.apache.commons.jexl2.internal.introspection.MethodKey$1 [WARNING] - org.apache.commons.jexl2.Main [WARNING] - org.apache.commons.jexl2.parser.ASTForeachStatement [WARNING] - org.apache.commons.jexl2.introspection.Sandbox [WARNING] - org.apache.commons.jexl2.internal.introspection.ClassMap [WARNING] - org.apache.commons.jexl2.parser.ASTFunctionNode [WARNING] - 168 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-annotations-2.6.0.jar define 58 overlapping classes: [WARNING] - com.fasterxml.jackson.annotation.JsonAutoDetect [WARNING] - com.fasterxml.jackson.annotation.JsonInclude [WARNING] - com.fasterxml.jackson.annotation.ObjectIdGenerators [WARNING] - com.fasterxml.jackson.annotation.JsonFormat$Features [WARNING] - com.fasterxml.jackson.annotation.JsonFormat$Feature [WARNING] - com.fasterxml.jackson.annotation.JsonIgnore [WARNING] - com.fasterxml.jackson.annotation.JsonSetter [WARNING] - com.fasterxml.jackson.annotation.JsonTypeInfo$None [WARNING] - com.fasterxml.jackson.annotation.JsonSubTypes [WARNING] - com.fasterxml.jackson.annotation.JsonFormat$Shape [WARNING] - 48 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, compress-lzf-1.0.3.jar define 42 overlapping classes: [WARNING] - com.ning.compress.lzf.LZFUncompressor [WARNING] - com.ning.compress.BufferRecycler [WARNING] - com.ning.compress.lzf.LZFEncoder [WARNING] - com.ning.compress.lzf.impl.UnsafeChunkEncoderBE [WARNING] - com.ning.compress.lzf.impl.UnsafeChunkEncoderLE [WARNING] - com.ning.compress.gzip.OptimizedGZIPInputStream [WARNING] - com.ning.compress.lzf.util.LZFFileOutputStream$Wrapper [WARNING] - com.ning.compress.lzf.util.LZFFileInputStream$1 [WARNING] - com.ning.compress.lzf.ChunkEncoder [WARNING] - com.ning.compress.lzf.impl.UnsafeChunkDecoder [WARNING] - 32 more... [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT.jar with /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT-shaded.jar [INFO] Dependency-reduced POM written at: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/dependency-reduced-pom.xml [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-cli --- [INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-cli --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-cli >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-cli <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! model contains 26 documentable templates [INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT-javadoc.jar [INFO] [INFO] --- appassembler-maven-plugin:1.10:assemble (default) @ mango-cli --- [INFO] Installing artifact /home/jenkins/.m2/repository/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro/1.8.2/avro-1.8.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro/1.8.2/avro-1.8.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/tukaani/xz/1.5/xz-1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar [INFO] Installing artifact /home/jenkins/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/curator/curator-client/2.7.1/curator-client-2.7.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/curator/curator-client/2.7.1/curator-client-2.7.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/zookeeper/zookeeper/3.4.6/zookeeper-3.4.6.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/zookeeper/zookeeper/3.4.6/zookeeper-3.4.6.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/fusesource/leveldbjni/leveldbjni-all/1.8/leveldbjni-all-1.8.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/fusesource/leveldbjni/leveldbjni-all/1.8/leveldbjni-all-1.8.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.8.1/parquet-avro-1.8.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/it/unimi/dsi/fastutil/6.5.7/fastutil-6.5.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.5.7/fastutil-6.5.7.jar [INFO] Installing artifact /home/jenkins/.m2/repository/commons-codec/commons-codec/1.10/commons-codec-1.10.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/commons-codec/commons-codec/1.10/commons-codec-1.10.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-tags_2.11/2.3.3/spark-tags_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-tags_2.11/2.3.3/spark-tags_2.11-2.3.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo-shaded/3.0.3/kryo-shaded-3.0.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/kryo-shaded/3.0.3/kryo-shaded-3.0.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/minlog/1.3.0/minlog-1.3.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/minlog/1.3.0/minlog-1.3.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-column/1.8.3/parquet-column-1.8.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.8.3/parquet-column-1.8.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-common/1.8.3/parquet-common-1.8.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.8.3/parquet-common-1.8.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-encoding/1.8.3/parquet-encoding-1.8.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.8.3/parquet-encoding-1.8.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-databind/2.6.7.1/jackson-databind-2.6.7.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-databind/2.6.7.1/jackson-databind-2.6.7.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-annotations/2.6.0/jackson-annotations-2.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-annotations/2.6.0/jackson-annotations-2.6.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-core/2.6.7/jackson-core-2.6.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-core/2.6.7/jackson-core-2.6.7.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/xbean/xbean-asm5-shaded/4.4/xbean-asm5-shaded-4.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/xbean/xbean-asm5-shaded/4.4/xbean-asm5-shaded-4.4.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/spark-project/spark/unused/1.0.0/unused-1.0.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/spark-project/spark/unused/1.0.0/unused-1.0.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-scala_2.10/1.8.3/parquet-scala_2.10-1.8.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/parquet/parquet-scala_2.10/1.8.3/parquet-scala_2.10-1.8.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-core_2.11/2.3.3/spark-core_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-core_2.11/2.3.3/spark-core_2.11-2.3.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro-mapred/1.7.7/avro-mapred-1.7.7-hadoop2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro-mapred/1.7.7/avro-mapred-1.7.7-hadoop2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro-ipc/1.7.7/avro-ipc-1.7.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro-ipc/1.7.7/avro-ipc-1.7.7.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro-ipc/1.7.7/avro-ipc-1.7.7-tests.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/avro/avro-ipc/1.7.7/avro-ipc-1.7.7-tests.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/chill_2.11/0.8.4/chill_2.11-0.8.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/twitter/chill_2.11/0.8.4/chill_2.11-0.8.4.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/chill-java/0.8.4/chill-java-0.8.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/twitter/chill-java/0.8.4/chill-java-0.8.4.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-launcher_2.11/2.3.3/spark-launcher_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-launcher_2.11/2.3.3/spark-launcher_2.11-2.3.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-kvstore_2.11/2.3.3/spark-kvstore_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-kvstore_2.11/2.3.3/spark-kvstore_2.11-2.3.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-network-common_2.11/2.3.3/spark-network-common_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-network-common_2.11/2.3.3/spark-network-common_2.11-2.3.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-network-shuffle_2.11/2.3.3/spark-network-shuffle_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-network-shuffle_2.11/2.3.3/spark-network-shuffle_2.11-2.3.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/spark/spark-unsafe_2.11/2.3.3/spark-unsafe_2.11-2.3.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/spark/spark-unsafe_2.11/2.3.3/spark-unsafe_2.11-2.3.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/net/java/dev/jets3t/jets3t/0.9.4/jets3t-0.9.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/java/dev/jets3t/jets3t/0.9.4/jets3t-0.9.4.jar [INFO] Installing artifact /home/jenkins/.m2/repository/javax/activation/activation/1.1.1/activation-1.1.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/activation/activation/1.1.1/activation-1.1.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bouncycastle/bcprov-jdk15on/1.52/bcprov-jdk15on-1.52.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bouncycastle/bcprov-jdk15on/1.52/bcprov-jdk15on-1.52.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/jamesmurty/utils/java-xmlbuilder/1.1/java-xmlbuilder-1.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/jamesmurty/utils/java-xmlbuilder/1.1/java-xmlbuilder-1.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/net/iharder/base64/2.3.8/base64-2.3.8.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/iharder/base64/2.3.8/base64-2.3.8.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/curator/curator-recipes/2.6.0/curator-recipes-2.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/curator/curator-recipes/2.6.0/curator-recipes-2.6.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/curator/curator-framework/2.6.0/curator-framework-2.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/curator/curator-framework/2.6.0/curator-framework-2.6.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/servlet/javax.servlet-api/3.1.0/javax.servlet-api-3.1.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-lang3/3.5/commons-lang3-3.5.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-math3/3.4.1/commons-math3-3.4.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-math3/3.4.1/commons-math3-3.4.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/jul-to-slf4j/1.7.16/jul-to-slf4j-1.7.16.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/jul-to-slf4j/1.7.16/jul-to-slf4j-1.7.16.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/jcl-over-slf4j/1.7.16/jcl-over-slf4j-1.7.16.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/jcl-over-slf4j/1.7.16/jcl-over-slf4j-1.7.16.jar [INFO] Installing artifact /home/jenkins/.m2/repository/log4j/log4j/1.2.17/log4j-1.2.17.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-log4j12/1.7.16/slf4j-log4j12-1.7.16.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.16/slf4j-log4j12-1.7.16.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/ning/compress-lzf/1.0.3/compress-lzf-1.0.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/ning/compress-lzf/1.0.3/compress-lzf-1.0.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/lz4/lz4-java/1.4.0/lz4-java-1.4.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/lz4/lz4-java/1.4.0/lz4-java-1.4.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/github/luben/zstd-jni/1.3.2-2/zstd-jni-1.3.2-2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/github/luben/zstd-jni/1.3.2-2/zstd-jni-1.3.2-2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/roaringbitmap/RoaringBitmap/0.5.11/RoaringBitmap-0.5.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/roaringbitmap/RoaringBitmap/0.5.11/RoaringBitmap-0.5.11.jar [INFO] Installing artifact /home/jenkins/.m2/repository/commons-net/commons-net/2.2/commons-net-2.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/commons-net/commons-net/2.2/commons-net-2.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/json4s/json4s-jackson_2.11/3.2.11/json4s-jackson_2.11-3.2.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/json4s/json4s-jackson_2.11/3.2.11/json4s-jackson_2.11-3.2.11.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/json4s/json4s-core_2.11/3.2.11/json4s-core_2.11-3.2.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/json4s/json4s-core_2.11/3.2.11/json4s-core_2.11-3.2.11.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/json4s/json4s-ast_2.11/3.2.11/json4s-ast_2.11-3.2.11.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/json4s/json4s-ast_2.11/3.2.11/json4s-ast_2.11-3.2.11.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/core/jersey-client/2.22.2/jersey-client-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/core/jersey-client/2.22.2/jersey-client-2.22.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/javax/ws/rs/javax.ws.rs-api/2.0.1/javax.ws.rs-api-2.0.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/ws/rs/javax.ws.rs-api/2.0.1/javax.ws.rs-api-2.0.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/hk2-api/2.4.0-b34/hk2-api-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/hk2-api/2.4.0-b34/hk2-api-2.4.0-b34.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/hk2-utils/2.4.0-b34/hk2-utils-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/hk2-utils/2.4.0-b34/hk2-utils-2.4.0-b34.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/external/aopalliance-repackaged/2.4.0-b34/aopalliance-repackaged-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/external/aopalliance-repackaged/2.4.0-b34/aopalliance-repackaged-2.4.0-b34.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/external/javax.inject/2.4.0-b34/javax.inject-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/external/javax.inject/2.4.0-b34/javax.inject-2.4.0-b34.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/hk2-locator/2.4.0-b34/hk2-locator-2.4.0-b34.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/hk2-locator/2.4.0-b34/hk2-locator-2.4.0-b34.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/javassist/javassist/3.18.1-GA/javassist-3.18.1-GA.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/javassist/javassist/3.18.1-GA/javassist-3.18.1-GA.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/core/jersey-common/2.22.2/jersey-common-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/core/jersey-common/2.22.2/jersey-common-2.22.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/javax/annotation/javax.annotation-api/1.2/javax.annotation-api-1.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/annotation/javax.annotation-api/1.2/javax.annotation-api-1.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/bundles/repackaged/jersey-guava/2.22.2/jersey-guava-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/bundles/repackaged/jersey-guava/2.22.2/jersey-guava-2.22.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/hk2/osgi-resource-locator/1.0.1/osgi-resource-locator-1.0.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/hk2/osgi-resource-locator/1.0.1/osgi-resource-locator-1.0.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/core/jersey-server/2.22.2/jersey-server-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/core/jersey-server/2.22.2/jersey-server-2.22.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/media/jersey-media-jaxb/2.22.2/jersey-media-jaxb-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/media/jersey-media-jaxb/2.22.2/jersey-media-jaxb-2.22.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/javax/validation/validation-api/1.1.0.Final/validation-api-1.1.0.Final.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/validation/validation-api/1.1.0.Final/validation-api-1.1.0.Final.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/containers/jersey-container-servlet/2.22.2/jersey-container-servlet-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/containers/jersey-container-servlet/2.22.2/jersey-container-servlet-2.22.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/glassfish/jersey/containers/jersey-container-servlet-core/2.22.2/jersey-container-servlet-core-2.22.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/glassfish/jersey/containers/jersey-container-servlet-core/2.22.2/jersey-container-servlet-core-2.22.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/io/netty/netty-all/4.1.17.Final/netty-all-4.1.17.Final.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/netty/netty-all/4.1.17.Final/netty-all-4.1.17.Final.jar [INFO] Installing artifact /home/jenkins/.m2/repository/io/netty/netty/3.9.9.Final/netty-3.9.9.Final.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/netty/netty/3.9.9.Final/netty-3.9.9.Final.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/clearspring/analytics/stream/2.7.0/stream-2.7.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/clearspring/analytics/stream/2.7.0/stream-2.7.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/io/dropwizard/metrics/metrics-core/3.1.5/metrics-core-3.1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/dropwizard/metrics/metrics-core/3.1.5/metrics-core-3.1.5.jar [INFO] Installing artifact /home/jenkins/.m2/repository/io/dropwizard/metrics/metrics-jvm/3.1.5/metrics-jvm-3.1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/dropwizard/metrics/metrics-jvm/3.1.5/metrics-jvm-3.1.5.jar [INFO] Installing artifact /home/jenkins/.m2/repository/io/dropwizard/metrics/metrics-json/3.1.5/metrics-json-3.1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/dropwizard/metrics/metrics-json/3.1.5/metrics-json-3.1.5.jar [INFO] Installing artifact /home/jenkins/.m2/repository/io/dropwizard/metrics/metrics-graphite/3.1.5/metrics-graphite-3.1.5.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/io/dropwizard/metrics/metrics-graphite/3.1.5/metrics-graphite-3.1.5.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/module/jackson-module-scala_2.11/2.6.7.1/jackson-module-scala_2.11-2.6.7.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/module/jackson-module-scala_2.11/2.6.7.1/jackson-module-scala_2.11-2.6.7.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/module/jackson-module-paranamer/2.7.9/jackson-module-paranamer-2.7.9.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/fasterxml/jackson/module/jackson-module-paranamer/2.7.9/jackson-module-paranamer-2.7.9.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/ivy/ivy/2.4.0/ivy-2.4.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/ivy/ivy/2.4.0/ivy-2.4.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/oro/oro/2.0.8/oro-2.0.8.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/oro/oro/2.0.8/oro-2.0.8.jar [INFO] Installing artifact /home/jenkins/.m2/repository/net/razorvine/pyrolite/4.13/pyrolite-4.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/razorvine/pyrolite/4.13/pyrolite-4.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/net/sf/py4j/py4j/0.10.7/py4j-0.10.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/sf/py4j/py4j/0.10.7/py4j-0.10.7.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-crypto/1.0.0/commons-crypto-1.0.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-crypto/1.0.0/commons-crypto-1.0.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli-spark2_2.11/0.26.0/adam-cli-spark2_2.11-0.26.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-cli-spark2_2.11/0.26.0/adam-cli-spark2_2.11-0.26.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-apis-spark2_2.11/0.26.0/adam-apis-spark2_2.11-0.26.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-apis-spark2_2.11/0.26.0/adam-apis-spark2_2.11-0.26.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/args4j/args4j/2.0.31/args4j-2.0.31.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/args4j/args4j/2.0.31/args4j-2.0.31.jar [INFO] Installing artifact /home/jenkins/.m2/repository/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/net/codingwell/scala-guice_2.11/4.2.1/scala-guice_2.11-4.2.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/inject/guice/4.2.0/guice-4.2.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/inject/guice/4.2.0/guice-4.2.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/javax/inject/javax.inject/1/javax.inject-1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/javax/inject/javax.inject/1/javax.inject-1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/aopalliance/aopalliance/1.0/aopalliance-1.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/aopalliance/aopalliance/1.0/aopalliance-1.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-core-spark2_2.11/0.26.0/adam-core-spark2_2.11-0.26.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core-spark2_2.11/0.26.0/adam-core-spark2_2.11-0.26.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/objenesis/objenesis/2.1/objenesis-2.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/objenesis/objenesis/2.1/objenesis-2.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/commons-io/commons-io/2.6/commons-io-2.6.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/commons-io/commons-io/2.6/commons-io-2.6.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.9.2/hadoop-bam-7.9.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/github/jsr203hadoop/jsr203hadoop/1.0.3/jsr203hadoop-1.0.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/github/samtools/htsjdk/2.16.1/htsjdk-2.16.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/github/samtools/htsjdk/2.16.1/htsjdk-2.16.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpclient/4.5.2/httpclient-4.5.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.5.2/httpclient-4.5.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpcore/4.4.4/httpcore-4.4.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.4.4/httpcore-4.4.4.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/guava/27.0-jre/guava-27.0-jre.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/failureaccess/1.0/failureaccess-1.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/guava/listenablefuture/9999.0-empty-to-avoid-conflict-with-guava/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/checkerframework/checker-qual/2.5.2/checker-qual-2.5.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/errorprone/error_prone_annotations/2.2.0/error_prone_annotations-2.2.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/j2objc/j2objc-annotations/1.1/j2objc-annotations-1.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/codehaus/mojo/animal-sniffer-annotations/1.17/animal-sniffer-annotations-1.17.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.26.0/adam-codegen-spark2_2.11-0.26.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.26.0/adam-codegen-spark2_2.11-0.26.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.12.0/bdg-formats-0.12.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.12.0/bdg-formats-0.12.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.13/utils-cli-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli-spark2_2.11/0.2.13/utils-cli-spark2_2.11-0.2.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.13/utils-misc-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc-spark2_2.11/0.2.13/utils-misc-spark2_2.11-0.2.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.13/utils-intervalrdd-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-intervalrdd-spark2_2.11/0.2.13/utils-intervalrdd-spark2_2.11-0.2.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.13/utils-metrics-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics-spark2_2.11/0.2.13/utils-metrics-spark2_2.11-0.2.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/servo/servo-core/0.12.12/servo-core-0.12.12.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.12.12/servo-core-0.12.12.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-server/9.4.15.v20190215/jetty-server-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-server/9.4.15.v20190215/jetty-server-9.4.15.v20190215.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-http/9.4.15.v20190215/jetty-http-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-http/9.4.15.v20190215/jetty-http-9.4.15.v20190215.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-util/9.4.15.v20190215/jetty-util-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-util/9.4.15.v20190215/jetty-util-9.4.15.v20190215.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-io/9.4.15.v20190215/jetty-io-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-io/9.4.15.v20190215/jetty-io-9.4.15.v20190215.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-webapp/9.4.15.v20190215/jetty-webapp-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-webapp/9.4.15.v20190215/jetty-webapp-9.4.15.v20190215.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-xml/9.4.15.v20190215/jetty-xml-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-xml/9.4.15.v20190215/jetty-xml-9.4.15.v20190215.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-servlet/9.4.15.v20190215/jetty-servlet-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-servlet/9.4.15.v20190215/jetty-servlet-9.4.15.v20190215.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/eclipse/jetty/jetty-security/9.4.15.v20190215/jetty-security-9.4.15.v20190215.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/eclipse/jetty/jetty-security/9.4.15.v20190215/jetty-security-9.4.15.v20190215.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-reflect/2.11.7/scala-reflect-2.11.7.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-reflect/2.11.7/scala-reflect-2.11.7.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-xml_2.11/1.0.2/scala-xml_2.11-1.0.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra_2.11/2.4.1/scalatra_2.11-2.4.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalatra-common_2.11/2.4.1/scalatra-common_2.11-2.4.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/clapper/grizzled-slf4j_2.11/1.0.2/grizzled-slf4j_2.11-1.0.2.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/clapper/grizzled-slf4j_2.11/1.0.2/grizzled-slf4j_2.11-1.0.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/rl/rl_2.11/0.4.10/rl_2.11-0.4.10.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/googlecode/juniversalchardet/juniversalchardet/1.0.3/juniversalchardet-1.0.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/eu/medsea/mimeutil/mime-util/2.1.3/mime-util-2.1.3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/joda-time/joda-time/2.9.1/joda-time-2.9.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/joda/joda-convert/1.8.1/joda-convert-1.8.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/modules/scala-parser-combinators_2.11/1.0.4/scala-parser-combinators_2.11-1.0.4.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-core_2.11/1.9.1/scalate-core_2.11-1.9.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scala-lang/scala-compiler/2.11.12/scala-compiler-2.11.12.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/scalatra/scalate/scalate-util_2.11/1.9.1/scalate-util_2.11-1.9.1.jar [INFO] Installing artifact /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-core/0.0.3-SNAPSHOT/mango-core-0.0.3-SNAPSHOT.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.13/utils-io-spark2_2.11-0.2.13.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io-spark2_2.11/0.2.13/utils-io-spark2_2.11-0.2.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java/3.0.0-beta-3/protobuf-java-3.0.0-beta-3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/com/google/protobuf/protobuf-java-util/3.0.0-beta-3/protobuf-java-util-3.0.0-beta-3.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/ga4gh/ga4gh-schemas/0.6.0a10/ga4gh-schemas-0.6.0a10.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-ga4gh/0.6.0/convert-ga4gh-0.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-ga4gh/0.6.0/convert-ga4gh-0.6.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert-htsjdk/0.6.0/convert-htsjdk-0.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert-htsjdk/0.6.0/convert-htsjdk-0.6.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/convert/convert/0.6.0/convert-0.6.0.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/convert/convert/0.6.0/convert-0.6.0.jar [INFO] Installing artifact /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/mango-cli-0.0.3-SNAPSHOT.jar to /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-cli/target/appassembler/repo/org/bdgenomics/mango/mango-cli/0.0.3-SNAPSHOT/mango-cli-0.0.3-SNAPSHOT.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Mango: Assembly 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ mango-assembly --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly --- [INFO] Request to add '/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-assembly --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-assembly --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-assembly --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-assembly --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-assembly --- [INFO] Test Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-assembly --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-assembly --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-assembly --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-assembly --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-assembly --- [INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar [INFO] [INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-assembly --- [INFO] Including org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT in the shaded jar. [INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar. [INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar. [INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar. [INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar. [INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar. [INFO] Including it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar. [INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar. [INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar. [INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar. [INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar. [INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar. [INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar. [INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.7 in the shaded jar. [INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar. [INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.12 in the shaded jar. [INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar. [INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar. [INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar. [INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar. [INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar. [INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar. [INFO] Including org.apache.curator:curator-client:jar:2.6.0 in the shaded jar. [INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar. [INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar. [INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar. [INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar. [INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar. [INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar. [INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar. [INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar. [INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar. [INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar. [INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar. [INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar. [INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar. [INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar. [INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar. [INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar. [INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar. [INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar. [INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar. [INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar. [INFO] Including org.scala-lang:scala-reflect:jar:2.11.8 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar. [INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar. [INFO] Including oro:oro:jar:2.0.8 in the shaded jar. [INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar. [INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar. [INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar. [INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar. [INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar. [INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar. [INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar. [INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar. [INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar. [INFO] Including org.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:2.16.1 in the shaded jar. [INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar. [INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar. [INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar. [INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar. [INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar. [INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar. [INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar. [INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar. [INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.scalatra:scalatra_2.11:jar:2.4.1 in the shaded jar. [INFO] Including org.scalatra:scalatra-common_2.11:jar:2.4.1 in the shaded jar. [INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.0.2 in the shaded jar. [INFO] Including org.scalatra.rl:rl_2.11:jar:0.4.10 in the shaded jar. [INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar. [INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar. [INFO] Including joda-time:joda-time:jar:2.9.1 in the shaded jar. [INFO] Including org.joda:joda-convert:jar:1.8.1 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.5 in the shaded jar. [INFO] Including org.scalatra.scalate:scalate-core_2.11:jar:1.9.1 in the shaded jar. [INFO] Including org.scala-lang:scala-compiler:jar:2.11.12 in the shaded jar. [INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.9.1 in the shaded jar. [INFO] Including org.bdgenomics.mango:mango-core:jar:0.0.3-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar. [INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar. [WARNING] mango-core-0.0.3-SNAPSHOT.jar, validation-api-1.1.0.Final.jar, mango-cli-0.0.3-SNAPSHOT.jar define 106 overlapping classes: [WARNING] - javax.validation.ConstraintDeclarationException [WARNING] - javax.validation.GroupDefinitionException [WARNING] - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder$LeafNodeBuilderDefinedContext [WARNING] - javax.validation.metadata.ParameterDescriptor [WARNING] - javax.validation.Validator [WARNING] - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder [WARNING] - javax.validation.constraints.AssertTrue$List [WARNING] - javax.validation.constraints.Past [WARNING] - javax.validation.metadata.GroupConversionDescriptor [WARNING] - javax.validation.constraints.Max [WARNING] - 96 more... [WARNING] javax.servlet-api-3.1.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 79 overlapping classes: [WARNING] - javax.servlet.http.Cookie [WARNING] - javax.servlet.ServletContext [WARNING] - javax.servlet.Registration [WARNING] - javax.servlet.http.HttpSessionListener [WARNING] - javax.servlet.http.HttpSessionContext [WARNING] - javax.servlet.FilterChain [WARNING] - javax.servlet.http.WebConnection [WARNING] - javax.servlet.http.HttpServletRequestWrapper [WARNING] - javax.servlet.http.HttpSessionAttributeListener [WARNING] - javax.servlet.annotation.HandlesTypes [WARNING] - 69 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, avro-ipc-1.7.7-tests.jar define 248 overlapping classes: [WARNING] - test.StringablesRecord$Builder [WARNING] - org.apache.avro.specific.TestSpecificRecordBuilder [WARNING] - org.apache.avro.test.TestRecordWithUnion$Builder [WARNING] - org.apache.avro.test.TestError [WARNING] - org.apache.avro.test.Kind [WARNING] - org.apache.avro.io.Perf$IntTest [WARNING] - org.apache.avro.Interop$1 [WARNING] - org.apache.avro.test.TestError$Builder [WARNING] - org.apache.avro.TestProtocolReflect$1 [WARNING] - org.apache.avro.ipc.trace.TestFileSpanStorage [WARNING] - 238 more... [WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, failureaccess-1.0.jar define 2 overlapping classes: [WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess [WARNING] - com.google.common.util.concurrent.internal.InternalFutures [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, jetty-servlet-9.4.15.v20190215.jar define 48 overlapping classes: [WARNING] - org.eclipse.jetty.servlet.ServletHandler$Default404Servlet [WARNING] - org.eclipse.jetty.servlet.FilterMapping [WARNING] - org.eclipse.jetty.servlet.ErrorPageErrorHandler$PageLookupTechnique [WARNING] - org.eclipse.jetty.servlet.ServletContextHandler [WARNING] - org.eclipse.jetty.servlet.Holder$1 [WARNING] - org.eclipse.jetty.servlet.FilterMapping$1 [WARNING] - org.eclipse.jetty.servlet.ServletContextHandler$ServletContainerInitializerCaller [WARNING] - org.eclipse.jetty.servlet.FilterHolder [WARNING] - org.eclipse.jetty.servlet.Invoker [WARNING] - org.eclipse.jetty.servlet.Holder [WARNING] - 38 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 760 overlapping classes: [WARNING] - shaded.com.google.protobuf.FieldMaskProto [WARNING] - org.bdgenomics.mango.filters.Discovery$$anonfun$4 [WARNING] - shaded.com.google.protobuf.DescriptorProtos$EnumValueDescriptorProto [WARNING] - shaded.com.google.protobuf.NioByteString$1 [WARNING] - scala.tools.nsc.plugins.Plugins$$anonfun$computePluginPhases$1$$anonfun$apply$6 [WARNING] - shaded.com.google.protobuf.GeneratedMessage$BuilderParent [WARNING] - org.bdgenomics.mango.models.LazyMaterialization$$anonfun$put$1$$anonfun$2 [WARNING] - org.bdgenomics.mango.io.BedReader$$anonfun$10$$anonfun$apply$1$$anonfun$apply$2 [WARNING] - shaded.com.google.protobuf.GeneratedMessage$4 [WARNING] - shaded.com.google.protobuf.TextFormat$UnknownFieldParseException [WARNING] - 750 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, htsjdk-2.16.1.jar define 983 overlapping classes: [WARNING] - htsjdk.samtools.cram.ref.ReferenceSource [WARNING] - htsjdk.samtools.HighAccuracyDownsamplingIterator [WARNING] - htsjdk.samtools.util.zip.DeflaterFactory [WARNING] - htsjdk.samtools.filter.DuplicateReadFilter [WARNING] - htsjdk.variant.vcf.VCFEncoder [WARNING] - htsjdk.samtools.util.CloserUtil [WARNING] - htsjdk.tribble.TribbleException$FeatureFileDoesntExist [WARNING] - htsjdk.tribble.index.tabix.TabixIndex [WARNING] - htsjdk.samtools.AbstractBAMFileIndex [WARNING] - htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder$1 [WARNING] - 973 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-io-spark2_2.11-0.2.13.jar, mango-cli-0.0.3-SNAPSHOT.jar define 23 overlapping classes: [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$3 [WARNING] - org.bdgenomics.utils.io.FileLocator [WARNING] - org.bdgenomics.utils.io.ByteAccess [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$readByteStream$1 [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$1 [WARNING] - org.bdgenomics.utils.io.ByteAccess$$anonfun$readFully$2 [WARNING] - org.bdgenomics.utils.io.LocalFileByteAccess [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$2 [WARNING] - org.bdgenomics.utils.io.HTTPFileLocator$ [WARNING] - 13 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, javassist-3.18.1-GA.jar define 390 overlapping classes: [WARNING] - javassist.util.proxy.ProxyFactory$3 [WARNING] - javassist.bytecode.FieldInfo [WARNING] - javassist.DirClassPath [WARNING] - javassist.ClassPool$1 [WARNING] - javassist.expr.Cast$ProceedForCast [WARNING] - javassist.URLClassPath [WARNING] - javassist.CtMethod$LongConstParameter [WARNING] - javassist.compiler.Javac$2 [WARNING] - javassist.bytecode.annotation.ClassMemberValue [WARNING] - javassist.bytecode.stackmap.TypeData$ClassName [WARNING] - 380 more... [WARNING] log4j-1.2.17.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 314 overlapping classes: [WARNING] - org.apache.log4j.or.sax.AttributesRenderer [WARNING] - org.apache.log4j.pattern.MessagePatternConverter [WARNING] - org.apache.log4j.chainsaw.ControlPanel$3 [WARNING] - org.apache.log4j.pattern.NameAbbreviator$DropElementAbbreviator [WARNING] - org.apache.log4j.jmx.MethodUnion [WARNING] - org.apache.log4j.lf5.viewer.LogTable [WARNING] - org.apache.log4j.BasicConfigurator [WARNING] - org.apache.log4j.rewrite.RewriteAppender [WARNING] - org.apache.log4j.lf5.viewer.LogBrokerMonitor$22 [WARNING] - org.apache.log4j.pattern.LoggingEventPatternConverter [WARNING] - 304 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, compress-lzf-1.0.3.jar define 42 overlapping classes: [WARNING] - com.ning.compress.lzf.LZFUncompressor [WARNING] - com.ning.compress.BufferRecycler [WARNING] - com.ning.compress.lzf.LZFEncoder [WARNING] - com.ning.compress.lzf.impl.UnsafeChunkEncoderBE [WARNING] - com.ning.compress.lzf.impl.UnsafeChunkEncoderLE [WARNING] - com.ning.compress.gzip.OptimizedGZIPInputStream [WARNING] - com.ning.compress.lzf.util.LZFFileOutputStream$Wrapper [WARNING] - com.ning.compress.lzf.util.LZFFileInputStream$1 [WARNING] - com.ning.compress.lzf.ChunkEncoder [WARNING] - com.ning.compress.lzf.impl.UnsafeChunkDecoder [WARNING] - 32 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, pyrolite-4.13.jar define 54 overlapping classes: [WARNING] - net.razorvine.pickle.objects.ByteArrayConstructor [WARNING] - net.razorvine.pyro.NameServerProxy [WARNING] - net.razorvine.pyro.serializer.PyroSerializer [WARNING] - net.razorvine.pickle.objects.DateTimeConstructor [WARNING] - net.razorvine.pickle.IObjectConstructor [WARNING] - net.razorvine.pickle.objects.ClassDictConstructor [WARNING] - net.razorvine.pyro.serializer.PyroUriSerpent [WARNING] - net.razorvine.pickle.objects.OperatorAttrGetterForCalendarTz$CalendarLocalizer [WARNING] - net.razorvine.pickle.objects.TimeZoneConstructor [WARNING] - net.razorvine.pyro.Config [WARNING] - 44 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, netty-all-4.1.17.Final.jar define 2501 overlapping classes: [WARNING] - io.netty.handler.codec.http.multipart.InterfaceHttpData$HttpDataType [WARNING] - io.netty.resolver.dns.InflightNameResolver$1 [WARNING] - io.netty.channel.AbstractChannel$AbstractUnsafe$8 [WARNING] - io.netty.handler.codec.smtp.DefaultSmtpRequest [WARNING] - io.netty.handler.codec.redis.RedisMessage [WARNING] - io.netty.handler.codec.memcache.binary.BinaryMemcacheResponse [WARNING] - io.netty.handler.timeout.IdleStateHandler [WARNING] - io.netty.buffer.FixedCompositeByteBuf$Component [WARNING] - io.netty.handler.codec.http.HttpHeaders [WARNING] - io.netty.handler.codec.http2.Http2ClientUpgradeCodec [WARNING] - 2491 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-metrics-spark2_2.11-0.2.13.jar, mango-cli-0.0.3-SNAPSHOT.jar define 407 overlapping classes: [WARNING] - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$reduceByKey$2$$anonfun$apply$33 [WARNING] - org.bdgenomics.utils.instrumentation.SimpleMonitorValueExtractor [WARNING] - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$fullOuterJoin$2 [WARNING] - org.bdgenomics.utils.instrumentation.MetricsListener$$anonfun$onTaskEnd$2 [WARNING] - org.bdgenomics.utils.metrics.Histogram$$anonfun$countSubset$1 [WARNING] - org.bdgenomics.utils.instrumentation.Alignment$ [WARNING] - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$saveAsHadoopFile$3 [WARNING] - org.bdgenomics.utils.instrumentation.Metrics$TreeNode$$anonfun$6 [WARNING] - org.apache.spark.rdd.InstrumentedRDD$$anonfun$reduce$1$$anonfun$apply$35 [WARNING] - org.apache.spark.rdd.InstrumentedRDD$$anonfun$aggregate$1$$anonfun$apply$39$$anonfun$apply$40 [WARNING] - 397 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, parquet-column-1.8.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 731 overlapping classes: [WARNING] - org.apache.parquet.it.unimi.dsi.fastutil.longs.LongComparator [WARNING] - org.apache.parquet.filter2.recordlevel.IncrementallyUpdatedFilterPredicateBuilder$25 [WARNING] - org.apache.parquet.column.values.dictionary.DictionaryValuesWriter$PlainIntegerDictionaryValuesWriter [WARNING] - org.apache.parquet.it.unimi.dsi.fastutil.ints.Int2IntLinkedOpenHashMap$MapEntry [WARNING] - org.apache.parquet.io.PrimitiveColumnIO [WARNING] - org.apache.parquet.io.api.Binary$ByteBufferBackedBinary [WARNING] - org.apache.parquet.column.statistics.BooleanStatistics [WARNING] - org.apache.parquet.column.values.boundedint.BoundedIntValuesReader [WARNING] - org.apache.parquet.schema.PrimitiveType$PrimitiveTypeName$3 [WARNING] - org.apache.parquet.it.unimi.dsi.fastutil.doubles.DoubleSortedSet [WARNING] - 721 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, leveldbjni-all-1.8.jar define 75 overlapping classes: [WARNING] - org.fusesource.leveldbjni.internal.NativeObject [WARNING] - org.fusesource.leveldbjni.internal.NativeDB$DBJNI [WARNING] - org.fusesource.leveldbjni.internal.NativeCache [WARNING] - org.fusesource.leveldbjni.internal.NativeComparator$ComparatorJNI [WARNING] - org.fusesource.leveldbjni.internal.NativeIterator [WARNING] - org.iq80.leveldb.WriteBatch [WARNING] - org.fusesource.hawtjni.runtime.ClassFlag [WARNING] - org.fusesource.leveldbjni.internal.NativeBuffer$1 [WARNING] - org.iq80.leveldb.DBComparator [WARNING] - org.fusesource.leveldbjni.internal.NativeBuffer$Pool [WARNING] - 65 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, slf4j-api-1.7.7.jar define 24 overlapping classes: [WARNING] - org.slf4j.helpers.SubstituteLogger [WARNING] - org.slf4j.ILoggerFactory [WARNING] - org.slf4j.MDC [WARNING] - org.slf4j.helpers.BasicMDCAdapter [WARNING] - org.slf4j.spi.MDCAdapter [WARNING] - org.slf4j.LoggerFactory [WARNING] - org.slf4j.helpers.Util [WARNING] - org.slf4j.helpers.NOPLogger [WARNING] - org.slf4j.helpers.NOPLoggerFactory [WARNING] - org.slf4j.helpers.SubstituteLoggerFactory [WARNING] - 14 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, convert-htsjdk-0.6.0.jar define 3 overlapping classes: [WARNING] - org.bdgenomics.convert.htsjdk.HtsjdkModule [WARNING] - org.bdgenomics.convert.htsjdk.ConversionStringencyToValidationStringency [WARNING] - org.bdgenomics.convert.htsjdk.ValidationStringencyToConversionStringency [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, scala-library-2.11.11.jar define 3828 overlapping classes: [WARNING] - scala.collection.mutable.SortedSet$class [WARNING] - scala.collection.immutable.IndexedSeq [WARNING] - scala.collection.SeqLike$$anonfun$reverseMap$2 [WARNING] - scala.Function2$mcDID$sp [WARNING] - scala.collection.immutable.IntMapValueIterator [WARNING] - scala.collection.MapLike$DefaultKeySet [WARNING] - scala.collection.parallel.FactoryOps$Otherwise [WARNING] - scala.math.Ordering$String$ [WARNING] - scala.util.Either$ [WARNING] - scala.collection.mutable.SetProxy [WARNING] - 3818 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, objenesis-2.1.jar define 37 overlapping classes: [WARNING] - org.objenesis.ObjenesisBase [WARNING] - org.objenesis.instantiator.gcj.GCJInstantiator [WARNING] - org.objenesis.strategy.SingleInstantiatorStrategy [WARNING] - org.objenesis.instantiator.sun.SunReflectionFactoryHelper [WARNING] - org.objenesis.ObjenesisHelper [WARNING] - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator [WARNING] - org.objenesis.instantiator.sun.SunReflectionFactoryInstantiator [WARNING] - org.objenesis.instantiator.basic.NullInstantiator [WARNING] - org.objenesis.instantiator.android.Android17Instantiator [WARNING] - org.objenesis.instantiator.ObjectInstantiator [WARNING] - 27 more... [WARNING] jersey-media-jaxb-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 47 overlapping classes: [WARNING] - org.glassfish.jersey.jaxb.internal.XmlRootElementJaxbProvider$App [WARNING] - org.glassfish.jersey.jaxb.internal.XmlJaxbElementProvider$General [WARNING] - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider$General [WARNING] - org.glassfish.jersey.jaxb.internal.JaxbStringReaderProvider$1 [WARNING] - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider [WARNING] - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$4 [WARNING] - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$General [WARNING] - org.glassfish.jersey.jaxb.internal.JaxbMessagingBinder [WARNING] - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$2 [WARNING] - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$Text [WARNING] - 37 more... [WARNING] chill_2.11-0.8.4.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 150 overlapping classes: [WARNING] - com.twitter.chill.Tuple11Serializer [WARNING] - com.twitter.chill.InnerClosureFinder [WARNING] - com.twitter.chill.Instantiators$$anonfun$reflectAsm$1 [WARNING] - com.twitter.chill.RichKryo$$anonfun$fromInputStream$1 [WARNING] - com.twitter.chill.package$$anon$3 [WARNING] - com.twitter.chill.JavaIterableWrapperSerializer [WARNING] - com.twitter.chill.Instantiators$$anonfun$newOrElse$1 [WARNING] - com.twitter.chill.SortedMapSerializer$$anonfun$write$1 [WARNING] - com.twitter.chill.package$$anon$5$$anonfun$apply$2 [WARNING] - com.twitter.chill.Tuple8Serializer [WARNING] - 140 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, animal-sniffer-annotations-1.17.jar define 1 overlapping classes: [WARNING] - org.codehaus.mojo.animal_sniffer.IgnoreJRERequirement [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, jetty-server-9.4.15.v20190215.jar define 302 overlapping classes: [WARNING] - org.eclipse.jetty.server.handler.ThreadLimitHandler$RFC7239 [WARNING] - org.eclipse.jetty.server.handler.ManagedAttributeListener [WARNING] - org.eclipse.jetty.server.ServletRequestHttpWrapper [WARNING] - org.eclipse.jetty.server.DebugListener$1 [WARNING] - org.eclipse.jetty.server.ShutdownMonitor$1 [WARNING] - org.eclipse.jetty.server.HttpInput$1 [WARNING] - org.eclipse.jetty.server.UserIdentity$Scope [WARNING] - org.eclipse.jetty.server.AcceptRateLimit$1 [WARNING] - org.eclipse.jetty.server.session.AbstractSessionDataStoreFactory [WARNING] - org.eclipse.jetty.server.AsyncContextState$1 [WARNING] - 292 more... [WARNING] stream-2.7.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 78 overlapping classes: [WARNING] - com.clearspring.analytics.stream.cardinality.HyperLogLog [WARNING] - com.clearspring.analytics.stream.membership.DataOutputBuffer [WARNING] - com.clearspring.analytics.stream.quantile.TDigest [WARNING] - com.clearspring.analytics.stream.cardinality.HyperLogLog$SerializationHolder [WARNING] - com.clearspring.analytics.util.ListNode2 [WARNING] - com.clearspring.analytics.stream.frequency.CountMinSketch [WARNING] - com.clearspring.analytics.util.DoublyLinkedList [WARNING] - com.clearspring.analytics.stream.cardinality.CountThenEstimate$CountThenEstimateMergeException [WARNING] - com.clearspring.analytics.stream.quantile.QDigest$1 [WARNING] - com.clearspring.analytics.stream.cardinality.HyperLogLog$HyperLogLogMergeException [WARNING] - 68 more... [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, jetty-webapp-9.4.15.v20190215.jar define 51 overlapping classes: [WARNING] - org.eclipse.jetty.webapp.FragmentDescriptor [WARNING] - org.eclipse.jetty.webapp.CachingWebAppClassLoader [WARNING] - org.eclipse.jetty.webapp.ClasspathPattern$ClassEntry [WARNING] - org.eclipse.jetty.webapp.WebAppContext [WARNING] - org.eclipse.jetty.webapp.ClasspathPattern$ByClass [WARNING] - org.eclipse.jetty.webapp.CloneConfiguration [WARNING] - org.eclipse.jetty.webapp.RelativeOrdering$1 [WARNING] - org.eclipse.jetty.webapp.Configuration$ClassList [WARNING] - org.eclipse.jetty.webapp.ClasspathPattern$ByModule [WARNING] - org.eclipse.jetty.webapp.StandardDescriptorProcessor$1 [WARNING] - 41 more... [WARNING] jersey-container-servlet-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 6 overlapping classes: [WARNING] - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl [WARNING] - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$ExtensionImpl [WARNING] - org.glassfish.jersey.servlet.init.JerseyServletContainerInitializer [WARNING] - org.glassfish.jersey.servlet.init.FilterUrlMappingsProviderImpl [WARNING] - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$1 [WARNING] - org.glassfish.jersey.servlet.init.internal.LocalizationMessages [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, joda-convert-1.8.1.jar define 94 overlapping classes: [WARNING] - org.joda.convert.JDKStringConverter$18 [WARNING] - org.joda.convert.JDKStringConverter$28 [WARNING] - org.joda.convert.factory.NumericArrayStringConverterFactory$FloatArrayStringConverter [WARNING] - org.joda.convert.JDKStringConverter$1 [WARNING] - org.joda.convert.factory.BooleanArrayStringConverterFactory [WARNING] - org.joda.convert.factory.NumericObjectArrayStringConverterFactory [WARNING] - org.joda.convert.FromString [WARNING] - org.joda.convert.StringConverter [WARNING] - org.joda.convert.StringConvert$1 [WARNING] - org.joda.convert.factory.CharObjectArrayStringConverterFactory$CharecterArrayStringConverter [WARNING] - 84 more... [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, guice-4.2.0.jar define 1 overlapping classes: [WARNING] - com.google.inject.internal.asm.$Item [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-network-common_2.11-2.3.3.jar define 1697 overlapping classes: [WARNING] - org.spark_project.guava.annotations.Beta [WARNING] - org.spark_project.guava.util.concurrent.UncaughtExceptionHandlers$Exiter [WARNING] - org.spark_project.guava.eventbus.Subscribe [WARNING] - org.spark_project.guava.collect.TreeRangeMap [WARNING] - org.spark_project.guava.collect.ImmutableList$SubList [WARNING] - org.spark_project.guava.cache.RemovalCause$1 [WARNING] - org.spark_project.guava.collect.ForwardingMultimap [WARNING] - org.spark_project.guava.io.LimitInputStream [WARNING] - org.spark_project.guava.math.BigIntegerMath [WARNING] - org.spark_project.guava.collect.Tables [WARNING] - 1687 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, json4s-core_2.11-3.2.11.jar, mango-cli-0.0.3-SNAPSHOT.jar define 407 overlapping classes: [WARNING] - org.json4s.CustomSerializer [WARNING] - org.json4s.reflect.Reflector$ClassDescriptorBuilder$$anonfun$constructorsAndCompanion$3$$anonfun$13$$anonfun$apply$3 [WARNING] - org.json4s.reflect.package$$anon$2 [WARNING] - org.json4s.DefaultReaders$JValueReader$ [WARNING] - org.json4s.StreamingJsonWriter$$anonfun$addJValue$1 [WARNING] - org.json4s.ParserUtil$RecycledSegment [WARNING] - org.json4s.package [WARNING] - org.json4s.DefaultReaders$ [WARNING] - org.json4s.Xml$$anonfun$directChildren$1$1 [WARNING] - org.json4s.JDoubleJObjectJsonWriter [WARNING] - 397 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, avro-mapred-1.7.7-hadoop2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 126 overlapping classes: [WARNING] - org.apache.avro.mapreduce.AvroMultipleOutputs [WARNING] - org.apache.avro.mapreduce.AvroKeyValueOutputFormat [WARNING] - org.apache.avro.mapred.SequenceFileReader$8 [WARNING] - org.apache.avro.hadoop.file.HadoopCodecFactory [WARNING] - org.apache.avro.mapred.Pair [WARNING] - org.apache.avro.mapred.AvroMultipleOutputs [WARNING] - org.apache.avro.mapred.FsInput [WARNING] - org.apache.avro.mapred.tether.InputProtocol$Callback [WARNING] - org.apache.avro.mapred.AvroOutputFormat$1 [WARNING] - org.apache.avro.hadoop.file.SortedKeyValueFile$Reader$Options [WARNING] - 116 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-core_2.11-2.3.3.jar define 8350 overlapping classes: [WARNING] - org.apache.spark.shuffle.BaseShuffleHandle [WARNING] - org.apache.spark.SparkContext$$anonfun$11 [WARNING] - org.spark_project.jetty.client.util.MultiPartContentProvider$1 [WARNING] - org.apache.spark.TaskContextImpl$$anonfun$markTaskFailed$1 [WARNING] - org.apache.spark.util.collection.PrimitiveVector$mcI$sp [WARNING] - org.spark_project.jetty.servlets.PushCacheFilter [WARNING] - org.apache.spark.util.Utils$$anonfun$downloadFile$1 [WARNING] - org.apache.spark.util.JsonProtocol$$anonfun$52 [WARNING] - org.apache.spark.ExecutorAllocationManager$$anonfun$org$apache$spark$ExecutorAllocationManager$$onExecutorAdded$2 [WARNING] - org.apache.spark.rdd.util.PeriodicRDDCheckpointer [WARNING] - 8340 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, ga4gh-schemas-0.6.0a10.jar define 541 overlapping classes: [WARNING] - ga4gh.AlleleAnnotations$TranscriptEffectOrBuilder [WARNING] - ga4gh.PeerServiceOuterClass$GetInfoResponse$1 [WARNING] - ga4gh.MetadataServiceOuterClass$GetDatasetRequestOrBuilder [WARNING] - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest [WARNING] - ga4gh.RnaQuantificationServiceOuterClass$SearchExpressionLevelsRequest$Builder [WARNING] - ga4gh.GenotypePhenotypeServiceOuterClass$EvidenceQuery$1 [WARNING] - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest$1 [WARNING] - ga4gh.ReferenceServiceOuterClass$ListReferenceBasesResponseOrBuilder [WARNING] - ga4gh.VariantServiceOuterClass$SearchCallSetsRequest [WARNING] - ga4gh.RnaQuantificationServiceOuterClass$GetExpressionLevelRequest [WARNING] - 531 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-graphite-3.1.5.jar, mango-cli-0.0.3-SNAPSHOT.jar define 10 overlapping classes: [WARNING] - com.codahale.metrics.graphite.PickledGraphite$MetricTuple [WARNING] - com.codahale.metrics.graphite.GraphiteReporter$Builder [WARNING] - com.codahale.metrics.graphite.Graphite [WARNING] - com.codahale.metrics.graphite.GraphiteRabbitMQ$1 [WARNING] - com.codahale.metrics.graphite.GraphiteSender [WARNING] - com.codahale.metrics.graphite.PickledGraphite [WARNING] - com.codahale.metrics.graphite.GraphiteUDP [WARNING] - com.codahale.metrics.graphite.GraphiteReporter [WARNING] - com.codahale.metrics.graphite.GraphiteReporter$1 [WARNING] - com.codahale.metrics.graphite.GraphiteRabbitMQ [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-logging-1.1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar define 6 overlapping classes: [WARNING] - org.apache.commons.logging.impl.SimpleLog$1 [WARNING] - org.apache.commons.logging.Log [WARNING] - org.apache.commons.logging.impl.SimpleLog [WARNING] - org.apache.commons.logging.LogConfigurationException [WARNING] - org.apache.commons.logging.impl.NoOpLog [WARNING] - org.apache.commons.logging.LogFactory [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-jexl-2.1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 178 overlapping classes: [WARNING] - org.apache.commons.jexl2.internal.AbstractExecutor$Get [WARNING] - org.apache.commons.jexl2.introspection.JexlPropertyGet [WARNING] - org.apache.commons.jexl2.parser.StringParser [WARNING] - org.apache.commons.jexl2.parser.ASTBitwiseOrNode [WARNING] - org.apache.commons.jexl2.internal.introspection.MethodKey$1 [WARNING] - org.apache.commons.jexl2.Main [WARNING] - org.apache.commons.jexl2.parser.ASTForeachStatement [WARNING] - org.apache.commons.jexl2.introspection.Sandbox [WARNING] - org.apache.commons.jexl2.internal.introspection.ClassMap [WARNING] - org.apache.commons.jexl2.parser.ASTFunctionNode [WARNING] - 168 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, metrics-core-3.1.5.jar define 115 overlapping classes: [WARNING] - com.codahale.metrics.JmxReporter$JmxGaugeMBean [WARNING] - com.codahale.metrics.ThreadLocalRandomProxy$InternalProvider [WARNING] - com.codahale.metrics.JmxReporter [WARNING] - com.codahale.metrics.EWMA [WARNING] - com.codahale.metrics.Gauge [WARNING] - com.codahale.metrics.MetricRegistry$MetricBuilder$1 [WARNING] - com.codahale.metrics.MetricFilter$1 [WARNING] - com.codahale.metrics.JmxReporter$JmxCounterMBean [WARNING] - com.codahale.metrics.InstrumentedExecutorService$InstrumentedRunnable [WARNING] - com.codahale.metrics.RatioGauge$Ratio [WARNING] - 105 more... [WARNING] jersey-client-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 111 overlapping classes: [WARNING] - org.glassfish.jersey.client.ChunkParser [WARNING] - org.glassfish.jersey.client.HttpUrlConnectorProvider [WARNING] - org.glassfish.jersey.client.JerseyInvocation$EntityPresence [WARNING] - org.glassfish.jersey.client.ResponseCallback [WARNING] - org.glassfish.jersey.client.authentication.RequestAuthenticationException [WARNING] - org.glassfish.jersey.client.JerseyInvocation$5 [WARNING] - org.glassfish.jersey.client.ClientConfig$State$4 [WARNING] - org.glassfish.jersey.client.ClientResponse$1 [WARNING] - org.glassfish.jersey.client.InboundJaxrsResponse$2 [WARNING] - org.glassfish.jersey.client.internal.HttpUrlConnector$5 [WARNING] - 101 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar define 3 overlapping classes: [WARNING] - org.apache.commons.logging.impl.SLF4JLogFactory [WARNING] - org.apache.commons.logging.impl.SLF4JLocationAwareLog [WARNING] - org.apache.commons.logging.impl.SLF4JLog [WARNING] mango-core-0.0.3-SNAPSHOT.jar, xz-1.5.jar, mango-cli-0.0.3-SNAPSHOT.jar define 105 overlapping classes: [WARNING] - org.tukaani.xz.lzma.LZMADecoder$LengthDecoder [WARNING] - org.tukaani.xz.index.IndexDecoder [WARNING] - org.tukaani.xz.lzma.LZMADecoder [WARNING] - org.tukaani.xz.lzma.LZMAEncoderFast [WARNING] - org.tukaani.xz.lzma.LZMAEncoder$LengthEncoder [WARNING] - org.tukaani.xz.BlockOutputStream [WARNING] - org.tukaani.xz.simple.SimpleFilter [WARNING] - org.tukaani.xz.rangecoder.RangeCoder [WARNING] - org.tukaani.xz.XZOutputStream [WARNING] - org.tukaani.xz.UncompressedLZMA2OutputStream [WARNING] - 95 more... [WARNING] mime-util-2.1.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 26 overlapping classes: [WARNING] - eu.medsea.mimeutil.detector.MagicMimeMimeDetector [WARNING] - eu.medsea.mimeutil.detector.OpendesktopMimeDetector$1 [WARNING] - eu.medsea.mimeutil.MimeDetectorRegistry [WARNING] - eu.medsea.mimeutil.detector.OpendesktopMimeDetector [WARNING] - eu.medsea.mimeutil.detector.InvalidMagicMimeEntryException [WARNING] - eu.medsea.mimeutil.TextMimeDetector [WARNING] - eu.medsea.util.ZipJarUtil [WARNING] - eu.medsea.mimeutil.detector.MagicMimeEntry [WARNING] - eu.medsea.mimeutil.detector.FileWatcher [WARNING] - eu.medsea.mimeutil.detector.WindowsRegistryMimeDetector$StreamReader [WARNING] - 16 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, oro-2.0.8.jar, mango-cli-0.0.3-SNAPSHOT.jar define 62 overlapping classes: [WARNING] - org.apache.oro.text.perl.MalformedPerl5PatternException [WARNING] - org.apache.oro.text.regex.Perl5Pattern [WARNING] - org.apache.oro.io.RegexFilenameFilter [WARNING] - org.apache.oro.util.Cache [WARNING] - org.apache.oro.text.GenericPatternCache [WARNING] - org.apache.oro.text.awk.DFAState [WARNING] - org.apache.oro.text.regex.StringSubstitution [WARNING] - org.apache.oro.text.awk.AwkCompiler [WARNING] - org.apache.oro.text.PatternCacheLRU [WARNING] - org.apache.oro.text.regex.Substitution [WARNING] - 52 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-kvstore_2.11-2.3.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 28 overlapping classes: [WARNING] - org.apache.spark.util.kvstore.LevelDB$TypeAliases [WARNING] - org.apache.spark.util.kvstore.LevelDB$1 [WARNING] - org.apache.spark.util.kvstore.LevelDB$PrefixCache [WARNING] - org.apache.spark.util.kvstore.LevelDBTypeInfo$Index [WARNING] - org.apache.spark.util.kvstore.KVStore [WARNING] - org.apache.spark.util.kvstore.KVTypeInfo [WARNING] - org.apache.spark.util.kvstore.KVIndex [WARNING] - org.apache.spark.util.kvstore.KVStoreIterator [WARNING] - org.apache.spark.util.kvstore.InMemoryStore$InMemoryView [WARNING] - org.apache.spark.util.kvstore.InMemoryStore$1 [WARNING] - 18 more... [WARNING] jetty-io-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 96 overlapping classes: [WARNING] - org.eclipse.jetty.io.ssl.ALPNProcessor [WARNING] - org.eclipse.jetty.io.CyclicTimeout$Wakeup [WARNING] - org.eclipse.jetty.io.AbstractEndPoint$2 [WARNING] - org.eclipse.jetty.io.CyclicTimeout$Timeout [WARNING] - org.eclipse.jetty.io.ChannelEndPoint$1 [WARNING] - org.eclipse.jetty.io.WriteFlusher$FailedState [WARNING] - org.eclipse.jetty.io.CyclicTimeout$1 [WARNING] - org.eclipse.jetty.io.ManagedSelector$Acceptor [WARNING] - org.eclipse.jetty.io.ssl.SslClientConnectionFactory$1 [WARNING] - org.eclipse.jetty.io.ByteBufferPool$Lease [WARNING] - 86 more... [WARNING] jetty-http-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 93 overlapping classes: [WARNING] - org.eclipse.jetty.http.pathmap.PathSpec [WARNING] - org.eclipse.jetty.http.MultiPartFormInputStream [WARNING] - org.eclipse.jetty.http.HttpParser$HttpHandler [WARNING] - org.eclipse.jetty.http.MultiPartFormInputStream$MultiPart [WARNING] - org.eclipse.jetty.http.BadMessageException [WARNING] - org.eclipse.jetty.http.HttpGenerator$PreparedResponse [WARNING] - org.eclipse.jetty.http.HttpComplianceSection [WARNING] - org.eclipse.jetty.http.HttpParser$IllegalCharacterException [WARNING] - org.eclipse.jetty.http.HttpParser$1 [WARNING] - org.eclipse.jetty.http.PathMap$PathSet [WARNING] - 83 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, args4j-2.0.31.jar define 71 overlapping classes: [WARNING] - org.kohsuke.args4j.spi.DoubleOptionHandler [WARNING] - org.kohsuke.args4j.spi.MethodSetter [WARNING] - org.kohsuke.args4j.spi.StringArrayOptionHandler [WARNING] - org.kohsuke.args4j.spi.MacAddressOptionHandler [WARNING] - org.kohsuke.args4j.spi.SubCommand [WARNING] - org.kohsuke.args4j.spi.PatternOptionHandler [WARNING] - org.kohsuke.args4j.ParserProperties$1 [WARNING] - org.kohsuke.args4j.OptionHandlerFilter$2 [WARNING] - org.kohsuke.args4j.spi.MultiFileOptionHandler [WARNING] - org.kohsuke.args4j.Localizable [WARNING] - 61 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-net-2.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 137 overlapping classes: [WARNING] - org.apache.commons.net.telnet.SimpleOptionHandler [WARNING] - org.apache.commons.net.ftp.parser.FTPFileEntryParserFactory [WARNING] - org.apache.commons.net.DefaultDatagramSocketFactory [WARNING] - org.apache.commons.net.ftp.parser.ConfigurableFTPFileEntryParserImpl [WARNING] - org.apache.commons.net.ntp.NTPUDPClient [WARNING] - org.apache.commons.net.util.SubnetUtils$1 [WARNING] - org.apache.commons.net.tftp.TFTP [WARNING] - org.apache.commons.net.ftp.FTPClient [WARNING] - org.apache.commons.net.echo.EchoTCPClient [WARNING] - org.apache.commons.net.telnet.Telnet [WARNING] - 127 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, utils-misc-spark2_2.11-0.2.13.jar define 11 overlapping classes: [WARNING] - org.bdgenomics.utils.misc.MathUtils [WARNING] - org.bdgenomics.utils.misc.Logging$ [WARNING] - org.bdgenomics.utils.misc.MathUtils$$anonfun$scalarArrayMultiply$1 [WARNING] - org.bdgenomics.utils.misc.Logging$class [WARNING] - org.bdgenomics.utils.misc.Logging$$anonfun$getContextOrClassLoader$1 [WARNING] - org.bdgenomics.utils.misc.MathUtils$$anonfun$aggregateArray$1 [WARNING] - org.bdgenomics.utils.misc.Logging [WARNING] - org.bdgenomics.utils.misc.HadoopUtil$ [WARNING] - org.bdgenomics.utils.misc.MathUtils$$anonfun$softmax$1 [WARNING] - org.bdgenomics.utils.misc.MathUtils$ [WARNING] - 1 more... [WARNING] jetty-util-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 285 overlapping classes: [WARNING] - org.eclipse.jetty.util.MemoryUtils$1 [WARNING] - org.eclipse.jetty.util.resource.URLResource [WARNING] - org.eclipse.jetty.util.Scanner$DiscreteListener [WARNING] - org.eclipse.jetty.util.MultiReleaseJarFile$VersionedJarEntry [WARNING] - org.eclipse.jetty.util.log.StacklessLogging [WARNING] - org.eclipse.jetty.util.component.Dumpable [WARNING] - org.eclipse.jetty.util.preventers.Java2DLeakPreventer [WARNING] - org.eclipse.jetty.util.InetAddressSet$LegacyInetRange [WARNING] - org.eclipse.jetty.util.resource.JarFileResource [WARNING] - org.eclipse.jetty.util.IncludeExcludeSet$SetContainsPredicate [WARNING] - 275 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, parquet-scala_2.10-1.8.3.jar define 19 overlapping classes: [WARNING] - org.apache.parquet.filter2.dsl.Dsl$SupportsEqNotEq [WARNING] - org.apache.parquet.filter2.dsl.Dsl$FloatColumn$ [WARNING] - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$Column$class [WARNING] - org.apache.parquet.filter2.dsl.Dsl [WARNING] - org.apache.parquet.filter2.dsl.Dsl$FloatColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$LongColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$BinaryColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$IntColumn$ [WARNING] - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn$ [WARNING] - 9 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, metrics-jvm-3.1.5.jar define 38 overlapping classes: [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$15 [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$3 [WARNING] - com.codahale.metrics.jvm.CachedThreadStatesGaugeSet [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$8 [WARNING] - com.codahale.metrics.jvm.ClassLoadingGaugeSet$1 [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$5 [WARNING] - com.codahale.metrics.jvm.BufferPoolMetricSet [WARNING] - com.codahale.metrics.jvm.ThreadStatesGaugeSet [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$10 [WARNING] - 28 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, chill-java-0.8.4.jar, mango-cli-0.0.3-SNAPSHOT.jar define 54 overlapping classes: [WARNING] - com.twitter.chill.java.ClosureSerializer [WARNING] - com.twitter.chill.config.JavaMapConfig [WARNING] - com.twitter.chill.java.IterableRegistrar [WARNING] - com.twitter.chill.java.SqlTimeSerializer [WARNING] - com.twitter.chill.KryoInstantiator [WARNING] - com.twitter.chill.java.PackageRegistrar [WARNING] - com.twitter.chill.config.ConfiguredInstantiator [WARNING] - com.twitter.chill.java.SimpleDateFormatSerializer [WARNING] - com.twitter.chill.KryoInstantiator$4 [WARNING] - com.twitter.chill.java.UnmodifiableSetSerializer [WARNING] - 44 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-logging-1.1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 22 overlapping classes: [WARNING] - org.apache.commons.logging.LogSource [WARNING] - org.apache.commons.logging.impl.ServletContextCleaner [WARNING] - org.apache.commons.logging.LogFactory$4 [WARNING] - org.apache.commons.logging.impl.WeakHashtable$1 [WARNING] - org.apache.commons.logging.LogFactory$3 [WARNING] - org.apache.commons.logging.LogFactory$2 [WARNING] - org.apache.commons.logging.impl.LogFactoryImpl$2 [WARNING] - org.apache.commons.logging.impl.LogKitLogger [WARNING] - org.apache.commons.logging.impl.LogFactoryImpl$3 [WARNING] - org.apache.commons.logging.impl.WeakHashtable$Entry [WARNING] - 12 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, zstd-jni-1.3.2-2.jar define 8 overlapping classes: [WARNING] - com.github.luben.zstd.ZstdDirectBufferDecompressingStream [WARNING] - com.github.luben.zstd.ZstdOutputStream [WARNING] - com.github.luben.zstd.ZstdDictCompress [WARNING] - com.github.luben.zstd.ZstdDictDecompress [WARNING] - com.github.luben.zstd.ZstdInputStream [WARNING] - com.github.luben.zstd.Zstd [WARNING] - com.github.luben.zstd.util.Native [WARNING] - com.github.luben.zstd.ZstdDirectBufferCompressingStream [WARNING] jackson-mapper-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 502 overlapping classes: [WARNING] - org.codehaus.jackson.map.ext.DOMSerializer [WARNING] - org.codehaus.jackson.node.POJONode [WARNING] - org.codehaus.jackson.map.ext.JodaDeserializers$LocalDateDeserializer [WARNING] - org.codehaus.jackson.map.ser.StdSerializers$UtilDateSerializer [WARNING] - org.codehaus.jackson.map.deser.std.JsonNodeDeserializer$ArrayDeserializer [WARNING] - org.codehaus.jackson.map.deser.std.PrimitiveArrayDeserializers$StringDeser [WARNING] - org.codehaus.jackson.map.util.Comparators$1 [WARNING] - org.codehaus.jackson.map.util.StdDateFormat [WARNING] - org.codehaus.jackson.map.KeyDeserializer [WARNING] - org.codehaus.jackson.map.MapperConfig$Impl [WARNING] - 492 more... [WARNING] spark-network-shuffle_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 41 overlapping classes: [WARNING] - org.apache.spark.network.shuffle.RetryingBlockFetcher$1 [WARNING] - org.apache.spark.network.shuffle.protocol.BlockTransferMessage$Type [WARNING] - org.apache.spark.network.shuffle.ShuffleIndexRecord [WARNING] - org.apache.spark.network.sasl.ShuffleSecretManager [WARNING] - org.apache.spark.network.shuffle.SimpleDownloadFile [WARNING] - org.apache.spark.network.shuffle.OneForOneBlockFetcher [WARNING] - org.apache.spark.network.shuffle.ExternalShuffleBlockResolver$2 [WARNING] - org.apache.spark.network.shuffle.ExternalShuffleBlockHandler$ManagedBufferIterator [WARNING] - org.apache.spark.network.shuffle.DownloadFileManager [WARNING] - org.apache.spark.network.shuffle.protocol.RegisterExecutor [WARNING] - 31 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, javax.ws.rs-api-2.0.1.jar define 125 overlapping classes: [WARNING] - javax.ws.rs.ext.RuntimeDelegate$HeaderDelegate [WARNING] - javax.ws.rs.DefaultValue [WARNING] - javax.ws.rs.core.StreamingOutput [WARNING] - javax.ws.rs.HEAD [WARNING] - javax.ws.rs.ext.WriterInterceptor [WARNING] - javax.ws.rs.core.Request [WARNING] - javax.ws.rs.ext.Providers [WARNING] - javax.ws.rs.container.Suspended [WARNING] - javax.ws.rs.container.ConnectionCallback [WARNING] - javax.ws.rs.client.FactoryFinder [WARNING] - 115 more... [WARNING] joda-time-2.9.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 246 overlapping classes: [WARNING] - org.joda.time.field.RemainderDateTimeField [WARNING] - org.joda.time.convert.ReadableDurationConverter [WARNING] - org.joda.time.convert.ReadableIntervalConverter [WARNING] - org.joda.time.field.SkipUndoDateTimeField [WARNING] - org.joda.time.format.DateTimeFormatterBuilder$TimeZoneName [WARNING] - org.joda.time.tz.DateTimeZoneBuilder$RuleSet [WARNING] - org.joda.time.chrono.BasicDayOfMonthDateTimeField [WARNING] - org.joda.time.Duration [WARNING] - org.joda.time.field.OffsetDateTimeField [WARNING] - org.joda.time.format.ISODateTimeFormat [WARNING] - 236 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, j2objc-annotations-1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 12 overlapping classes: [WARNING] - com.google.j2objc.annotations.Property [WARNING] - com.google.j2objc.annotations.RetainedWith [WARNING] - com.google.j2objc.annotations.RetainedLocalRef [WARNING] - com.google.j2objc.annotations.J2ObjCIncompatible [WARNING] - com.google.j2objc.annotations.AutoreleasePool [WARNING] - com.google.j2objc.annotations.LoopTranslation$LoopStyle [WARNING] - com.google.j2objc.annotations.ReflectionSupport$Level [WARNING] - com.google.j2objc.annotations.ReflectionSupport [WARNING] - com.google.j2objc.annotations.Weak [WARNING] - com.google.j2objc.annotations.WeakOuter [WARNING] - 2 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jackson-databind-2.6.7.1.jar define 563 overlapping classes: [WARNING] - com.fasterxml.jackson.databind.BeanDescription [WARNING] - com.fasterxml.jackson.databind.deser.impl.BeanAsArrayBuilderDeserializer [WARNING] - com.fasterxml.jackson.databind.SerializerProvider [WARNING] - com.fasterxml.jackson.databind.introspect.AnnotatedMethodMap [WARNING] - com.fasterxml.jackson.databind.ser.std.StaticListSerializerBase [WARNING] - com.fasterxml.jackson.databind.ser.std.NumberSerializers$ShortSerializer [WARNING] - com.fasterxml.jackson.databind.ser.BeanSerializerFactory [WARNING] - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonMapFormatVisitor [WARNING] - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatTypes [WARNING] - com.fasterxml.jackson.databind.deser.impl.MethodProperty [WARNING] - 553 more... [WARNING] juniversalchardet-1.0.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 62 overlapping classes: [WARNING] - org.mozilla.universalchardet.prober.distributionanalysis.EUCJPDistributionAnalysis [WARNING] - org.mozilla.universalchardet.prober.SJISProber [WARNING] - org.mozilla.universalchardet.prober.statemachine.ISO2022KRSMModel [WARNING] - org.mozilla.universalchardet.prober.sequence.Latin7Model [WARNING] - org.mozilla.universalchardet.prober.CharsetProber$ProbingState [WARNING] - org.mozilla.universalchardet.prober.distributionanalysis.JISDistributionAnalysis [WARNING] - org.mozilla.universalchardet.prober.UTF8Prober [WARNING] - org.mozilla.universalchardet.prober.sequence.Koi8rModel [WARNING] - org.mozilla.universalchardet.prober.contextanalysis.JapaneseContextAnalysis [WARNING] - org.mozilla.universalchardet.prober.sequence.MacCyrillicModel [WARNING] - 52 more... [WARNING] javax.inject-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, javax.inject-1.jar define 6 overlapping classes: [WARNING] - javax.inject.Inject [WARNING] - javax.inject.Singleton [WARNING] - javax.inject.Named [WARNING] - javax.inject.Scope [WARNING] - javax.inject.Provider [WARNING] - javax.inject.Qualifier [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, hk2-locator-2.4.0-b34.jar define 95 overlapping classes: [WARNING] - org.jvnet.hk2.internal.PerLocatorUtilities$1 [WARNING] - org.jvnet.hk2.internal.Utilities$4 [WARNING] - org.jvnet.hk2.internal.ProxyUtilities$2 [WARNING] - org.jvnet.hk2.internal.ServiceLocatorImpl$12 [WARNING] - org.jvnet.hk2.internal.MethodInterceptorInvocationHandler [WARNING] - org.jvnet.hk2.internal.ClazzCreator [WARNING] - org.jvnet.hk2.internal.ValidationInformationImpl [WARNING] - org.jvnet.hk2.internal.ServiceLocatorImpl$6 [WARNING] - org.jvnet.hk2.internal.ConstructorInterceptorHandler$1 [WARNING] - org.jvnet.hk2.internal.ServiceLocatorImpl$IgdValue [WARNING] - 85 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jackson-core-2.6.7.jar define 93 overlapping classes: [WARNING] - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer$Bucket [WARNING] - com.fasterxml.jackson.core.FormatSchema [WARNING] - com.fasterxml.jackson.core.io.InputDecorator [WARNING] - com.fasterxml.jackson.core.JsonGenerator$Feature [WARNING] - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer [WARNING] - com.fasterxml.jackson.core.type.ResolvedType [WARNING] - com.fasterxml.jackson.core.io.SegmentedStringWriter [WARNING] - com.fasterxml.jackson.core.TreeNode [WARNING] - com.fasterxml.jackson.core.sym.Name [WARNING] - com.fasterxml.jackson.core.util.JsonGeneratorDelegate [WARNING] - 83 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, aopalliance-1.0.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: [WARNING] - org.aopalliance.intercept.ConstructorInterceptor [WARNING] - org.aopalliance.intercept.MethodInvocation [WARNING] - org.aopalliance.intercept.MethodInterceptor [WARNING] - org.aopalliance.intercept.Invocation [WARNING] - org.aopalliance.aop.AspectException [WARNING] - org.aopalliance.intercept.Interceptor [WARNING] - org.aopalliance.intercept.Joinpoint [WARNING] - org.aopalliance.aop.Advice [WARNING] - org.aopalliance.intercept.ConstructorInvocation [WARNING] mango-core-0.0.3-SNAPSHOT.jar, curator-framework-2.6.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 167 overlapping classes: [WARNING] - org.apache.curator.framework.imps.TempGetDataBuilderImpl [WARNING] - org.apache.curator.framework.imps.GetDataBuilderImpl$2 [WARNING] - org.apache.curator.framework.imps.CuratorFrameworkImpl$4 [WARNING] - org.apache.curator.framework.state.ConnectionState [WARNING] - org.apache.curator.framework.api.CreateModable [WARNING] - org.apache.curator.framework.imps.SetDataBuilderImpl$4 [WARNING] - org.apache.curator.framework.imps.PathAndBytes [WARNING] - org.apache.curator.framework.api.ACLVersionBackgroundPathable [WARNING] - org.apache.curator.framework.api.ACLCreateModeBackgroundPathAndBytesable [WARNING] - org.apache.curator.framework.listen.ListenerContainer [WARNING] - 157 more... [WARNING] jersey-container-servlet-core-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 51 overlapping classes: [WARNING] - org.glassfish.jersey.servlet.WebComponent$3 [WARNING] - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder [WARNING] - org.glassfish.jersey.servlet.internal.LocalizationMessages [WARNING] - org.glassfish.jersey.servlet.WebConfig [WARNING] - org.glassfish.jersey.servlet.spi.FilterUrlMappingsProvider [WARNING] - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder$3 [WARNING] - org.glassfish.jersey.servlet.ServletPropertiesDelegate [WARNING] - org.glassfish.jersey.servlet.WebComponent$7 [WARNING] - org.glassfish.jersey.servlet.internal.ResponseWriter [WARNING] - org.glassfish.jersey.servlet.WebAppResourcesScanner$1 [WARNING] - 41 more... [WARNING] lz4-java-1.4.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 77 overlapping classes: [WARNING] - net.jpountz.xxhash.AbstractStreamingXXHash32Java [WARNING] - net.jpountz.lz4.LZ4BlockInputStream [WARNING] - net.jpountz.lz4.LZ4FrameOutputStream [WARNING] - net.jpountz.xxhash.XXHash32JNI [WARNING] - net.jpountz.lz4.LZ4BlockOutputStream [WARNING] - net.jpountz.lz4.LZ4JNI [WARNING] - net.jpountz.lz4.LZ4JavaUnsafeFastDecompressor [WARNING] - net.jpountz.lz4.LZ4SafeUtils [WARNING] - net.jpountz.xxhash.StreamingXXHash32JNI$Factory [WARNING] - net.jpountz.util.UnsafeUtils [WARNING] - 67 more... [WARNING] adam-cli-spark2_2.11-0.26.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 130 overlapping classes: [WARNING] - org.bdgenomics.adam.cli.PrintADAMArgs [WARNING] - org.bdgenomics.adam.cli.Reads2Coverage$$anonfun$1$$anonfun$apply$1 [WARNING] - org.bdgenomics.adam.cli.TransformVariants$$anonfun$maybeCoalesce$2 [WARNING] - org.bdgenomics.adam.cli.FlagStat$ [WARNING] - org.bdgenomics.adam.cli.TransformAlignments$$anonfun$7 [WARNING] - org.bdgenomics.adam.cli.TransformVariants$ [WARNING] - org.bdgenomics.adam.cli.View$$anonfun$getFilter$1$1 [WARNING] - org.bdgenomics.adam.cli.TransformAlignments$$anonfun$maybeCoalesce$2 [WARNING] - org.bdgenomics.adam.cli.TransformAlignments$$anonfun$4 [WARNING] - org.bdgenomics.adam.cli.ADAMMain$$anonfun$1 [WARNING] - 120 more... [WARNING] parquet-common-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 32 overlapping classes: [WARNING] - org.apache.parquet.SemanticVersion$SemanticVersionParseException [WARNING] - org.apache.parquet.glob.GlobNode$GlobNodeSequence [WARNING] - org.apache.parquet.Ints [WARNING] - org.apache.parquet.Version [WARNING] - org.apache.parquet.glob.GlobNode$Atom [WARNING] - org.apache.parquet.SemanticVersion$NumberOrString [WARNING] - org.apache.parquet.Files [WARNING] - org.apache.parquet.ParquetRuntimeException [WARNING] - org.apache.parquet.glob.GlobNode [WARNING] - org.apache.parquet.io.InputFile [WARNING] - 22 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-xml_2.11-1.0.5.jar, mango-cli-0.0.3-SNAPSHOT.jar define 421 overlapping classes: [WARNING] - scala.xml.PrettyPrinter$Para [WARNING] - scala.xml.Group$ [WARNING] - scala.xml.PrettyPrinter$$anonfun$traverse$1 [WARNING] - scala.xml.MetaData [WARNING] - scala.xml.MalformedAttributeException [WARNING] - scala.xml.pull.EvComment [WARNING] - scala.xml.parsing.TokenTests$$anonfun$isSpace$1 [WARNING] - scala.xml.Properties [WARNING] - scala.xml.parsing.MarkupParser$$anonfun$1 [WARNING] - scala.xml.pull.EvEntityRef$ [WARNING] - 411 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, lift-json_2.11-3.3.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 390 overlapping classes: [WARNING] - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$deserialize$2 [WARNING] - net.liftweb.json.TypeInfo$ [WARNING] - net.liftweb.json.JsonAST$JString$ [WARNING] - net.liftweb.json.JsonAST$RenderSettings$ [WARNING] - net.liftweb.json.JsonAST$JDouble$ [WARNING] - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$classFor$2 [WARNING] - net.liftweb.json.JsonAST$RenderSpecialDoubleValuesAsIs$ [WARNING] - net.liftweb.json.Meta$$anonfun$net$liftweb$json$Meta$$fieldMapping$1$4 [WARNING] - net.liftweb.json.Meta$DeclaredConstructor [WARNING] - net.liftweb.json.Formats$$anonfun$customSerializer$1 [WARNING] - 380 more... [WARNING] httpcore-4.4.4.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 254 overlapping classes: [WARNING] - org.apache.http.protocol.HttpRequestHandler [WARNING] - org.apache.http.impl.io.ChunkedOutputStream [WARNING] - org.apache.http.protocol.ChainBuilder [WARNING] - org.apache.http.impl.entity.DisallowIdentityContentLengthStrategy [WARNING] - org.apache.http.impl.ConnSupport [WARNING] - org.apache.http.impl.io.DefaultHttpResponseParserFactory [WARNING] - org.apache.http.HttpClientConnection [WARNING] - org.apache.http.NameValuePair [WARNING] - org.apache.http.protocol.HttpExpectationVerifier [WARNING] - org.apache.http.protocol.UriPatternMatcher [WARNING] - 244 more... [WARNING] javax.annotation-api-1.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 15 overlapping classes: [WARNING] - javax.annotation.ManagedBean [WARNING] - javax.annotation.PreDestroy [WARNING] - javax.annotation.Generated [WARNING] - javax.annotation.Resource$AuthenticationType [WARNING] - javax.annotation.security.DeclareRoles [WARNING] - javax.annotation.Priority [WARNING] - javax.annotation.Resource [WARNING] - javax.annotation.security.DenyAll [WARNING] - javax.annotation.security.RunAs [WARNING] - javax.annotation.sql.DataSourceDefinitions [WARNING] - 5 more... [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, scalatra-common_2.11-2.4.1.jar define 21 overlapping classes: [WARNING] - org.scalatra.servlet.HasMultipartConfig$$anonfun$org$scalatra$servlet$HasMultipartConfig$$multipartConfigFromContext$1$$anonfun$apply$3 [WARNING] - org.scalatra.servlet.HasMultipartConfig$$anonfun$org$scalatra$servlet$HasMultipartConfig$$multipartConfigFromContext$1$$anonfun$apply$2 [WARNING] - org.scalatra.servlet.ScalatraAsyncSupport [WARNING] - org.scalatra.servlet.HasMultipartConfig [WARNING] - org.scalatra.servlet.MountConfig [WARNING] - org.scalatra.servlet.HasMultipartConfig$ [WARNING] - org.scalatra.servlet.MultipartConfig$ [WARNING] - org.scalatra.servlet.HasMultipartConfig$$anonfun$org$scalatra$servlet$HasMultipartConfig$$multipartConfigFromContext$1$$anonfun$apply$1 [WARNING] - org.scalatra.servlet.MultipartConfig$$anonfun$toMultipartConfigElement$2 [WARNING] - org.scalatra.servlet.HasMultipartConfig$$anonfun$initialize$1 [WARNING] - 11 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, scalap-2.11.11.jar define 581 overlapping classes: [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigEntryParsers$$anonfun$25$$anonfun$apply$13 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$_pmt$1$1 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigParser$$anonfun$scalaSigFromAnnotation$2 [WARNING] - scala.tools.scalap.scalax.rules.StateRules$$anonfun$anyOf$2 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ConstantType$ [WARNING] - scala.tools.scalap.scalax.rules.scalasig.Symbol$class [WARNING] - scala.tools.scalap.scalax.rules.Rule$$anonfun$flatMap$1 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$printSymbolAttributes$1 [WARNING] - scala.tools.scalap.scalax.rules.InRule$$anonfun$unary_$bang$1$$anonfun$apply$1 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.NoType$ [WARNING] - 571 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, py4j-0.10.7.jar define 67 overlapping classes: [WARNING] - py4j.reflection.TypeConverter [WARNING] - py4j.Py4JJavaServer [WARNING] - py4j.Py4JNetworkException [WARNING] - py4j.reflection.PythonProxyHandler [WARNING] - py4j.reflection.MethodInvoker$1 [WARNING] - py4j.commands.JVMViewCommand [WARNING] - py4j.Py4JClientConnection [WARNING] - py4j.model.Py4JClass [WARNING] - py4j.commands.ReflectionCommand [WARNING] - py4j.commands.MemoryCommand [WARNING] - 57 more... [WARNING] ngs-java-2.9.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 73 overlapping classes: [WARNING] - ngs.itf.ReadItf [WARNING] - gov.nih.nlm.ncbi.ngs.error.cause.JvmErrorCause [WARNING] - ngs.ReferenceIterator [WARNING] - gov.nih.nlm.ncbi.ngs.Manager$1 [WARNING] - gov.nih.nlm.ncbi.ngs.LMProperties [WARNING] - gov.nih.nlm.ncbi.ngs.error.LibraryLoadError [WARNING] - gov.nih.nlm.ncbi.ngs.LibDependencies [WARNING] - gov.nih.nlm.ncbi.ngs.error.cause.ConnectionProblemCause [WARNING] - ngs.itf.PileupEventItf [WARNING] - gov.nih.nlm.ncbi.ngs.LibManager$Location [WARNING] - 63 more... [WARNING] scalatra_2.11-2.4.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 936 overlapping classes: [WARNING] - org.scalatra.util.FileCharset$ [WARNING] - org.scalatra.ApiFormats$$anonfun$requestFormat$1 [WARNING] - org.scalatra.ScalatraBase$$anonfun$11 [WARNING] - org.scalatra.SinatraRouteMatcher$BuilderGeneratorParser$$anonfun$org$scalatra$SinatraRouteMatcher$BuilderGeneratorParser$$prefixedOptional$5 [WARNING] - org.scalatra.util.conversion.Conversions$SeqConversion [WARNING] - org.scalatra.Route$$anonfun$appendMatcher$1 [WARNING] - org.scalatra.Route [WARNING] - org.scalatra.FutureSupport$$anonfun$renderFutureResult$1$1$$anonfun$apply$2 [WARNING] - org.scalatra.PreconditionFailed$ [WARNING] - org.scalatra.util.conversion.DefaultImplicitConversions$$anonfun$17 [WARNING] - 926 more... [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, adam-apis-spark2_2.11-0.26.0.jar define 133 overlapping classes: [WARNING] - org.bdgenomics.adam.api.java.FeaturesToFragmentsConverter [WARNING] - org.bdgenomics.adam.api.java.GenotypesToCoverageConverter [WARNING] - org.bdgenomics.adam.api.java.GenotypesToFragmentsConverter [WARNING] - org.bdgenomics.adam.api.java.ToVariantDatasetConversion$class [WARNING] - org.bdgenomics.adam.api.java.ToCoverageDatasetConversion$class [WARNING] - org.bdgenomics.adam.api.java.FeaturesToVariantsDatasetConverter [WARNING] - org.bdgenomics.adam.api.java.ToVariantDatasetConversion$$typecreator7$1 [WARNING] - org.bdgenomics.adam.api.java.VariantContextsToContigsConverter [WARNING] - org.bdgenomics.adam.api.java.VariantsToContigsDatasetConverter [WARNING] - org.bdgenomics.adam.api.java.VariantsToVariantsConverter [WARNING] - 123 more... [WARNING] convert-ga4gh-0.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 20 overlapping classes: [WARNING] - org.bdgenomics.convert.ga4gh.CigarOperatorToOperation$1 [WARNING] - org.bdgenomics.convert.ga4gh.BdgenomicsVariantToGa4ghVariant [WARNING] - org.bdgenomics.convert.ga4gh.CigarToCigarUnits [WARNING] - org.bdgenomics.convert.ga4gh.BdgenomicsFeatureToGa4ghFeature [WARNING] - org.bdgenomics.convert.ga4gh.StringToOntologyTerm [WARNING] - org.bdgenomics.convert.ga4gh.ProgramToProcessingStep [WARNING] - org.bdgenomics.convert.ga4gh.Ga4ghReadGroupToBdgenomicsReadGroup [WARNING] - org.bdgenomics.convert.ga4gh.Ga4ghOntologyTermToBdgenomicsOntologyTerm [WARNING] - org.bdgenomics.convert.ga4gh.ProcessingStepToProgram [WARNING] - org.bdgenomics.convert.ga4gh.BdgenomicsStrandToGa4ghStrand [WARNING] - 10 more... [WARNING] avro-1.8.2.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1172 overlapping classes: [WARNING] - org.apache.avro.message.SchemaStore [WARNING] - avro.shaded.com.google.common.collect.SingletonImmutableList [WARNING] - org.apache.avro.io.EncoderFactory$DefaultEncoderFactory [WARNING] - avro.shaded.com.google.common.collect.Iterables$15 [WARNING] - org.apache.avro.GuavaClasses [WARNING] - avro.shaded.com.google.common.collect.Sets$PowerSet$1$1 [WARNING] - avro.shaded.com.google.common.collect.RegularImmutableMap [WARNING] - org.apache.avro.generic.GenericDatumReader$2 [WARNING] - avro.shaded.com.google.common.collect.Synchronized$SynchronizedSortedSet [WARNING] - org.apache.avro.file.BZip2Codec [WARNING] - 1162 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jackson-annotations-2.6.7.jar define 58 overlapping classes: [WARNING] - com.fasterxml.jackson.annotation.JsonAutoDetect [WARNING] - com.fasterxml.jackson.annotation.JsonInclude [WARNING] - com.fasterxml.jackson.annotation.ObjectIdGenerators [WARNING] - com.fasterxml.jackson.annotation.JsonFormat$Features [WARNING] - com.fasterxml.jackson.annotation.JsonFormat$Feature [WARNING] - com.fasterxml.jackson.annotation.JsonIgnore [WARNING] - com.fasterxml.jackson.annotation.JsonSetter [WARNING] - com.fasterxml.jackson.annotation.JsonTypeInfo$None [WARNING] - com.fasterxml.jackson.annotation.JsonSubTypes [WARNING] - com.fasterxml.jackson.annotation.JsonFormat$Shape [WARNING] - 48 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-tags_2.11-2.3.3.jar define 11 overlapping classes: [WARNING] - org.apache.spark.annotation.Since [WARNING] - org.apache.spark.annotation.InterfaceStability$Stable [WARNING] - org.apache.spark.annotation.package [WARNING] - org.apache.spark.annotation.DeveloperApi [WARNING] - org.apache.spark.annotation.InterfaceStability$Evolving [WARNING] - org.apache.spark.annotation.package$ [WARNING] - org.apache.spark.annotation.Experimental [WARNING] - org.apache.spark.annotation.AlphaComponent [WARNING] - org.apache.spark.annotation.Private [WARNING] - org.apache.spark.annotation.InterfaceStability [WARNING] - 1 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, osgi-resource-locator-1.0.1.jar define 12 overlapping classes: [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$1 [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoader$ProviderFactory [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoader [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$ProvidersPerBundle [WARNING] - org.glassfish.hk2.osgiresourcelocator.ResourceFinderImpl [WARNING] - org.glassfish.hk2.osgiresourcelocator.ResourceFinder [WARNING] - org.glassfish.hk2.osgiresourcelocator.Activator [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$DefaultFactory [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$BundleTracker [WARNING] - 2 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-common-2.22.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 474 overlapping classes: [WARNING] - org.glassfish.jersey.internal.inject.ContextInjectionResolver$Binder [WARNING] - org.glassfish.jersey.internal.ServiceFinder$ServiceIteratorProvider [WARNING] - org.glassfish.jersey.message.internal.HttpHeaderReader$1 [WARNING] - org.glassfish.jersey.internal.util.collection.KeyComparatorHashMap$1 [WARNING] - org.glassfish.jersey.uri.UriTemplate$1ValuesFromArrayStrategy [WARNING] - org.glassfish.jersey.message.internal.TracingLogger$Level [WARNING] - org.glassfish.jersey.internal.util.PropertyAlias [WARNING] - org.glassfish.jersey.uri.UriTemplate$3 [WARNING] - org.glassfish.jersey.model.internal.ComponentBag$7 [WARNING] - org.glassfish.jersey.spi.AbstractThreadPoolProvider [WARNING] - 464 more... [WARNING] json4s-jackson_2.11-3.2.11.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 27 overlapping classes: [WARNING] - org.json4s.jackson.JsonMethods$class [WARNING] - org.json4s.jackson.Json [WARNING] - org.json4s.jackson.Json$ [WARNING] - org.json4s.jackson.JValueSerializerResolver$ [WARNING] - org.json4s.jackson.Json4sModule$ [WARNING] - org.json4s.jackson.JsonMethods$$anonfun$parseOpt$1 [WARNING] - org.json4s.jackson.JValueDeserializerResolver$ [WARNING] - org.json4s.jackson.package [WARNING] - org.json4s.jackson.package$ [WARNING] - org.json4s.jackson.Json4sScalaModule$ [WARNING] - 17 more... [WARNING] avro-ipc-1.7.7.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 114 overlapping classes: [WARNING] - org.apache.avro.ipc.HandshakeRequest$1 [WARNING] - org.apache.avro.ipc.stats.Histogram [WARNING] - org.apache.avro.ipc.stats.Histogram$Entry [WARNING] - org.apache.avro.ipc.trace.Span$Builder [WARNING] - org.apache.avro.ipc.trace.TraceNode [WARNING] - org.apache.avro.ipc.specific.SpecificRequestor [WARNING] - org.apache.avro.ipc.stats.Histogram$SegmenterException [WARNING] - org.apache.avro.ipc.SaslSocketServer$AnonymousServer [WARNING] - org.apache.avro.ipc.stats.Histogram$Segmenter [WARNING] - org.apache.avro.ipc.SaslSocketServer$2 [WARNING] - 104 more... [WARNING] scala-reflect-2.11.8.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 2792 overlapping classes: [WARNING] - scala.reflect.runtime.ReflectionUtils [WARNING] - scala.reflect.internal.Types$LazyType [WARNING] - scala.reflect.internal.Scopes$LookupInaccessible$ [WARNING] - scala.reflect.internal.Definitions$DefinitionsClass$$anonfun$newT1NullaryMethod$1 [WARNING] - scala.reflect.internal.SymbolPairs$Cursor [WARNING] - scala.reflect.internal.Types$StaticallyAnnotatedType$ [WARNING] - scala.reflect.runtime.SynchronizedOps$SynchronizedScope$$anonfun$isEmpty$1 [WARNING] - scala.reflect.internal.Kinds$TypeConKind$$anonfun$buildState$3 [WARNING] - scala.reflect.api.StandardLiftables$StandardUnliftableInstances$$anonfun$unliftTuple18$1 [WARNING] - scala.reflect.runtime.SynchronizedSymbols$SynchronizedClassSymbol [WARNING] - 2782 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, parquet-avro-1.8.1.jar define 83 overlapping classes: [WARNING] - org.apache.parquet.avro.AvroRecordConverter$AvroCollectionConverter$1 [WARNING] - org.apache.parquet.avro.AvroParquetInputFormat [WARNING] - org.apache.parquet.avro.AvroRecordConverter$AvroArrayConverter$7 [WARNING] - org.apache.parquet.avro.AvroConverters$AvroPrimitiveConverter [WARNING] - org.apache.parquet.avro.AvroWriteSupport$TwoLevelListWriter [WARNING] - org.apache.parquet.avro.AvroConverters$FieldIntegerConverter [WARNING] - org.apache.parquet.avro.AvroCompatRecordMaterializer [WARNING] - org.apache.parquet.avro.AvroIndexedRecordConverter$AvroArrayConverter$1 [WARNING] - org.apache.parquet.avro.AvroWriteSupport$ListWriter [WARNING] - org.apache.parquet.avro.AvroConverters$FieldByteBufferConverter [WARNING] - 73 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, gson-2.3.jar, mango-cli-0.0.3-SNAPSHOT.jar define 165 overlapping classes: [WARNING] - com.google.gson.internal.bind.JsonTreeWriter [WARNING] - com.google.gson.internal.Excluder [WARNING] - com.google.gson.JsonDeserializationContext [WARNING] - com.google.gson.FieldNamingPolicy$5 [WARNING] - com.google.gson.internal.LinkedTreeMap$KeySet [WARNING] - com.google.gson.internal.$Gson$Types [WARNING] - com.google.gson.internal.UnsafeAllocator$2 [WARNING] - com.google.gson.internal.bind.SqlDateTypeAdapter$1 [WARNING] - com.google.gson.FieldAttributes [WARNING] - com.google.gson.internal.$Gson$Types$ParameterizedTypeImpl [WARNING] - 155 more... [WARNING] jsr203hadoop-1.0.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 27 overlapping classes: [WARNING] - hdfs.jsr203.HadoopDirectoryStream [WARNING] - hdfs.jsr203.HadoopPath [WARNING] - hdfs.jsr203.HadoopFileSystem$1 [WARNING] - hdfs.jsr203.HadoopFileOwnerAttributeView [WARNING] - hdfs.jsr203.HadoopUserPrincipal [WARNING] - hdfs.jsr203.IAttributeReader [WARNING] - hdfs.jsr203.HadoopPath$1 [WARNING] - hdfs.jsr203.HadoopBasicFileAttributes [WARNING] - hdfs.jsr203.HadoopDirectoryStream$1 [WARNING] - hdfs.jsr203.package-info [WARNING] - 17 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, adam-core-spark2_2.11-0.26.0.jar define 2708 overlapping classes: [WARNING] - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$74$$anonfun$apply$77 [WARNING] - org.bdgenomics.adam.rdd.feature.FeatureDataset$$anonfun$filterToTranscript$2$$anonfun$apply$9$$anonfun$apply$10 [WARNING] - org.bdgenomics.adam.rdd.read.AlignmentRecordDataset$$typecreator9$1 [WARNING] - org.bdgenomics.adam.sql.VariantCallingAnnotations$$anonfun$toAvro$58 [WARNING] - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$63 [WARNING] - org.bdgenomics.adam.rdd.feature.DatasetBoundFeatureDataset$$anonfun$filterByAttribute$1 [WARNING] - org.bdgenomics.adam.io.InterleavedFastqInputFormat [WARNING] - org.bdgenomics.adam.util.FileMerger$$anonfun$mergeFilesAcrossFilesystems$4 [WARNING] - org.bdgenomics.adam.rdd.fragment.DatasetBoundFragmentDataset [WARNING] - org.bdgenomics.adam.sql.VariantAnnotation$$anonfun$fromAvro$80 [WARNING] - 2698 more... [WARNING] commons-crypto-1.0.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 46 overlapping classes: [WARNING] - org.apache.commons.crypto.stream.PositionedCryptoInputStream [WARNING] - org.apache.commons.crypto.cipher.OpenSsl [WARNING] - org.apache.commons.crypto.random.CryptoRandomFactory$RandomProvider [WARNING] - org.apache.commons.crypto.cipher.OpenSsl$AlgorithmMode [WARNING] - org.apache.commons.crypto.utils.Utils$DefaultPropertiesHolder [WARNING] - org.apache.commons.crypto.Crypto [WARNING] - org.apache.commons.crypto.cipher.OpenSsl$Transform [WARNING] - org.apache.commons.crypto.OpenSslInfoNative [WARNING] - org.apache.commons.crypto.stream.CtrCryptoOutputStream [WARNING] - org.apache.commons.crypto.jna.OpenSslNativeJna [WARNING] - 36 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, kryo-shaded-3.0.3.jar define 14 overlapping classes: [WARNING] - com.esotericsoftware.kryo.serializers.VersionFieldSerializer [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Context [WARNING] - com.esotericsoftware.kryo.serializers.EnumNameSerializer [WARNING] - com.esotericsoftware.kryo.serializers.ClosureSerializer [WARNING] - com.esotericsoftware.kryo.pool.KryoPool [WARNING] - com.esotericsoftware.kryo.pool.SoftReferenceQueue [WARNING] - com.esotericsoftware.kryo.pool.KryoCallback [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.TypePath [WARNING] - com.esotericsoftware.reflectasm.PublicConstructorAccess [WARNING] - com.esotericsoftware.kryo.pool.KryoPoolQueueImpl [WARNING] - 4 more... [WARNING] hk2-utils-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 80 overlapping classes: [WARNING] - org.glassfish.hk2.utilities.cache.Cache$1 [WARNING] - org.jvnet.hk2.component.MultiMap$1 [WARNING] - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperImpl$4 [WARNING] - org.glassfish.hk2.utilities.cache.internal.WeakCARCacheImpl$1 [WARNING] - org.glassfish.hk2.utilities.cache.LRUHybridCache [WARNING] - org.glassfish.hk2.utilities.cache.LRUCache [WARNING] - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperUtilities [WARNING] - org.glassfish.hk2.utilities.reflection.ClassReflectionHelper [WARNING] - org.glassfish.hk2.utilities.cache.CacheEntry [WARNING] - org.glassfish.hk2.utilities.reflection.ReflectionHelper [WARNING] - 70 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, httpclient-4.5.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 463 overlapping classes: [WARNING] - org.apache.http.impl.cookie.RFC2109Spec [WARNING] - org.apache.http.impl.execchain.MainClientExec [WARNING] - org.apache.http.conn.routing.RouteInfo$TunnelType [WARNING] - org.apache.http.client.methods.HttpGet [WARNING] - org.apache.http.impl.cookie.BrowserCompatSpecFactory [WARNING] - org.apache.http.impl.client.HttpAuthenticator [WARNING] - org.apache.http.conn.ManagedClientConnection [WARNING] - org.apache.http.client.protocol.RequestAuthCache [WARNING] - org.apache.http.conn.params.ConnConnectionParamBean [WARNING] - org.apache.http.impl.client.IdleConnectionEvictor [WARNING] - 453 more... [WARNING] commons-lang3-3.5.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 260 overlapping classes: [WARNING] - org.apache.commons.lang3.time.StopWatch$State$1 [WARNING] - org.apache.commons.lang3.ThreadUtils$1 [WARNING] - org.apache.commons.lang3.ThreadUtils$ThreadGroupPredicate [WARNING] - org.apache.commons.lang3.builder.MultilineRecursiveToStringStyle [WARNING] - org.apache.commons.lang3.concurrent.AbstractCircuitBreaker [WARNING] - org.apache.commons.lang3.SerializationUtils [WARNING] - org.apache.commons.lang3.time.FastDatePrinter$TwentyFourHourField [WARNING] - org.apache.commons.lang3.LocaleUtils [WARNING] - org.apache.commons.lang3.concurrent.ConcurrentException [WARNING] - org.apache.commons.lang3.CharRange [WARNING] - 250 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, slf4j-log4j12-1.7.16.jar, mango-cli-0.0.3-SNAPSHOT.jar define 6 overlapping classes: [WARNING] - org.slf4j.impl.Log4jLoggerAdapter [WARNING] - org.slf4j.impl.Log4jMDCAdapter [WARNING] - org.slf4j.impl.StaticMarkerBinder [WARNING] - org.slf4j.impl.Log4jLoggerFactory [WARNING] - org.slf4j.impl.StaticLoggerBinder [WARNING] - org.slf4j.impl.StaticMDCBinder [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, metrics-json-3.1.5.jar define 11 overlapping classes: [WARNING] - com.codahale.metrics.json.MetricsModule$MetricRegistrySerializer [WARNING] - com.codahale.metrics.json.HealthCheckModule$HealthCheckResultSerializer [WARNING] - com.codahale.metrics.json.HealthCheckModule [WARNING] - com.codahale.metrics.json.MetricsModule$TimerSerializer [WARNING] - com.codahale.metrics.json.MetricsModule$GaugeSerializer [WARNING] - com.codahale.metrics.json.MetricsModule$1 [WARNING] - com.codahale.metrics.json.MetricsModule$MeterSerializer [WARNING] - com.codahale.metrics.json.MetricsModule [WARNING] - com.codahale.metrics.json.MetricsModule$HistogramSerializer [WARNING] - com.codahale.metrics.json.MetricsModule$CounterSerializer [WARNING] - 1 more... [WARNING] scala-guice_2.11-4.2.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 95 overlapping classes: [WARNING] - net.codingwell.scalaguice.ScalaModule$ [WARNING] - net.codingwell.scalaguice.ScalaModule$ScalaScopedBindingBuilder [WARNING] - net.codingwell.scalaguice.InternalModule$BindingBuilder$$typecreator1$2 [WARNING] - net.codingwell.scalaguice.InjectorExtensions$ScalaInjector$$typecreator2$1 [WARNING] - net.codingwell.scalaguice.ScalaModule$ScalaLinkedBindingBuilder$$anon$2$$typecreator1$1 [WARNING] - net.codingwell.scalaguice.binder.ScopedBindingBuilderProxy [WARNING] - net.codingwell.scalaguice.ScalaModule$$anonfun$filterTrace$2 [WARNING] - net.codingwell.scalaguice.ScalaPrivateModule$ElementBuilder [WARNING] - net.codingwell.scalaguice.binder.LinkedBindingBuilderProxy$class [WARNING] - net.codingwell.scalaguice.ScalaModule$ScalaAnnotatedBindingBuilder [WARNING] - 85 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, checker-qual-2.5.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 302 overlapping classes: [WARNING] - org.checkerframework.checker.formatter.FormatUtil [WARNING] - org.checkerframework.checker.units.qual.MixedUnits [WARNING] - org.checkerframework.checker.units.qual.PolyUnit [WARNING] - org.checkerframework.checker.regex.qual.PolyRegex [WARNING] - org.checkerframework.checker.units.qual.C [WARNING] - org.checkerframework.checker.formatter.FormatUtil$IllegalFormatConversionCategoryException [WARNING] - org.checkerframework.framework.qual.Unqualified [WARNING] - org.checkerframework.common.reflection.qual.UnknownMethod [WARNING] - org.checkerframework.framework.qual.EnsuresQualifierIf [WARNING] - org.checkerframework.checker.signedness.SignednessUtil [WARNING] - 292 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, zookeeper-3.4.6.jar define 440 overlapping classes: [WARNING] - org.apache.zookeeper.server.NettyServerCnxn$DumpCommand [WARNING] - org.apache.zookeeper.proto.GetMaxChildrenRequest [WARNING] - org.apache.jute.XmlInputArchive$XMLParser [WARNING] - org.apache.zookeeper.server.NettyServerCnxn$SendBufferWriter [WARNING] - org.apache.jute.CsvInputArchive$1 [WARNING] - org.apache.zookeeper.KeeperException$CodeDeprecated [WARNING] - org.apache.zookeeper.server.ZooKeeperServerMXBean [WARNING] - org.apache.zookeeper.server.NettyServerCnxn$EnvCommand [WARNING] - org.apache.zookeeper.server.quorum.Learner$PacketInFlight [WARNING] - org.apache.zookeeper.Op$Check [WARNING] - 430 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, adam-codegen-spark2_2.11-0.26.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 18 overlapping classes: [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$ [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$getters$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$setters$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$apply$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$ [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$fields$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$$anonfun$fields$1 [WARNING] - 8 more... [WARNING] bcprov-jdk15on-1.52.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 2430 overlapping classes: [WARNING] - org.bouncycastle.crypto.modes.gcm.Tables8kGCMMultiplier [WARNING] - org.bouncycastle.crypto.tls.HeartbeatMode [WARNING] - org.bouncycastle.pqc.math.linearalgebra.GF2nPolynomialElement [WARNING] - org.bouncycastle.jcajce.provider.asymmetric.ecgost.KeyFactorySpi [WARNING] - org.bouncycastle.jcajce.provider.symmetric.AES$AlgParamsCCM [WARNING] - org.bouncycastle.asn1.tsp.TimeStampResp [WARNING] - org.bouncycastle.jcajce.provider.digest.SHA384$Mappings [WARNING] - org.bouncycastle.jcajce.provider.asymmetric.elgamal.AlgorithmParameterGeneratorSpi [WARNING] - org.bouncycastle.asn1.x509.CRLNumber [WARNING] - org.bouncycastle.jcajce.provider.digest.SM3 [WARNING] - 2420 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jersey-guava-2.22.2.jar define 753 overlapping classes: [WARNING] - jersey.repackaged.com.google.common.collect.AbstractNavigableMap$DescendingMap [WARNING] - jersey.repackaged.com.google.common.collect.AbstractMultiset$ElementSet [WARNING] - jersey.repackaged.com.google.common.collect.Collections2$OrderedPermutationCollection [WARNING] - jersey.repackaged.com.google.common.collect.StandardTable$TableSet [WARNING] - jersey.repackaged.com.google.common.base.Splitter [WARNING] - jersey.repackaged.com.google.common.util.concurrent.Futures$1$1 [WARNING] - jersey.repackaged.com.google.common.base.CharMatcher$5 [WARNING] - jersey.repackaged.com.google.common.collect.SortedMapDifference [WARNING] - jersey.repackaged.com.google.common.collect.ImmutableListMultimap [WARNING] - jersey.repackaged.com.google.common.cache.LocalCache$AbstractReferenceEntry [WARNING] - 743 more... [WARNING] RoaringBitmap-0.5.11.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 69 overlapping classes: [WARNING] - org.roaringbitmap.ReverseRunContainerShortIterator [WARNING] - org.roaringbitmap.ShortIterator [WARNING] - org.roaringbitmap.Util [WARNING] - org.roaringbitmap.buffer.RawMappeableRunContainerShortIterator [WARNING] - org.roaringbitmap.buffer.MappeableBitmapContainer [WARNING] - org.roaringbitmap.buffer.BufferFastAggregation$2 [WARNING] - org.roaringbitmap.buffer.MappeableBitmapContainerShortIterator [WARNING] - org.roaringbitmap.RunContainerShortIterator [WARNING] - org.roaringbitmap.buffer.ReverseMappeableArrayContainerShortIterator [WARNING] - org.roaringbitmap.buffer.MappeableContainerPointer [WARNING] - 59 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, base64-2.3.8.jar, mango-cli-0.0.3-SNAPSHOT.jar define 4 overlapping classes: [WARNING] - net.iharder.Base64$InputStream [WARNING] - net.iharder.Base64$OutputStream [WARNING] - net.iharder.Base64$1 [WARNING] - net.iharder.Base64 [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, hadoop-bam-7.9.2.jar define 115 overlapping classes: [WARNING] - org.seqdoop.hadoop_bam.BAMSplitGuesser [WARNING] - org.seqdoop.hadoop_bam.util.SAMHeaderReader [WARNING] - org.seqdoop.hadoop_bam.QseqInputFormat [WARNING] - org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter [WARNING] - org.seqdoop.hadoop_bam.FastaInputFormat$1 [WARNING] - org.seqdoop.hadoop_bam.util.SAMOutputPreparer$1 [WARNING] - org.seqdoop.hadoop_bam.QseqOutputFormat$QseqRecordWriter [WARNING] - org.seqdoop.hadoop_bam.FastaInputFormat [WARNING] - org.seqdoop.hadoop_bam.LineReader [WARNING] - org.seqdoop.hadoop_bam.util.BGZFCodec [WARNING] - 105 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, fastutil-6.5.7.jar, mango-cli-0.0.3-SNAPSHOT.jar define 10653 overlapping classes: [WARNING] - it.unimi.dsi.fastutil.doubles.Double2IntRBTreeMap$Submap$KeySet [WARNING] - it.unimi.dsi.fastutil.longs.Long2CharAVLTreeMap$2$1 [WARNING] - it.unimi.dsi.fastutil.bytes.Byte2ObjectLinkedOpenHashMap$EntryIterator [WARNING] - it.unimi.dsi.fastutil.shorts.Short2FloatOpenCustomHashMap$KeySet [WARNING] - it.unimi.dsi.fastutil.ints.Int2ReferenceRBTreeMap$Submap [WARNING] - it.unimi.dsi.fastutil.bytes.Byte2BooleanRBTreeMap$Submap$1 [WARNING] - it.unimi.dsi.fastutil.floats.AbstractFloat2ShortSortedMap$ValuesCollection [WARNING] - it.unimi.dsi.fastutil.longs.Long2ReferenceRBTreeMap$Submap$2 [WARNING] - it.unimi.dsi.fastutil.chars.AbstractChar2LongSortedMap$ValuesIterator [WARNING] - it.unimi.dsi.fastutil.doubles.DoubleHeaps [WARNING] - 10643 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, paranamer-2.8.jar define 21 overlapping classes: [WARNING] - com.thoughtworks.paranamer.PositionalParanamer [WARNING] - com.thoughtworks.paranamer.JavadocParanamer [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer$Type [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer$1 [WARNING] - com.thoughtworks.paranamer.JavadocParanamer$DirJavadocProvider [WARNING] - com.thoughtworks.paranamer.AnnotationParanamer$Jsr330Helper [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer$TypeCollector [WARNING] - com.thoughtworks.paranamer.AnnotationParanamer [WARNING] - com.thoughtworks.paranamer.NullParanamer [WARNING] - 11 more... [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, scalate-core_2.11-1.9.1.jar define 1372 overlapping classes: [WARNING] - org.fusesource.scalate.mustache.MustacheParser$$anonfun$open$1 [WARNING] - org.fusesource.scalate.scuery.support.CssParser$$anonfun$attrib$3$$anonfun$apply$26 [WARNING] - org.fusesource.scalate.support.TemplateFinder$$anonfun$org$fusesource$scalate$support$TemplateFinder$$findTemplateAlias$1$1$$anonfun$apply$3 [WARNING] - org.fusesource.scalate.ssp.SspParser$$anonfun$scalaExpression$3 [WARNING] - org.fusesource.scalate.scuery.support.InvalidCssSelectorException [WARNING] - org.fusesource.scalate.support.ScalaParseSupport$$anonfun$octalEscapeSeq$3 [WARNING] - org.fusesource.scalate.scuery.support.CssParser$$anonfun$functional_nth_pseudo$4 [WARNING] - org.fusesource.scalate.scaml.ScamlParser$$anonfun$expression$6$$anonfun$apply$30$$anonfun$apply$33 [WARNING] - org.fusesource.scalate.scaml.ScamlParser$$anonfun$haml_comment_statement$4 [WARNING] - org.fusesource.scalate.support.ScalaParseSupport$$anonfun$someUpto$3$$anonfun$apply$17 [WARNING] - 1362 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, minlog-1.3.0.jar, minlog-1.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 2 overlapping classes: [WARNING] - com.esotericsoftware.minlog.Log [WARNING] - com.esotericsoftware.minlog.Log$Logger [WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-intervalrdd-spark2_2.11-0.2.13.jar, mango-cli-0.0.3-SNAPSHOT.jar define 51 overlapping classes: [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$ [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$collect$2 [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$4 [WARNING] - org.bdgenomics.utils.interval.array.Interval$class [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$get$1 [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$4 [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$1 [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$ [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$filter$1 [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$mapValues$1 [WARNING] - 41 more... [WARNING] parquet-encoding-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 184 overlapping classes: [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer14 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer24 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer10 [WARNING] - org.apache.parquet.column.values.bitpacking.LemireBitPackingBE$Packer7 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer20 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer7 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer30 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer13 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer23 [WARNING] - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$Packer19 [WARNING] - 174 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, netty-3.9.9.Final.jar define 879 overlapping classes: [WARNING] - org.jboss.netty.handler.traffic.TrafficCounter$TrafficMonitoringTask [WARNING] - org.jboss.netty.handler.codec.spdy.SpdyGoAwayFrame [WARNING] - org.jboss.netty.util.internal.jzlib.Deflate [WARNING] - org.jboss.netty.channel.socket.ServerSocketChannelConfig [WARNING] - org.jboss.netty.util.internal.ConcurrentHashMap$HashIterator [WARNING] - org.jboss.netty.handler.codec.serialization.ObjectDecoder [WARNING] - org.jboss.netty.util.internal.jzlib.Tree [WARNING] - org.jboss.netty.util.internal.ConcurrentIdentityWeakKeyHashMap$Segment [WARNING] - org.jboss.netty.util.internal.ConcurrentIdentityHashMap$ValueIterator [WARNING] - org.jboss.netty.handler.codec.http.multipart.HttpPostRequestEncoder [WARNING] - 869 more... [WARNING] bdg-formats-0.12.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 61 overlapping classes: [WARNING] - org.bdgenomics.formats.avro.VariantCallingAnnotations$Builder [WARNING] - org.bdgenomics.formats.avro.VariantAnnotation$Builder [WARNING] - org.bdgenomics.formats.avro.Reference$1 [WARNING] - org.bdgenomics.formats.avro.VariantAnnotationMessage [WARNING] - org.bdgenomics.formats.avro.OntologyTerm$1 [WARNING] - org.bdgenomics.formats.avro.Feature$1 [WARNING] - org.bdgenomics.formats.avro.AlignmentRecord [WARNING] - org.bdgenomics.formats.avro.Sequence$1 [WARNING] - org.bdgenomics.formats.avro.ReadGroup$Builder [WARNING] - org.bdgenomics.formats.avro.ReadGroup [WARNING] - 51 more... [WARNING] jackson-core-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 121 overlapping classes: [WARNING] - org.codehaus.jackson.annotate.JsonManagedReference [WARNING] - org.codehaus.jackson.util.DefaultPrettyPrinter$FixedSpaceIndenter [WARNING] - org.codehaus.jackson.JsonGenerationException [WARNING] - org.codehaus.jackson.util.BufferRecycler$CharBufferType [WARNING] - org.codehaus.jackson.io.UTF32Reader [WARNING] - org.codehaus.jackson.sym.Name1 [WARNING] - org.codehaus.jackson.util.MinimalPrettyPrinter [WARNING] - org.codehaus.jackson.impl.JsonParserBase [WARNING] - org.codehaus.jackson.annotate.JsonValue [WARNING] - org.codehaus.jackson.sym.CharsToNameCanonicalizer$Bucket [WARNING] - 111 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, servo-core-0.12.12.jar, mango-cli-0.0.3-SNAPSHOT.jar define 162 overlapping classes: [WARNING] - com.netflix.servo.util.Objects [WARNING] - com.netflix.servo.util.Clock [WARNING] - com.netflix.servo.monitor.MaxGauge [WARNING] - com.netflix.servo.publish.LocalJmxConnector [WARNING] - com.netflix.servo.publish.MonitorRegistryMetricPoller$MonitorValueCallable [WARNING] - com.netflix.servo.util.ExpiringCache$Entry [WARNING] - com.netflix.servo.util.ThreadCpuStats$CpuUsage [WARNING] - com.netflix.servo.tag.SmallTagMap$Builder [WARNING] - com.netflix.servo.stats.StatsConfig [WARNING] - com.netflix.servo.monitor.Monitors$CounterFactory [WARNING] - 152 more... [WARNING] spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 18 overlapping classes: [WARNING] - org.apache.spark.unsafe.types.UTF8String [WARNING] - org.apache.spark.unsafe.memory.HeapMemoryAllocator [WARNING] - org.apache.spark.unsafe.array.LongArray [WARNING] - org.apache.spark.unsafe.types.UTF8String$LongWrapper [WARNING] - org.apache.spark.unsafe.bitset.BitSetMethods [WARNING] - org.apache.spark.unsafe.memory.UnsafeMemoryAllocator [WARNING] - org.apache.spark.sql.catalyst.expressions.HiveHasher [WARNING] - org.apache.spark.unsafe.KVIterator [WARNING] - org.apache.spark.unsafe.types.CalendarInterval [WARNING] - org.apache.spark.unsafe.memory.MemoryBlock [WARNING] - 8 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jsr305-1.3.9.jar, mango-cli-0.0.3-SNAPSHOT.jar define 35 overlapping classes: [WARNING] - javax.annotation.RegEx [WARNING] - javax.annotation.concurrent.Immutable [WARNING] - javax.annotation.meta.TypeQualifierDefault [WARNING] - javax.annotation.meta.TypeQualifier [WARNING] - javax.annotation.Syntax [WARNING] - javax.annotation.CheckReturnValue [WARNING] - javax.annotation.CheckForNull [WARNING] - javax.annotation.Nonnull [WARNING] - javax.annotation.meta.TypeQualifierNickname [WARNING] - javax.annotation.MatchesPattern [WARNING] - 25 more... [WARNING] error_prone_annotations-2.2.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 22 overlapping classes: [WARNING] - com.google.errorprone.annotations.NoAllocation [WARNING] - com.google.errorprone.annotations.Var [WARNING] - com.google.errorprone.annotations.IncompatibleModifiers [WARNING] - com.google.errorprone.annotations.CompatibleWith [WARNING] - com.google.errorprone.annotations.concurrent.LockMethod [WARNING] - com.google.errorprone.annotations.FormatString [WARNING] - com.google.errorprone.annotations.DoNotCall [WARNING] - com.google.errorprone.annotations.Immutable [WARNING] - com.google.errorprone.annotations.RestrictedApi [WARNING] - com.google.errorprone.annotations.CompileTimeConstant [WARNING] - 12 more... [WARNING] jetty-xml-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 14 overlapping classes: [WARNING] - org.eclipse.jetty.xml.ConfigurationProcessorFactory [WARNING] - org.eclipse.jetty.xml.XmlParser$Node [WARNING] - org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration$AttrOrElementNode [WARNING] - org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration [WARNING] - org.eclipse.jetty.xml.ConfigurationProcessor [WARNING] - org.eclipse.jetty.xml.XmlParser$Handler [WARNING] - org.eclipse.jetty.xml.XmlConfiguration [WARNING] - org.eclipse.jetty.xml.XmlConfiguration$1 [WARNING] - org.eclipse.jetty.xml.XmlConfiguration$JettyXmlConfiguration$1 [WARNING] - org.eclipse.jetty.xml.XmlParser [WARNING] - 4 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-server-2.22.2.jar, mango-cli-0.0.3-SNAPSHOT.jar define 665 overlapping classes: [WARNING] - org.glassfish.jersey.server.internal.inject.ParamConverters$TypeFromString [WARNING] - org.glassfish.jersey.server.internal.inject.QueryParamValueFactoryProvider [WARNING] - org.glassfish.jersey.server.internal.inject.ParamInjectionResolver [WARNING] - org.glassfish.jersey.server.internal.InternalServerProperties [WARNING] - org.glassfish.jersey.server.internal.inject.ParameterInjectionBinder$5 [WARNING] - jersey.repackaged.org.objectweb.asm.FieldWriter [WARNING] - org.glassfish.jersey.server.internal.RuntimeDelegateImpl [WARNING] - org.glassfish.jersey.server.internal.inject.ParamConverterFactory [WARNING] - org.glassfish.jersey.server.internal.monitoring.RequestEventImpl$Builder [WARNING] - org.glassfish.jersey.server.ContainerRequest [WARNING] - 655 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, scala-compiler-2.11.12.jar define 9084 overlapping classes: [WARNING] - scala.tools.nsc.doc.base.CommentFactoryBase$SimpleTagKey [WARNING] - scala.tools.jline_embedded.Terminal [WARNING] - scala.tools.nsc.Global$$anonfun$scala$tools$nsc$Global$$writeICode$1 [WARNING] - scala.tools.nsc.backend.opt.ClosureElimination$ClosureElim$$anonfun$analyzeMethod$1$$anonfun$apply$2 [WARNING] - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$typedCase$2$$anonfun$apply$27 [WARNING] - scala.tools.nsc.backend.icode.analysis.TypeFlowAnalysis$MTFAGrowable$$anonfun$scala$tools$nsc$backend$icode$analysis$TypeFlowAnalysis$MTFAGrowable$$putOnRadar$1$$anonfun$3 [WARNING] - scala.tools.nsc.interpreter.ILoop$$anonfun$standardCommands$3 [WARNING] - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$isReferencedFrom$1 [WARNING] - scala.tools.nsc.typechecker.Typers$Typer$dyna$ [WARNING] - scala.tools.nsc.transform.patmat.MatchAnalysis$MatchAnalyzer$NegativeExample$$anonfun$23 [WARNING] - 9074 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-launcher_2.11-2.3.3.jar define 34 overlapping classes: [WARNING] - org.apache.spark.launcher.AbstractAppHandle [WARNING] - org.apache.spark.launcher.SparkAppHandle$State [WARNING] - org.apache.spark.launcher.SparkAppHandle$Listener [WARNING] - org.apache.spark.launcher.ChildProcAppHandle [WARNING] - org.apache.spark.launcher.LauncherProtocol [WARNING] - org.apache.spark.launcher.LauncherProtocol$Stop [WARNING] - org.apache.spark.launcher.SparkSubmitOptionParser [WARNING] - org.apache.spark.launcher.LauncherProtocol$Message [WARNING] - org.apache.spark.launcher.CommandBuilderUtils [WARNING] - org.apache.spark.launcher.SparkSubmitCommandBuilder$OptionParser [WARNING] - 24 more... [WARNING] jetty-security-9.4.15.v20190215.jar, mango-cli-0.0.3-SNAPSHOT.jar define 61 overlapping classes: [WARNING] - org.eclipse.jetty.security.SpnegoUserPrincipal [WARNING] - org.eclipse.jetty.security.authentication.DigestAuthenticator [WARNING] - org.eclipse.jetty.security.UserDataConstraint [WARNING] - org.eclipse.jetty.security.PropertyUserStore$UserListener [WARNING] - org.eclipse.jetty.security.authentication.FormAuthenticator [WARNING] - org.eclipse.jetty.security.UserAuthentication [WARNING] - org.eclipse.jetty.security.DefaultAuthenticatorFactory [WARNING] - org.eclipse.jetty.security.SecurityHandler [WARNING] - org.eclipse.jetty.security.IdentityService [WARNING] - org.eclipse.jetty.security.authentication.ConfigurableSpnegoAuthenticator$UserIdentityHolder [WARNING] - 51 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, java-xmlbuilder-1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 5 overlapping classes: [WARNING] - com.jamesmurty.utils.NamespaceContextImpl [WARNING] - com.jamesmurty.utils.BaseXMLBuilder [WARNING] - com.jamesmurty.utils.XMLBuilder [WARNING] - com.jamesmurty.utils.XMLBuilder2 [WARNING] - com.jamesmurty.utils.XMLBuilderRuntimeException [WARNING] mango-core-0.0.3-SNAPSHOT.jar, snappy-java-1.0.5.jar, mango-cli-0.0.3-SNAPSHOT.jar define 12 overlapping classes: [WARNING] - org.xerial.snappy.SnappyLoader [WARNING] - org.xerial.snappy.SnappyOutputStream [WARNING] - org.xerial.snappy.SnappyErrorCode [WARNING] - org.xerial.snappy.SnappyBundleActivator [WARNING] - org.xerial.snappy.SnappyError [WARNING] - org.xerial.snappy.SnappyNativeAPI [WARNING] - org.xerial.snappy.SnappyException [WARNING] - org.xerial.snappy.Snappy [WARNING] - org.xerial.snappy.SnappyNative [WARNING] - org.xerial.snappy.OSInfo [WARNING] - 2 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, ivy-2.4.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 744 overlapping classes: [WARNING] - org.apache.ivy.ant.IvyDeliver [WARNING] - org.apache.ivy.plugins.resolver.util.ApacheHttpURLLister [WARNING] - org.apache.ivy.ant.BuildOBRTask [WARNING] - org.apache.ivy.osgi.p2.P2MetadataParser$UnitsHandler$1 [WARNING] - org.apache.ivy.core.cache.ResolutionCacheManager [WARNING] - org.apache.ivy.osgi.repo.EditableRepoDescriptor [WARNING] - org.apache.ivy.plugins.parser.AbstractModuleDescriptorParser$AbstractParser [WARNING] - org.apache.ivy.plugins.latest.LatestLexicographicStrategy$1 [WARNING] - org.apache.ivy.osgi.repo.FSManifestIterable$3 [WARNING] - org.apache.ivy.util.url.HttpClientHandler [WARNING] - 734 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, utils-cli-spark2_2.11-0.2.13.jar, mango-cli-0.0.3-SNAPSHOT.jar define 23 overlapping classes: [WARNING] - org.bdgenomics.utils.cli.Args4j [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$4 [WARNING] - org.bdgenomics.utils.cli.ParquetArgs [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$3 [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$class [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$2 [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$run$1 [WARNING] - org.bdgenomics.utils.cli.ParquetArgs$class [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$1 [WARNING] - org.bdgenomics.utils.cli.SaveArgs [WARNING] - 13 more... [WARNING] scalate-util_2.11-1.9.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 219 overlapping classes: [WARNING] - org.fusesource.scalate.util.StringResource [WARNING] - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$12$$anonfun$apply$3$$anonfun$apply$19 [WARNING] - org.fusesource.scalate.util.ClassPathBuilder$$anonfun$findManifestEntries$1$$anonfun$apply$3 [WARNING] - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$18 [WARNING] - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$12$$anonfun$apply$3$$anonfun$apply$5$$anonfun$apply$6$$anonfun$apply$9$$anonfun$apply$10 [WARNING] - org.fusesource.scalate.util.ResourceLoader [WARNING] - org.fusesource.scalate.util.SourceMapStratum$$anonfun$7 [WARNING] - org.fusesource.scalate.util.SourceMap$SmapParser$$anonfun$20$$anonfun$apply$45 [WARNING] - org.fusesource.scalate.util.ProductReflector$ [WARNING] - org.fusesource.scalate.util.ClassFinder$$anonfun$discoverCommandClasses$1 [WARNING] - 209 more... [WARNING] commons-compress-1.8.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 64 overlapping classes: [WARNING] - org.apache.commons.compress.archivers.sevenz.Coders$LZMADecoder [WARNING] - org.apache.commons.compress.archivers.sevenz.SevenZArchiveEntry [WARNING] - org.apache.commons.compress.archivers.sevenz.SevenZOutputFile$1 [WARNING] - org.apache.commons.compress.changes.ChangeSetPerformer$ArchiveEntryIterator [WARNING] - org.apache.commons.compress.archivers.sevenz.Coder [WARNING] - org.apache.commons.compress.archivers.sevenz.Coders$BCJDecoder$1 [WARNING] - org.apache.commons.compress.compressors.gzip.GzipParameters [WARNING] - org.apache.commons.compress.compressors.lzma.LZMACompressorInputStream [WARNING] - org.apache.commons.compress.compressors.snappy.SnappyCompressorInputStream [WARNING] - org.apache.commons.compress.archivers.sevenz.Coders$BCJDecoder [WARNING] - 54 more... [WARNING] rl_2.11-0.4.10.jar, mango-cli-0.0.3-SNAPSHOT.jar define 126 overlapping classes: [WARNING] - rl.StringQueryString$ [WARNING] - rl.PathOps$class [WARNING] - rl.MapQueryString$$anonfun$mkString$1$$anonfun$apply$4 [WARNING] - rl.EmptyFragment$ [WARNING] - rl.StringFragment [WARNING] - rl.IPv6Address$$anon$3 [WARNING] - rl.DomainParser$PublicSuffix$ [WARNING] - rl.DomainParser$PublicSuffix [WARNING] - rl.MapQueryString$$anonfun$10 [WARNING] - rl.EmptyHost$$anon$5 [WARNING] - 116 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-codec-1.12.jar, mango-cli-0.0.3-SNAPSHOT.jar define 92 overlapping classes: [WARNING] - org.apache.commons.codec.language.Nysiis [WARNING] - org.apache.commons.codec.language.bm.Rule$1 [WARNING] - org.apache.commons.codec.language.bm.Rule$RPattern [WARNING] - org.apache.commons.codec.language.ColognePhonetic$CologneInputBuffer [WARNING] - org.apache.commons.codec.digest.HmacUtils [WARNING] - org.apache.commons.codec.language.bm.BeiderMorseEncoder [WARNING] - org.apache.commons.codec.digest.UnixCrypt [WARNING] - org.apache.commons.codec.language.Soundex [WARNING] - org.apache.commons.codec.binary.BinaryCodec [WARNING] - org.apache.commons.codec.language.bm.Languages$1 [WARNING] - 82 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, convert-0.6.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 23 overlapping classes: [WARNING] - org.bdgenomics.convert.bdgenomics.SliceToRead [WARNING] - org.bdgenomics.convert.bdgenomics.SliceToSequence [WARNING] - org.bdgenomics.convert.bdgenomics.BdgenomicsModule [WARNING] - org.bdgenomics.convert.ConversionException [WARNING] - org.bdgenomics.convert.bdgenomics.OntologyTermToString [WARNING] - org.bdgenomics.convert.bdgenomics.StringToVariantAnnotationMessage [WARNING] - org.bdgenomics.convert.ConversionStringency [WARNING] - org.bdgenomics.convert.bdgenomics.ReadToSlice [WARNING] - org.bdgenomics.convert.Converter [WARNING] - org.bdgenomics.convert.bdgenomics.ReadToSequence [WARNING] - 13 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, aopalliance-repackaged-2.4.0-b34.jar define 17 overlapping classes: [WARNING] - org.aopalliance.reflect.ClassLocator [WARNING] - org.aopalliance.reflect.Metadata [WARNING] - org.aopalliance.instrument.Instrumentation [WARNING] - org.aopalliance.reflect.Field [WARNING] - org.aopalliance.intercept.FieldInterceptor [WARNING] - org.aopalliance.reflect.Method [WARNING] - org.aopalliance.reflect.CodeLocator [WARNING] - org.aopalliance.intercept.FieldAccess [WARNING] - org.aopalliance.reflect.ProgramUnit [WARNING] - org.aopalliance.instrument.UndoNotSupportedException [WARNING] - 7 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-module-paranamer-2.7.9.jar, mango-cli-0.0.3-SNAPSHOT.jar define 26 overlapping classes: [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.NullParanamer [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.ParameterNamesNotFoundException [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$1 [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$MethodCollector [WARNING] - com.fasterxml.jackson.module.paranamer.SerializableParanamer [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.JavadocParanamer$DirJavadocProvider [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$Type [WARNING] - com.fasterxml.jackson.module.paranamer.ParanamerAnnotationIntrospector [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.CachingParanamer$WithoutWeakReferences [WARNING] - com.fasterxml.jackson.module.paranamer.ParanamerOnJacksonAnnotationIntrospector [WARNING] - 16 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, curator-recipes-2.6.0.jar define 190 overlapping classes: [WARNING] - org.apache.curator.framework.recipes.atomic.DistributedAtomicNumber [WARNING] - org.apache.curator.framework.recipes.locks.Reaper$State [WARNING] - org.apache.curator.framework.recipes.locks.InterProcessReadWriteLock [WARNING] - org.apache.curator.framework.recipes.queue.QueueBase [WARNING] - org.apache.curator.framework.recipes.locks.ChildReaper$1 [WARNING] - org.apache.curator.framework.recipes.cache.Operation [WARNING] - org.apache.curator.framework.recipes.shared.SharedValue$1 [WARNING] - org.apache.curator.framework.recipes.locks.Revoker [WARNING] - org.apache.curator.framework.recipes.queue.QueueSharderPolicies [WARNING] - org.apache.curator.framework.recipes.locks.StandardLockInternalsDriver [WARNING] - 180 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, commons-io-2.6.jar define 127 overlapping classes: [WARNING] - org.apache.commons.io.FileCleaningTracker [WARNING] - org.apache.commons.io.comparator.SizeFileComparator [WARNING] - org.apache.commons.io.input.CloseShieldInputStream [WARNING] - org.apache.commons.io.ByteOrderParser [WARNING] - org.apache.commons.io.filefilter.EmptyFileFilter [WARNING] - org.apache.commons.io.monitor.FileEntry [WARNING] - org.apache.commons.io.output.ThresholdingOutputStream [WARNING] - org.apache.commons.io.input.TailerListener [WARNING] - org.apache.commons.io.IOExceptionWithCause [WARNING] - org.apache.commons.io.filefilter.NotFileFilter [WARNING] - 117 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, json4s-ast_2.11-3.2.11.jar define 68 overlapping classes: [WARNING] - org.json4s.Merge$Mergeable [WARNING] - org.json4s.Merge$Mergeable$MergeSyntax [WARNING] - org.json4s.Merge$$anonfun$mergeRec$2$1 [WARNING] - org.json4s.BigDecimalMode$class [WARNING] - org.json4s.JsonAST$JBool$ [WARNING] - org.json4s.JsonAST$JField$ [WARNING] - org.json4s.DoubleMode$class [WARNING] - org.json4s.JsonAST$JString [WARNING] - org.json4s.LowPriorityMergeDep$class [WARNING] - org.json4s.JsonAST [WARNING] - 58 more... [WARNING] curator-client-2.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 56 overlapping classes: [WARNING] - org.apache.curator.HandleHolder$Helper [WARNING] - org.apache.curator.utils.PathUtils [WARNING] - org.apache.curator.ensemble.exhibitor.ExhibitorEnsembleProvider$1 [WARNING] - org.apache.curator.utils.CloseableScheduledExecutorService [WARNING] - org.apache.curator.utils.EnsurePath$InitialHelper$1 [WARNING] - org.apache.curator.SessionFailRetryLoop$2 [WARNING] - org.apache.curator.utils.ZKPaths$PathAndNode [WARNING] - org.apache.curator.ensemble.exhibitor.DefaultExhibitorRestClient [WARNING] - org.apache.curator.TimeTrace [WARNING] - org.apache.curator.HandleHolder$1$1 [WARNING] - 46 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, scala-parser-combinators_2.11-1.0.4.jar define 352 overlapping classes: [WARNING] - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$whitespace$1$$anonfun$apply$20$$anonfun$apply$21 [WARNING] - scala.util.parsing.combinator.ImplicitConversions$$anonfun$flatten5$1 [WARNING] - scala.util.parsing.combinator.Parsers$$anonfun$rep$1 [WARNING] - scala.util.parsing.json.Lexer$$anonfun$number$1$$anonfun$apply$16 [WARNING] - scala.util.parsing.combinator.Parsers$NoSuccess$$anonfun$1 [WARNING] - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$3$$anonfun$apply$3$$anonfun$apply$4 [WARNING] - scala.util.parsing.combinator.token.StdTokens$class [WARNING] - scala.util.parsing.json.Lexer$$anonfun$charSeq$10 [WARNING] - scala.util.parsing.combinator.Parsers$Parser$$anonfun$$tilde$greater$1 [WARNING] - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$5 [WARNING] - 342 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, hk2-api-2.4.0-b34.jar, mango-cli-0.0.3-SNAPSHOT.jar define 165 overlapping classes: [WARNING] - org.glassfish.hk2.api.ActiveDescriptor [WARNING] - org.glassfish.hk2.api.Proxiable [WARNING] - org.glassfish.hk2.utilities.InjecteeImpl [WARNING] - org.glassfish.hk2.api.ProxyCtl [WARNING] - org.glassfish.hk2.api.DynamicConfiguration [WARNING] - org.glassfish.hk2.internal.ImmediateHelper$1 [WARNING] - org.glassfish.hk2.api.InjectionResolver [WARNING] - org.glassfish.hk2.utilities.ServiceLocatorUtilities$3 [WARNING] - org.glassfish.hk2.api.Validator [WARNING] - org.glassfish.hk2.api.PopulatorPostProcessor [WARNING] - 155 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, activation-1.1.1.jar, mango-cli-0.0.3-SNAPSHOT.jar define 38 overlapping classes: [WARNING] - javax.activation.DataContentHandlerFactory [WARNING] - javax.activation.ObjectDataContentHandler [WARNING] - javax.activation.DataContentHandler [WARNING] - com.sun.activation.registries.MimeTypeEntry [WARNING] - com.sun.activation.viewers.TextViewer [WARNING] - com.sun.activation.registries.LogSupport [WARNING] - javax.activation.CommandObject [WARNING] - javax.activation.SecuritySupport$2 [WARNING] - com.sun.activation.viewers.TextEditor [WARNING] - com.sun.activation.viewers.ImageViewerCanvas [WARNING] - 28 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, kryo-shaded-3.0.3.jar, kryo-2.24.0.jar define 193 overlapping classes: [WARNING] - com.esotericsoftware.kryo.serializers.BeanSerializer$1 [WARNING] - com.esotericsoftware.kryo.Registration [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor [WARNING] - com.esotericsoftware.kryo.util.IntMap$Values [WARNING] - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer [WARNING] - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl [WARNING] - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField [WARNING] - com.esotericsoftware.kryo.serializers.JavaSerializer [WARNING] - 183 more... [WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1955 overlapping classes: [WARNING] - com.google.common.collect.CompactHashMap$Itr [WARNING] - com.google.common.collect.ImmutableMapValues$1 [WARNING] - com.google.common.util.concurrent.AbstractService$5 [WARNING] - com.google.common.io.LineProcessor [WARNING] - com.google.common.io.BaseEncoding$StandardBaseEncoding$2 [WARNING] - com.google.common.io.ByteProcessor [WARNING] - com.google.common.math.package-info [WARNING] - com.google.common.util.concurrent.SimpleTimeLimiter [WARNING] - com.google.common.cache.AbstractCache$StatsCounter [WARNING] - com.google.common.util.concurrent.CycleDetectingLockFactory$Policies [WARNING] - 1945 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, guice-4.2.0.jar define 572 overlapping classes: [WARNING] - com.google.inject.Scope [WARNING] - com.google.inject.Binding [WARNING] - com.google.inject.internal.cglib.core.$EmitUtils$3 [WARNING] - com.google.inject.spi.TypeConverter [WARNING] - com.google.inject.internal.ConstructionProxy [WARNING] - com.google.inject.spi.InjectionPoint [WARNING] - com.google.inject.spi.StaticInjectionRequest [WARNING] - com.google.inject.internal.cglib.proxy.$FixedValueGenerator [WARNING] - com.google.inject.internal.cglib.proxy.$DispatcherGenerator [WARNING] - com.google.inject.spi.Elements$ElementsAsModule [WARNING] - 562 more... [WARNING] commons-math3-3.4.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 1215 overlapping classes: [WARNING] - org.apache.commons.math3.optim.linear.LinearOptimizer [WARNING] - org.apache.commons.math3.linear.LUDecomposition$Solver [WARNING] - org.apache.commons.math3.analysis.function.Gaussian$Parametric [WARNING] - org.apache.commons.math3.stat.descriptive.WeightedEvaluation [WARNING] - org.apache.commons.math3.analysis.FunctionUtils$3 [WARNING] - org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic [WARNING] - org.apache.commons.math3.ml.clustering.FuzzyKMeansClusterer [WARNING] - org.apache.commons.math3.analysis.FunctionUtils$3$1 [WARNING] - org.apache.commons.math3.ode.nonstiff.MidpointStepInterpolator [WARNING] - org.apache.commons.math3.ode.ParameterConfiguration [WARNING] - 1205 more... [WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, spark-launcher_2.11-2.3.3.jar, spark-tags_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar, spark-kvstore_2.11-2.3.3.jar, mango-cli-0.0.3-SNAPSHOT.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: [WARNING] - org.apache.spark.unused.UnusedStubClass [WARNING] commons-compress-1.8.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 127 overlapping classes: [WARNING] - org.apache.commons.compress.archivers.dump.ShortFileException [WARNING] - org.apache.commons.compress.utils.CountingInputStream [WARNING] - org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream [WARNING] - org.apache.commons.compress.compressors.bzip2.CRC [WARNING] - org.apache.commons.compress.archivers.dump.DumpArchiveEntry [WARNING] - org.apache.commons.compress.compressors.bzip2.BlockSort [WARNING] - org.apache.commons.compress.archivers.tar.TarArchiveEntry [WARNING] - org.apache.commons.compress.archivers.dump.UnsupportedCompressionAlgorithmException [WARNING] - org.apache.commons.compress.archivers.zip.AbstractUnicodeExtraField [WARNING] - org.apache.commons.compress.archivers.dump.InvalidFormatException [WARNING] - 117 more... [WARNING] jackson-module-scala_2.11-2.6.7.1.jar, mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar define 403 overlapping classes: [WARNING] - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializer$$anonfun$2 [WARNING] - com.fasterxml.jackson.module.scala.deser.UnsortedSetDeserializerModule [WARNING] - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializerModule$class [WARNING] - com.fasterxml.jackson.module.scala.JacksonModule$$anonfun$1 [WARNING] - com.fasterxml.jackson.module.scala.deser.SortedSetDeserializer$$anonfun$4 [WARNING] - com.fasterxml.jackson.module.scala.util.Options$class [WARNING] - com.fasterxml.jackson.module.scala.util.EnumResolver$ [WARNING] - com.fasterxml.jackson.module.scala.ser.OptionSerializer$$anonfun$serialize$1 [WARNING] - com.fasterxml.jackson.module.scala.ser.OptionSerializerModule [WARNING] - com.fasterxml.jackson.module.scala.modifiers.CollectionLikeTypeModifier$$anonfun$modifyType$3 [WARNING] - 393 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jets3t-0.9.4.jar define 616 overlapping classes: [WARNING] - org.jets3t.service.acl.GroupGrantee [WARNING] - org.jets3t.service.multithread.CreateObjectsEvent [WARNING] - org.jets3t.service.model.S3BucketLoggingStatus [WARNING] - contribs.com.centerkey.utils.BareBonesBrowserLaunch [WARNING] - org.jets3t.service.impl.rest.CloudFrontXmlResponsesSaxParser$CacheBehaviorHandler [WARNING] - org.jets3t.apps.uploader.XmlGenerator$ObjectAndSignatureRequestDetails [WARNING] - org.jets3t.service.MultipartUploadChunk [WARNING] - org.jets3t.apps.cockpit.Cockpit$27 [WARNING] - org.jets3t.service.model.S3DeleteMarker [WARNING] - org.jets3t.gui.TableSorter$Row [WARNING] - 606 more... [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, scala-compiler-2.11.12.jar define 11 overlapping classes: [WARNING] - scala.tools.asm.CurrentFrame [WARNING] - scala.tools.nsc.transform.patmat.MatchCodeGen$OptimizedCodegen$optimizedCodegen$$anonfun$2$$anonfun$3 [WARNING] - scala.tools.nsc.symtab.classfile.ICodeReader$$anonfun$parseInstruction$1$2 [WARNING] - scala.tools.nsc.interpreter.jline.FileBackedHistory$$anonfun$2 [WARNING] - scala.tools.nsc.interpreter.jline.FileBackedHistory$$anonfun$secure$1 [WARNING] - scala.tools.nsc.interpreter.jline_embedded.FileBackedHistory$$anonfun$2 [WARNING] - scala.tools.nsc.GenericRunnerSettings$$anonfun$1 [WARNING] - scala.tools.nsc.transform.patmat.MatchCodeGen$OptimizedCodegen$optimizedCodegen$$anonfun$2$$anonfun$4 [WARNING] - scala.tools.nsc.interpreter.jline_embedded.FileBackedHistory$$anonfun$secure$1 [WARNING] - scala.tools.util.PathResolverBase$Calculated$$anonfun$okay$1$1 [WARNING] - 1 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, jul-to-slf4j-1.7.16.jar define 1 overlapping classes: [WARNING] - org.slf4j.bridge.SLF4JBridgeHandler [WARNING] mango-core-0.0.3-SNAPSHOT.jar, mango-cli-0.0.3-SNAPSHOT.jar, xbean-asm5-shaded-4.4.jar define 81 overlapping classes: [WARNING] - org.apache.xbean.asm5.FieldWriter [WARNING] - org.apache.xbean.asm5.commons.GeneratorAdapter [WARNING] - org.apache.xbean.asm5.AnnotationWriter [WARNING] - org.apache.xbean.asm5.tree.IntInsnNode [WARNING] - org.apache.xbean.asm5.Type [WARNING] - org.apache.xbean.asm5.commons.RemappingClassAdapter [WARNING] - org.apache.xbean.asm5.tree.FieldInsnNode [WARNING] - org.apache.xbean.asm5.tree.MultiANewArrayInsnNode [WARNING] - org.apache.xbean.asm5.tree.IincInsnNode [WARNING] - org.apache.xbean.asm5.tree.InsnList$InsnListIterator [WARNING] - 71 more... [WARNING] mango-cli-0.0.3-SNAPSHOT.jar, grizzled-slf4j_2.11-1.0.2.jar define 4 overlapping classes: [WARNING] - grizzled.slf4j.Logger$ [WARNING] - grizzled.slf4j.Logging [WARNING] - grizzled.slf4j.Logging$class [WARNING] - grizzled.slf4j.Logger [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 /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar with /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT-shaded.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-assembly --- [INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-assembly --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-assembly >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-assembly --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-assembly --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ mango-assembly --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ mango-assembly --- [INFO] Request to add '/home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/java-templates' folder. Not added since it does not exist. [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-assembly --- [INFO] Source directory: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-assembly <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-assembly --- model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango: Distribution 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-distribution --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-distribution --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-distribution --- [INFO] No sources to compile [INFO] [INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-distribution --- [INFO] Replacing original artifact with shaded artifact. [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-distribution --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-distribution --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-distribution >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-distribution --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-distribution --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-distribution <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-distribution --- [INFO] No source files found [INFO] [INFO] --- maven-assembly-plugin:2.4.1:single (default) @ mango-distribution --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [INFO] Building tar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.tar.gz [INFO] Building tar: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.tar.bz2 [INFO] Building zip: /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.zip [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] mango .............................................. SUCCESS [ 3.226 s] [INFO] mango: CORE ........................................ SUCCESS [ 40.974 s] [INFO] mango: CLI ......................................... SUCCESS [01:00 min] [INFO] Mango: Assembly .................................... SUCCESS [ 54.313 s] [INFO] mango: Distribution ................................ SUCCESS [ 33.285 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 03:12 min [INFO] Finished at: 2019-05-13T18:11:52-07:00 [INFO] Final Memory: 96M/1503M [INFO] ------------------------------------------------------------------------ # make sure that the distribution package contains an assembly jar # if no assembly jar is found, this will exit with code 1 and fail the build tar tzvf mango-distribution/target/mango-distribution*-bin.tar.gz | \ grep mango-assembly | \ grep jar | \ grep -v -e sources -e javadoc + grep mango-assembly + grep jar + tar tzvf mango-distribution/target/mango-distribution-0.0.3-SNAPSHOT-bin.tar.gz + grep -v -e sources -e javadoc -rw-r--r-- jenkins/jenkins 126865002 2019-05-13 18:11 mango-distribution-0.0.3-SNAPSHOT/repo/mango-assembly-0.0.3-SNAPSHOT.jar # we are done with maven, so clean up the maven temp dir find ${MANGO_MVN_TMP_DIR} + find /tmp/mangoTestMvnYNWYORu /tmp/mangoTestMvnYNWYORu /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/._references.avro.crc /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/._readGroups.avro.crc /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/_readGroups.avro /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/._partitionedByStartPos.crc /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/_references.avro /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/_partitionedByStartPos /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/._SUCCESS.crc /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/_SUCCESS /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/_processingSteps.avro /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=1 /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=1/positionBin=26 /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=1/positionBin=26/part-00000-d00b4b8b-850d-4556-8365-8133d01c0188.c000.snappy.parquet /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=1/positionBin=26/.part-00000-d00b4b8b-850d-4556-8365-8133d01c0188.c000.snappy.parquet.crc /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=1/positionBin=240 /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=1/positionBin=240/part-00000-d00b4b8b-850d-4556-8365-8133d01c0188.c000.snappy.parquet /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=1/positionBin=240/.part-00000-d00b4b8b-850d-4556-8365-8133d01c0188.c000.snappy.parquet.crc /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/._processingSteps.avro.crc /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=2 /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=2/positionBin=189 /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=2/positionBin=189/part-00000-d00b4b8b-850d-4556-8365-8133d01c0188.c000.snappy.parquet /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496.adam/referenceName=2/positionBin=189/.part-00000-d00b4b8b-850d-4556-8365-8133d01c0188.c000.snappy.parquet.crc /tmp/mangoTestMvnYNWYORu/scalate-8714131601268770740-workdir /tmp/mangoTestMvnYNWYORu/scalate-8714131601268770740-workdir/classes /tmp/mangoTestMvnYNWYORu/scalate-8714131601268770740-workdir/src /tmp/mangoTestMvnYNWYORu/scalate-8714131601268770740-workdir/src/WEB-INF /tmp/mangoTestMvnYNWYORu/scalate-8714131601268770740-workdir/src/WEB-INF/layouts /tmp/mangoTestMvnYNWYORu/scalate-8714131601268770740-workdir/src/WEB-INF/layouts/overall.ssp.scala /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028 /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045 /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/_header /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/._references.avro.crc /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/_samples.avro /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/._partitionedByStartPos.crc /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/_references.avro /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/_partitionedByStartPos /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/._SUCCESS.crc /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/_SUCCESS /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/referenceName=1 /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/referenceName=1/positionBin=0 /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/referenceName=1/positionBin=0/.part-00000-4a74512f-ac0a-40b7-82e7-0e1cbd9120eb.c000.snappy.parquet.crc /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/referenceName=1/positionBin=0/part-00000-4a74512f-ac0a-40b7-82e7-0e1cbd9120eb.c000.snappy.parquet /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/._header.crc /tmp/mangoTestMvnYNWYORu/TempSuite4013823256088161045.adam/._samples.avro.crc /tmp/mangoTestMvnYNWYORu/mmbroken3562880171554863656.genome /tmp/mangoTestMvnYNWYORu/invalidBuild.genome4955499409958557840 /tmp/mangoTestMvnYNWYORu/4515610687178373043 /tmp/mangoTestMvnYNWYORu/4515610687178373043/anoGam1.genome /tmp/mangoTestMvnYNWYORu/5501840225073725920 /tmp/mangoTestMvnYNWYORu/1195722755323740462 /tmp/mangoTestMvnYNWYORu/1195722755323740462/anoGam1.genome /tmp/mangoTestMvnYNWYORu/genomes1382471159330844540 /tmp/mangoTestMvnYNWYORu/genomes1382471159330844540/hg19.genome /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/_header /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/._references.avro.crc /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/_samples.avro /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/._partitionedByStartPos.crc /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/_references.avro /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/_partitionedByStartPos /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/._SUCCESS.crc /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/_SUCCESS /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/referenceName=1 /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/referenceName=1/positionBin=0 /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/referenceName=1/positionBin=0/.part-00000-0a46f80b-83b4-4520-a231-d3f20ea5b1b8.c000.snappy.parquet.crc /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/referenceName=1/positionBin=0/part-00000-0a46f80b-83b4-4520-a231-d3f20ea5b1b8.c000.snappy.parquet /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/._header.crc /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874.adam/._samples.avro.crc /tmp/mangoTestMvnYNWYORu/TempSuite3954987065639747496 /tmp/mangoTestMvnYNWYORu/genomes4195821665678429653 /tmp/mangoTestMvnYNWYORu/genomes4195821665678429653/hg19.genome /tmp/mangoTestMvnYNWYORu/scalate-2506416923854648376-workdir /tmp/mangoTestMvnYNWYORu/scalate-2506416923854648376-workdir/classes /tmp/mangoTestMvnYNWYORu/scalate-2506416923854648376-workdir/src /tmp/mangoTestMvnYNWYORu/scalate-2506416923854648376-workdir/src/WEB-INF /tmp/mangoTestMvnYNWYORu/scalate-2506416923854648376-workdir/src/WEB-INF/layouts /tmp/mangoTestMvnYNWYORu/scalate-2506416923854648376-workdir/src/WEB-INF/layouts/browser.ssp.scala /tmp/mangoTestMvnYNWYORu/mmbroken2515467134427844047.genome /tmp/mangoTestMvnYNWYORu/invalidBuild.genome8186798859170278095 /tmp/mangoTestMvnYNWYORu/TempSuite3550606786348769874 /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/._references.avro.crc /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/._readGroups.avro.crc /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/_readGroups.avro /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/._partitionedByStartPos.crc /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/_references.avro /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/_partitionedByStartPos /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/._SUCCESS.crc /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/_SUCCESS /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/_processingSteps.avro /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=1 /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=1/positionBin=26 /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=1/positionBin=26/.part-00000-1eeba885-d09e-4f20-a21e-df3092b68467.c000.snappy.parquet.crc /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=1/positionBin=26/part-00000-1eeba885-d09e-4f20-a21e-df3092b68467.c000.snappy.parquet /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=1/positionBin=240 /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=1/positionBin=240/.part-00000-1eeba885-d09e-4f20-a21e-df3092b68467.c000.snappy.parquet.crc /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=1/positionBin=240/part-00000-1eeba885-d09e-4f20-a21e-df3092b68467.c000.snappy.parquet /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/._processingSteps.avro.crc /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=2 /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=2/positionBin=189 /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=2/positionBin=189/.part-00000-1eeba885-d09e-4f20-a21e-df3092b68467.c000.snappy.parquet.crc /tmp/mangoTestMvnYNWYORu/TempSuite218932584361363028.adam/referenceName=2/positionBin=189/part-00000-1eeba885-d09e-4f20-a21e-df3092b68467.c000.snappy.parquet /tmp/mangoTestMvnYNWYORu/3434478720771933309 /tmp/mangoTestMvnYNWYORu/snappy-1.0.5-libsnappyjava.so /tmp/mangoTestMvnYNWYORu/scalate-6014617488776307181-workdir /tmp/mangoTestMvnYNWYORu/scalate-6014617488776307181-workdir/classes /tmp/mangoTestMvnYNWYORu/scalate-6014617488776307181-workdir/src /tmp/mangoTestMvnYNWYORu/scalate-6014617488776307181-workdir/src/WEB-INF /tmp/mangoTestMvnYNWYORu/scalate-6014617488776307181-workdir/src/WEB-INF/layouts /tmp/mangoTestMvnYNWYORu/scalate-6014617488776307181-workdir/src/WEB-INF/layouts/browser.ssp.scala /tmp/mangoTestMvnYNWYORu/scalate-4725509192055939583-workdir /tmp/mangoTestMvnYNWYORu/scalate-4725509192055939583-workdir/classes /tmp/mangoTestMvnYNWYORu/scalate-4725509192055939583-workdir/src /tmp/mangoTestMvnYNWYORu/scalate-4725509192055939583-workdir/src/WEB-INF /tmp/mangoTestMvnYNWYORu/scalate-4725509192055939583-workdir/src/WEB-INF/layouts /tmp/mangoTestMvnYNWYORu/scalate-4725509192055939583-workdir/src/WEB-INF/layouts/overall.ssp.scala rm -rf ${MANGO_MVN_TMP_DIR} + rm -rf /tmp/mangoTestMvnYNWYORu find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${MANGO_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \ {} \; + find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/mangoTestMvnYNWYORu:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' # run integration tests # prebuilt spark distributions are scala 2.11 for spark 2.x if [[ ${SCALAVER} == 2.11 ]]; then # make a temp directory MANGO_TMP_DIR=$(mktemp -d -t mangoTestXXXXXXX) MANGO_TMP_DIR=$MANGO_TMP_DIR/deleteMePleaseThisIsNoLongerNeeded mkdir $MANGO_TMP_DIR # set the TMPDIR envar, which is used by python to choose where to make temp directories export TMPDIR=${MANGO_TMP_DIR} pushd $PROJECT_ROOT # Copy the jar into our temp space for testing cp -r . $MANGO_TMP_DIR popd pushd $MANGO_TMP_DIR # what hadoop version are we on? format string for downloading spark assembly if [[ $HADOOP_VERSION =~ ^2\.6 ]]; then HADOOP=hadoop2.6 elif [[ $HADOOP_VERSION =~ ^2\.7 ]]; then HADOOP=hadoop2.7 else echo "Unknown Hadoop version." exit 1 fi # set spark artifact string for downloading assembly SPARK=spark-${SPARK_VERSION} # download prepackaged spark assembly curl \ -L "https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/${SPARK}/${SPARK}-bin-${HADOOP}.tgz" \ -o ${SPARK}-bin-${HADOOP}.tgz tar xzvf ${SPARK}-bin-${HADOOP}.tgz export SPARK_HOME=${MANGO_TMP_DIR}/${SPARK}-bin-${HADOOP} # add pyspark to the python path PY4J_ZIP="$(ls -1 "${SPARK_HOME}/python/lib" | grep py4j)" export PYTHONPATH=${SPARK_HOME}/python:${SPARK_HOME}/python/lib/${PY4J_ZIP}:${PYTHONPATH} # put mango jar on the pyspark path ASSEMBLY_DIR="${MANGO_TMP_DIR}/mango-assembly/target" ASSEMBLY_JAR="$(ls -1 "$ASSEMBLY_DIR" | grep "^mango-assembly[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true)" export PYSPARK_SUBMIT_ARGS="--jars ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} --driver-class-path ${ASSEMBLY_DIR}/${ASSEMBLY_JAR} pyspark-shell" # create a conda environment for python build, if necessary pythons=( 2.7 3.6 ) for python in ${pythons[*]} do uuid=$(uuidgen) conda create -y -q -n mango-build-${uuid} python=${python} source activate mango-build-${uuid} # install npm and node in the venv for mango-viz conda install -y nodejs # prepare mango python pushd mango-python make prepare popd # we can run the python build, now that we have a spark executable mvn -U \ -P python,distribution \ package \ -DskipTests \ -Dhadoop.version=${HADOOP_VERSION} \ -Dspark.version=${SPARK_VERSION} # clean mango python pushd mango-python make clean popd # prepare mango viz pushd mango-viz make prepare popd # run the widgets tests (mango-viz) mvn -P widgets test # clean mango viz pushd mango-viz make clean popd # make sure that the distribution package contains an egg # if no assembly jar is found, this will exit with code 1 and fail the build tar tzvf mango-distribution/target/mango-distribution*-bin.tar.gz | \ grep bdgenomics.mango | \ grep egg # test mango notebook, output to temporary log file MANGO_NOTEBOOK_LOGS=${MANGO_TMP_DIR}/mango-notebook.log bash -xv ${PROJECT_ROOT}/bin/mango-notebook &> ${MANGO_NOTEBOOK_LOGS} & # sleep for 2 seconds to let mango-notebook start up sleep 2 # if mango-notebook fails, then trying to kill the process will fail if kill $! ; then echo "Mango Notebook Succeeded" else echo "Mango Notebook failed with logs:" cat ${MANGO_NOTEBOOK_LOGS} # clean up rm -rf ${MANGO_TMP_DIR} exit 1 fi # copy python targets back cp -r mango-python/target ${PROJECT_ROOT}/mango-python/ # deactivate and remove the conda env source deactivate conda remove -y --name mango-build-${uuid} --all done # test mango submit MANGO_BROWSER_LOGS=mango-submit.log bash -xv ${PROJECT_ROOT}/example-files/browser-scripts/run-example.sh &> ${MANGO_BROWSER_LOGS} & # sleep for 10 seconds to let mango-browser start up sleep 10 # make sure server responds to POST for reads and variants curl \ --header "Content-type: application/json" \ --request POST \ --data "{\"pageToken\":null,\"pageSize\":200,\"readGroupIds\":[\"chr17_7500000-7515000_sam\"],\"referenceId\":\"chr17\",\"start\":1,\"end\":100}" \ http://localhost:8080/reads/search curl \ --header "Content-type: application/json" \ --request POST \ --data "{\"variantSetId\":\"ALL_chr17_7500000-7515000_phase3_shapeit2_mvncall_integrated_v5a_20130502_genotypes_vcf\",\"pageToken\":null,\"pageSize\":400,\"referenceName\":\"chr17\",\"callSetIds\":[],\"start\":7500000,\"end\":7515000}" \ http://localhost:8080/variants/search # get processes with mango prefix PROCESSES=( $(ps aux | grep -F 'browser-scripts/run-example.sh' | grep -v -F 'grep' | awk '{ print $2 }') ) # There should be processes running for mango-browser if [ "${#PROCESSES[@]}" -gt 0 ] ; then echo "Mango Browser Succeeded" # kill all Mango Browser related processes kill ${PROCESSES}; else echo "Mango Browser failed with logs:" cat ${MANGO_BROWSER_LOGS} # clean up rm -rf ${MANGO_TMP_DIR} exit 1 fi # test genome builds TEST_GENOME="anoGam1" bash -xv ${PROJECT_ROOT}/bin/make_genome ${TEST_GENOME} ${MANGO_TMP_DIR} unzip ${MANGO_TMP_DIR}/${TEST_GENOME}.genome -d ${MANGO_TMP_DIR}/${TEST_GENOME} pushd ${MANGO_TMP_DIR}/${TEST_GENOME} cat properties.txt cat ${TEST_GENOME}.chrom.sizes popd rm -rf ${MANGO_TMP_DIR}/${TEST_GENOME}* # clean up rm -rf ${MANGO_TMP_DIR} fi + [[ 2.11 == 2.11 ]] mktemp -d -t mangoTestXXXXXXX ++ mktemp -d -t mangoTestXXXXXXX + MANGO_TMP_DIR=/tmp/mangoTestcbqUd3G + MANGO_TMP_DIR=/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded + mkdir /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded + export TMPDIR=/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded + TMPDIR=/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded + pushd /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/.. ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu + cp -r . /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded + popd ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu + pushd /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu + [[ 2.7.5 =~ ^2\.6 ]] + [[ 2.7.5 =~ ^2\.7 ]] + HADOOP=hadoop2.7 + SPARK=spark-2.3.3 + curl -L 'https://www.apache.org/dyn/mirrors/mirrors.cgi?action=download&filename=spark/spark-2.3.3/spark-2.3.3-bin-hadoop2.7.tgz' -o spark-2.3.3-bin-hadoop2.7.tgz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 215M 0 4093 0 0 9381 0 6:41:34 --:--:-- 6:41:34 9381 0 215M 0 780k 0 0 542k 0 0:06:47 0:00:01 0:06:46 774k 0 215M 0 1846k 0 0 755k 0 0:04:52 0:00:02 0:04:50 917k 1 215M 1 2856k 0 0 814k 0 0:04:30 0:00:03 0:04:27 929k 1 215M 1 3666k 0 0 792k 0 0:04:38 0:00:04 0:04:34 874k 1 215M 1 3841k 0 0 707k 0 0:05:12 0:00:05 0:05:07 768k 2 215M 2 4558k 0 0 708k 0 0:05:11 0:00:06 0:05:05 755k 2 215M 2 5698k 0 0 766k 0 0:04:48 0:00:07 0:04:41 771k 3 215M 3 6942k 0 0 822k 0 0:04:28 0:00:08 0:04:20 827k 3 215M 3 7040k 0 0 739k 0 0:04:58 0:00:09 0:04:49 688k 3 215M 3 7044k 0 0 664k 0 0:05:32 0:00:10 0:05:22 619k 3 215M 3 7160k 0 0 622k 0 0:05:54 0:00:11 0:05:43 514k 3 215M 3 7218k 0 0 577k 0 0:06:21 0:00:12 0:06:09 300k 3 215M 3 7283k 0 0 541k 0 0:06:47 0:00:13 0:06:34 69821 3 215M 3 7447k 0 0 515k 0 0:07:07 0:00:14 0:06:53 84881 3 215M 3 7753k 0 0 502k 0 0:07:19 0:00:15 0:07:04 146k 3 215M 3 8277k 0 0 503k 0 0:07:18 0:00:16 0:07:02 226k 4 215M 4 9157k 0 0 525k 0 0:07:00 0:00:17 0:06:43 392k 4 215M 4 9553k 0 0 516k 0 0:07:07 0:00:18 0:06:49 449k 4 215M 4 9618k 0 0 493k 0 0:07:27 0:00:19 0:07:08 429k 4 215M 4 9991k 0 0 488k 0 0:07:31 0:00:20 0:07:11 447k 4 215M 4 10.7M 0 0 510k 0 0:07:11 0:00:21 0:06:50 535k 5 215M 5 11.2M 0 0 513k 0 0:07:09 0:00:22 0:06:47 471k 5 215M 5 11.7M 0 0 515k 0 0:07:08 0:00:23 0:06:45 512k 5 215M 5 12.4M 0 0 519k 0 0:07:04 0:00:24 0:06:40 622k 6 215M 6 13.0M 0 0 523k 0 0:07:01 0:00:25 0:06:36 666k 6 215M 6 13.5M 0 0 526k 0 0:06:59 0:00:26 0:06:33 591k 6 215M 6 14.2M 0 0 532k 0 0:06:54 0:00:27 0:06:27 619k 7 215M 7 15.1M 0 0 547k 0 0:06:43 0:00:28 0:06:15 695k 7 215M 7 16.0M 0 0 560k 0 0:06:34 0:00:29 0:06:05 757k 7 215M 7 17.1M 0 0 575k 0 0:06:23 0:00:30 0:05:53 832k 8 215M 8 18.0M 0 0 586k 0 0:06:16 0:00:31 0:05:45 906k 8 215M 8 18.9M 0 0 597k 0 0:06:09 0:00:32 0:05:37 955k 9 215M 9 19.9M 0 0 611k 0 0:06:01 0:00:33 0:05:28 975k 9 215M 9 20.9M 0 0 624k 0 0:05:53 0:00:34 0:05:19 1001k 10 215M 10 22.0M 0 0 635k 0 0:05:47 0:00:35 0:05:12 1010k 10 215M 10 23.0M 0 0 647k 0 0:05:40 0:00:36 0:05:04 1032k 11 215M 11 24.1M 0 0 655k 0 0:05:36 0:00:37 0:04:59 1005k 11 215M 11 24.1M 0 0 642k 0 0:05:43 0:00:38 0:05:05 851k 11 215M 11 24.2M 0 0 630k 0 0:05:49 0:00:39 0:05:10 678k 11 215M 11 24.3M 0 0 615k 0 0:05:58 0:00:40 0:05:18 475k 11 215M 11 24.4M 0 0 604k 0 0:06:05 0:00:41 0:05:24 290k 11 215M 11 24.6M 0 0 595k 0 0:06:10 0:00:42 0:05:28 115k 11 215M 11 25.1M 0 0 591k 0 0:06:13 0:00:43 0:05:30 192k 11 215M 11 25.8M 0 0 595k 0 0:06:10 0:00:44 0:05:26 314k 12 215M 12 27.1M 0 0 611k 0 0:06:01 0:00:45 0:05:16 573k 12 215M 12 27.9M 0 0 615k 0 0:05:58 0:00:46 0:05:12 706k 12 215M 12 28.0M 0 0 604k 0 0:06:05 0:00:47 0:05:18 682k 13 215M 13 28.1M 0 0 594k 0 0:06:11 0:00:48 0:05:23 615k 13 215M 13 28.6M 0 0 594k 0 0:06:11 0:00:49 0:05:22 583k 13 215M 13 30.0M 0 0 610k 0 0:06:01 0:00:50 0:05:11 609k 14 215M 14 30.3M 0 0 603k 0 0:06:05 0:00:51 0:05:14 491k 14 215M 14 30.4M 0 0 593k 0 0:06:11 0:00:52 0:05:19 492k 14 215M 14 30.8M 0 0 590k 0 0:06:13 0:00:53 0:05:20 555k 14 215M 14 31.9M 0 0 601k 0 0:06:06 0:00:54 0:05:12 675k 15 215M 15 32.5M 0 0 600k 0 0:06:07 0:00:55 0:05:12 498k 15 215M 15 32.5M 0 0 589k 0 0:06:14 0:00:56 0:05:18 446k 15 215M 15 32.6M 0 0 582k 0 0:06:19 0:00:57 0:05:22 457k 15 215M 15 32.7M 0 0 573k 0 0:06:24 0:00:58 0:05:26 395k 15 215M 15 32.7M 0 0 564k 0 0:06:31 0:00:59 0:05:32 167k 15 215M 15 32.9M 0 0 556k 0 0:06:36 0:01:00 0:05:36 66993 15 215M 15 33.0M 0 0 551k 0 0:06:40 0:01:01 0:05:39 104k 15 215M 15 33.4M 0 0 548k 0 0:06:42 0:01:02 0:05:40 155k 15 215M 15 34.0M 0 0 550k 0 0:06:41 0:01:03 0:05:38 275k 16 215M 16 35.0M 0 0 557k 0 0:06:36 0:01:04 0:05:32 467k 16 215M 16 35.1M 0 0 550k 0 0:06:41 0:01:05 0:05:36 465k 16 215M 16 35.2M 0 0 542k 0 0:06:46 0:01:06 0:05:40 436k 16 215M 16 35.6M 0 0 541k 0 0:06:47 0:01:07 0:05:40 450k 17 215M 17 36.9M 0 0 552k 0 0:06:39 0:01:08 0:05:31 576k 17 215M 17 38.1M 0 0 562k 0 0:06:32 0:01:09 0:05:23 628k 17 215M 17 38.2M 0 0 554k 0 0:06:37 0:01:10 0:05:27 619k 17 215M 17 38.2M 0 0 546k 0 0:06:43 0:01:11 0:05:32 597k 17 215M 17 38.2M 0 0 538k 0 0:06:49 0:01:12 0:05:37 506k 17 215M 17 38.2M 0 0 531k 0 0:06:55 0:01:13 0:05:42 253k 17 215M 17 38.2M 0 0 523k 0 0:07:01 0:01:14 0:05:47 24439 17 215M 17 38.3M 0 0 520k 0 0:07:04 0:01:15 0:05:49 29205 17 215M 17 38.4M 0 0 514k 0 0:07:09 0:01:16 0:05:53 40667 17 215M 17 38.4M 0 0 508k 0 0:07:14 0:01:17 0:05:57 52446 17 215M 17 38.5M 0 0 503k 0 0:07:18 0:01:18 0:06:00 82550 18 215M 18 38.8M 0 0 500k 0 0:07:20 0:01:19 0:06:01 136k 18 215M 18 39.3M 0 0 500k 0 0:07:20 0:01:20 0:06:00 205k 18 215M 18 40.1M 0 0 505k 0 0:07:17 0:01:21 0:05:56 362k 19 215M 19 41.2M 0 0 511k 0 0:07:11 0:01:22 0:05:49 562k 19 215M 19 42.3M 0 0 519k 0 0:07:04 0:01:23 0:05:41 766k 19 215M 19 42.7M 0 0 518k 0 0:07:05 0:01:24 0:05:41 795k 19 215M 19 42.8M 0 0 513k 0 0:07:10 0:01:25 0:05:45 710k 19 215M 19 43.0M 0 0 509k 0 0:07:13 0:01:26 0:05:47 582k 20 215M 20 43.8M 0 0 514k 0 0:07:09 0:01:27 0:05:42 551k 20 215M 20 44.1M 0 0 511k 0 0:07:11 0:01:28 0:05:43 369k 20 215M 20 44.2M 0 0 506k 0 0:07:15 0:01:29 0:05:46 311k 20 215M 20 44.9M 0 0 508k 0 0:07:14 0:01:30 0:05:44 431k 21 215M 21 45.7M 0 0 511k 0 0:07:11 0:01:31 0:05:40 545k 21 215M 21 45.9M 0 0 508k 0 0:07:13 0:01:32 0:05:41 415k 21 215M 21 46.4M 0 0 508k 0 0:07:13 0:01:33 0:05:40 472k 22 215M 22 47.6M 0 0 517k 0 0:07:06 0:01:34 0:05:32 705k 22 215M 22 48.8M 0 0 523k 0 0:07:02 0:01:35 0:05:27 774k 22 215M 22 48.8M 0 0 517k 0 0:07:06 0:01:36 0:05:30 619k 22 215M 22 48.8M 0 0 513k 0 0:07:09 0:01:37 0:05:32 603k 22 215M 22 48.8M 0 0 507k 0 0:07:14 0:01:38 0:05:36 490k 22 215M 22 48.8M 0 0 502k 0 0:07:19 0:01:39 0:05:40 239k 22 215M 22 49.0M 0 0 499k 0 0:07:21 0:01:40 0:05:41 31590 22 215M 22 49.0M 0 0 495k 0 0:07:25 0:01:41 0:05:44 43597 22 215M 22 49.1M 0 0 490k 0 0:07:29 0:01:42 0:05:47 55460 22 215M 22 49.3M 0 0 488k 0 0:07:32 0:01:43 0:05:49 93066 23 215M 23 49.6M 0 0 486k 0 0:07:33 0:01:44 0:05:49 152k 23 215M 23 50.1M 0 0 487k 0 0:07:32 0:01:45 0:05:47 241k 23 215M 23 51.0M 0 0 491k 0 0:07:29 0:01:46 0:05:43 414k 23 215M 23 51.4M 0 0 490k 0 0:07:29 0:01:47 0:05:42 484k 23 215M 23 51.5M 0 0 486k 0 0:07:33 0:01:48 0:05:45 455k 24 215M 24 52.0M 0 0 486k 0 0:07:33 0:01:49 0:05:44 488k 24 215M 24 52.8M 0 0 490k 0 0:07:30 0:01:50 0:05:40 553k 24 215M 24 53.0M 0 0 487k 0 0:07:33 0:01:51 0:05:42 393k 24 215M 24 53.0M 0 0 483k 0 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spark-2.3.3-bin-hadoop2.7/bin/docker-image-tool.sh spark-2.3.3-bin-hadoop2.7/bin/find-spark-home spark-2.3.3-bin-hadoop2.7/bin/find-spark-home.cmd spark-2.3.3-bin-hadoop2.7/bin/load-spark-env.cmd spark-2.3.3-bin-hadoop2.7/bin/load-spark-env.sh spark-2.3.3-bin-hadoop2.7/bin/pyspark spark-2.3.3-bin-hadoop2.7/bin/pyspark.cmd spark-2.3.3-bin-hadoop2.7/bin/pyspark2.cmd spark-2.3.3-bin-hadoop2.7/bin/run-example spark-2.3.3-bin-hadoop2.7/bin/run-example.cmd spark-2.3.3-bin-hadoop2.7/bin/spark-class spark-2.3.3-bin-hadoop2.7/bin/spark-class.cmd spark-2.3.3-bin-hadoop2.7/bin/spark-class2.cmd spark-2.3.3-bin-hadoop2.7/bin/spark-shell spark-2.3.3-bin-hadoop2.7/bin/spark-shell.cmd spark-2.3.3-bin-hadoop2.7/bin/spark-shell2.cmd spark-2.3.3-bin-hadoop2.7/bin/spark-sql spark-2.3.3-bin-hadoop2.7/bin/spark-sql.cmd spark-2.3.3-bin-hadoop2.7/bin/spark-sql2.cmd spark-2.3.3-bin-hadoop2.7/bin/spark-submit spark-2.3.3-bin-hadoop2.7/bin/spark-submit.cmd spark-2.3.3-bin-hadoop2.7/bin/spark-submit2.cmd spark-2.3.3-bin-hadoop2.7/bin/sparkR spark-2.3.3-bin-hadoop2.7/bin/sparkR.cmd spark-2.3.3-bin-hadoop2.7/bin/sparkR2.cmd spark-2.3.3-bin-hadoop2.7/conf/ spark-2.3.3-bin-hadoop2.7/conf/docker.properties.template spark-2.3.3-bin-hadoop2.7/conf/fairscheduler.xml.template spark-2.3.3-bin-hadoop2.7/conf/log4j.properties.template spark-2.3.3-bin-hadoop2.7/conf/metrics.properties.template spark-2.3.3-bin-hadoop2.7/conf/slaves.template spark-2.3.3-bin-hadoop2.7/conf/spark-defaults.conf.template spark-2.3.3-bin-hadoop2.7/conf/spark-env.sh.template spark-2.3.3-bin-hadoop2.7/data/ spark-2.3.3-bin-hadoop2.7/data/graphx/ spark-2.3.3-bin-hadoop2.7/data/graphx/followers.txt spark-2.3.3-bin-hadoop2.7/data/graphx/users.txt spark-2.3.3-bin-hadoop2.7/data/mllib/ spark-2.3.3-bin-hadoop2.7/data/mllib/als/ spark-2.3.3-bin-hadoop2.7/data/mllib/als/sample_movielens_ratings.txt spark-2.3.3-bin-hadoop2.7/data/mllib/als/test.data spark-2.3.3-bin-hadoop2.7/data/mllib/gmm_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/images/ spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/ spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/29.5.a_b_EGDP022204.jpg spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/54893.jpg spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/DP153539.jpg spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/DP802813.jpg spark-2.3.3-bin-hadoop2.7/data/mllib/images/kittens/not-image.txt spark-2.3.3-bin-hadoop2.7/data/mllib/images/license.txt spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/ spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/BGRA.png spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/BGRA_alpha_60.png spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/chr30.4.184.jpg spark-2.3.3-bin-hadoop2.7/data/mllib/images/multi-channel/grayscale.jpg spark-2.3.3-bin-hadoop2.7/data/mllib/iris_libsvm.txt spark-2.3.3-bin-hadoop2.7/data/mllib/kmeans_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/pagerank_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/pic_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/ridge-data/ spark-2.3.3-bin-hadoop2.7/data/mllib/ridge-data/lpsa.data spark-2.3.3-bin-hadoop2.7/data/mllib/sample_binary_classification_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_fpgrowth.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_isotonic_regression_libsvm_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_kmeans_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_lda_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_lda_libsvm_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_libsvm_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_linear_regression_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_movielens_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_multiclass_classification_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/sample_svm_data.txt spark-2.3.3-bin-hadoop2.7/data/mllib/streaming_kmeans_data_test.txt spark-2.3.3-bin-hadoop2.7/data/streaming/ spark-2.3.3-bin-hadoop2.7/data/streaming/AFINN-111.txt spark-2.3.3-bin-hadoop2.7/examples/ spark-2.3.3-bin-hadoop2.7/examples/jars/ spark-2.3.3-bin-hadoop2.7/examples/jars/scopt_2.11-3.7.0.jar spark-2.3.3-bin-hadoop2.7/examples/jars/spark-examples_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/examples/src/ spark-2.3.3-bin-hadoop2.7/examples/src/main/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaHdfsLR.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaLogQuery.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaPageRank.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaSparkPi.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaStatusTrackerDemo.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaTC.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/JavaWordCount.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaAFTSurvivalRegressionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaALSExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBinarizerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBisectingKMeansExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBucketedRandomProjectionLSHExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaBucketizerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaChiSqSelectorExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaChiSquareTestExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaCorrelationExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaCountVectorizerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDCTExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDecisionTreeClassificationExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDecisionTreeRegressionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaDocument.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaElementwiseProductExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaEstimatorTransformerParamExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaFeatureHasherExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaFPGrowthExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGaussianMixtureExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGeneralizedLinearRegressionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeClassifierExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaGradientBoostedTreeRegressorExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaImputerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaIndexToStringExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaInteractionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaIsotonicRegressionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaKMeansExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLabeledDocument.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLDAExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLinearRegressionWithElasticNetExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLinearSVCExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionSummaryExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaLogisticRegressionWithElasticNetExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMaxAbsScalerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMinHashLSHExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMinMaxScalerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaModelSelectionViaCrossValidationExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaModelSelectionViaTrainValidationSplitExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMulticlassLogisticRegressionWithElasticNetExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaMultilayerPerceptronClassifierExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaNaiveBayesExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaNGramExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaNormalizerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaOneHotEncoderEstimatorExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaOneVsRestExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPCAExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPipelineExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaPolynomialExpansionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaQuantileDiscretizerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaRandomForestClassifierExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaRandomForestRegressorExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaRFormulaExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaSQLTransformerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaStandardScalerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaStopWordsRemoverExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaStringIndexerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaTfIdfExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaTokenizerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorAssemblerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorIndexerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorSizeHintExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaVectorSlicerExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/ml/JavaWord2VecExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaALS.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaAssociationRulesExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaBinaryClassificationMetricsExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaBisectingKMeansExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaChiSqSelectorExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaCorrelationsExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaDecisionTreeClassificationExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaDecisionTreeRegressionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaElementwiseProductExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaGaussianMixtureExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaGradientBoostingClassificationExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaGradientBoostingRegressionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaHypothesisTestingExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaHypothesisTestingKolmogorovSmirnovTestExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaIsotonicRegressionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaKernelDensityEstimationExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaKMeansExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLatentDirichletAllocationExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLBFGSExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLinearRegressionWithSGDExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaLogisticRegressionWithLBFGSExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaMulticlassClassificationMetricsExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaMultiLabelClassificationMetricsExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaNaiveBayesExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaPCAExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaPowerIterationClusteringExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaPrefixSpanExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRandomForestClassificationExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRandomForestRegressionExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRankingMetricsExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRecommendationExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaRegressionMetricsExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaSimpleFPGrowth.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaStratifiedSamplingExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaStreamingTestExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaSummaryStatisticsExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaSVDExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/mllib/JavaSVMWithSGDExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/hive/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/hive/JavaSparkHiveExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaSparkSQLExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaSQLDataSourceExample.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaUserDefinedTypedAggregation.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/JavaUserDefinedUntypedAggregation.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredKafkaWordCount.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredNetworkWordCount.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredNetworkWordCountWindowed.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/sql/streaming/JavaStructuredSessionization.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/ spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaCustomReceiver.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaDirectKafkaWordCount.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaNetworkWordCount.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaQueueStream.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaRecord.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaRecoverableNetworkWordCount.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaSqlNetworkWordCount.java spark-2.3.3-bin-hadoop2.7/examples/src/main/java/org/apache/spark/examples/streaming/JavaStatefulNetworkWordCount.java spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ spark-2.3.3-bin-hadoop2.7/examples/src/main/python/als.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/avro_inputformat.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/kmeans.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/logistic_regression.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/ spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/aft_survival_regression.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/als_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/binarizer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/bisecting_k_means_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/bucketed_random_projection_lsh_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/bucketizer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/chi_square_test_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/chisq_selector_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/correlation_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/count_vectorizer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/cross_validator.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/dataframe_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/dct_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/decision_tree_classification_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/decision_tree_regression_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/elementwise_product_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/estimator_transformer_param_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/feature_hasher_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/fpgrowth_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/gaussian_mixture_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/generalized_linear_regression_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/gradient_boosted_tree_classifier_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/gradient_boosted_tree_regressor_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/imputer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/index_to_string_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/isotonic_regression_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/kmeans_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/lda_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/linear_regression_with_elastic_net.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/linearsvc.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/logistic_regression_summary_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/logistic_regression_with_elastic_net.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/max_abs_scaler_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/min_hash_lsh_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/min_max_scaler_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/multiclass_logistic_regression_with_elastic_net.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/multilayer_perceptron_classification.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/n_gram_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/naive_bayes_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/normalizer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/one_vs_rest_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/onehot_encoder_estimator_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/pca_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/pipeline_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/polynomial_expansion_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/quantile_discretizer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/random_forest_classifier_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/random_forest_regressor_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/rformula_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/sql_transformer.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/standard_scaler_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/stopwords_remover_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/string_indexer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/tf_idf_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/tokenizer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/train_validation_split.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/vector_assembler_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/vector_indexer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/vector_size_hint_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/vector_slicer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/ml/word2vec_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/ spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/binary_classification_metrics_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/bisecting_k_means_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/correlations.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/correlations_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/decision_tree_classification_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/decision_tree_regression_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/elementwise_product_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/fpgrowth_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/gaussian_mixture_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/gaussian_mixture_model.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/gradient_boosting_classification_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/gradient_boosting_regression_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/hypothesis_testing_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/hypothesis_testing_kolmogorov_smirnov_test_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/isotonic_regression_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/k_means_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/kernel_density_estimation_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/kmeans.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/latent_dirichlet_allocation_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/linear_regression_with_sgd_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/logistic_regression.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/logistic_regression_with_lbfgs_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/multi_class_metrics_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/multi_label_metrics_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/naive_bayes_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/normalizer_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/pca_rowmatrix_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/power_iteration_clustering_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/random_forest_classification_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/random_forest_regression_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/random_rdd_generation.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/ranking_metrics_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/recommendation_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/regression_metrics_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/sampled_rdds.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/standard_scaler_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/stratified_sampling_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/streaming_k_means_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/streaming_linear_regression_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/summary_statistics_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/svd_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/svm_with_sgd_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/tf_idf_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/word2vec.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/mllib/word2vec_example.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/pagerank.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/parquet_inputformat.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/pi.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sort.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/ spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/arrow.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/basic.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/datasource.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/hive.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/streaming/ spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/streaming/structured_kafka_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/streaming/structured_network_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/sql/streaming/structured_network_wordcount_windowed.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/status_api_demo.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/ spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/direct_kafka_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/flume_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/hdfs_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/kafka_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/network_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/network_wordjoinsentiments.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/queue_stream.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/recoverable_network_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/sql_network_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/streaming/stateful_network_wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/transitive_closure.py spark-2.3.3-bin-hadoop2.7/examples/src/main/python/wordcount.py spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ spark-2.3.3-bin-hadoop2.7/examples/src/main/r/data-manipulation.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/dataframe.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/ spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/als.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/bisectingKmeans.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/decisionTree.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/fpm.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/gaussianMixture.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/gbt.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/glm.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/isoreg.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/kmeans.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/kstest.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/lda.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/logit.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/ml.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/mlp.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/naiveBayes.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/randomForest.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/survreg.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/ml/svmLinear.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/RSparkSQLExample.R spark-2.3.3-bin-hadoop2.7/examples/src/main/r/streaming/ spark-2.3.3-bin-hadoop2.7/examples/src/main/r/streaming/structured_network_wordcount.R spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/ spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/employees.json spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/full_user.avsc spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/kv1.txt spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/people.csv spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/people.json spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/people.txt spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/user.avsc spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/users.avro spark-2.3.3-bin-hadoop2.7/examples/src/main/resources/users.parquet spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/BroadcastTest.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/DFSReadWriteTest.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/DriverSubmissionTest.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ExceptionHandlingTest.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/AggregateMessagesExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/Analytics.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/ComprehensiveExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/ConnectedComponentsExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/LiveJournalPageRank.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/PageRankExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/SSSPExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/SynthBenchmark.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/graphx/TriangleCountingExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/GroupByTest.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/HdfsTest.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalALS.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalFileLR.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalKMeans.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalLR.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LocalPi.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/LogQuery.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/AFTSurvivalRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ALSExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BinarizerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BisectingKMeansExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BucketedRandomProjectionLSHExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/BucketizerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ChiSqSelectorExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ChiSquareTestExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/CorrelationExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/CountVectorizerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DataFrameExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DCTExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeClassificationExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DecisionTreeRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/DeveloperApiExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ElementwiseProductExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/EstimatorTransformerParamExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/FeatureHasherExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/FPGrowthExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GaussianMixtureExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GBTExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GeneralizedLinearRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GradientBoostedTreeClassifierExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/GradientBoostedTreeRegressorExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ImputerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/IndexToStringExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/InteractionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/IsotonicRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/KMeansExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LDAExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LinearRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LinearRegressionWithElasticNetExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LinearSVCExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LogisticRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LogisticRegressionSummaryExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/LogisticRegressionWithElasticNetExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MaxAbsScalerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MinHashLSHExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MinMaxScalerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ModelSelectionViaCrossValidationExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/ModelSelectionViaTrainValidationSplitExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MulticlassLogisticRegressionWithElasticNetExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/MultilayerPerceptronClassifierExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/NaiveBayesExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/NGramExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/NormalizerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/OneHotEncoderEstimatorExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/OneVsRestExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PCAExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PipelineExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/PolynomialExpansionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/QuantileDiscretizerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RandomForestClassifierExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RandomForestExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RandomForestRegressorExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/RFormulaExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/SQLTransformerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/StandardScalerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/StopWordsRemoverExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/StringIndexerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/TfIdfExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/TokenizerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/UnaryTransformerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorAssemblerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorIndexerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorSizeHintExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/VectorSlicerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/ml/Word2VecExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/AbstractParams.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/AssociationRulesExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/BinaryClassification.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/BinaryClassificationMetricsExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/BisectingKMeansExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/ChiSqSelectorExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/Correlations.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/CorrelationsExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/CosineSimilarity.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/DecisionTreeClassificationExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/DecisionTreeRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/DecisionTreeRunner.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/DenseKMeans.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/ElementwiseProductExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/FPGrowthExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GaussianMixtureExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostedTreesRunner.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostingClassificationExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/GradientBoostingRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/HypothesisTestingExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/HypothesisTestingKolmogorovSmirnovTestExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/IsotonicRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/KernelDensityEstimationExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/KMeansExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LatentDirichletAllocationExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LBFGSExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LDAExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LinearRegression.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LinearRegressionWithSGDExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/LogisticRegressionWithLBFGSExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MovieLensALS.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MulticlassMetricsExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MultiLabelMetricsExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/MultivariateSummarizer.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/NaiveBayesExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/NormalizerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnRowMatrixExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PCAOnSourceVectorExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PMMLModelExportExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PowerIterationClusteringExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/PrefixSpanExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestClassificationExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomForestRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RandomRDDGeneration.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RankingMetricsExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RecommendationExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/RegressionMetricsExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SampledRDDs.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SimpleFPGrowth.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SparseNaiveBayes.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StandardScalerExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StratifiedSamplingExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingKMeansExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLinearRegressionExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingLogisticRegression.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/StreamingTestExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SummaryStatisticsExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SVDExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/SVMWithSGDExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnyPCA.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TallSkinnySVD.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/TFIDFExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/mllib/Word2VecExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/MultiBroadcastTest.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/pythonconverters/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/pythonconverters/AvroConverters.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SimpleSkewedGroupByTest.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SkewedGroupByTest.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkALS.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkHdfsLR.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkKMeans.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkLR.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkPageRank.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkPi.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/SparkTC.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/hive/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/hive/SparkHiveExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/RDDRelation.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/SparkSQLExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/SQLDataSourceExample.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredKafkaWordCount.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCount.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredNetworkWordCountWindowed.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/streaming/StructuredSessionization.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedTypedAggregation.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/sql/UserDefinedUntypedAggregation.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/ spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewGenerator.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/clickstream/PageViewStream.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/CustomReceiver.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/DirectKafkaWordCount.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/HdfsWordCount.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/NetworkWordCount.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/QueueStream.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/RawNetworkGrep.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/RecoverableNetworkWordCount.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/SqlNetworkWordCount.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/StatefulNetworkWordCount.scala spark-2.3.3-bin-hadoop2.7/examples/src/main/scala/org/apache/spark/examples/streaming/StreamingExamples.scala spark-2.3.3-bin-hadoop2.7/jars/ spark-2.3.3-bin-hadoop2.7/jars/activation-1.1.1.jar spark-2.3.3-bin-hadoop2.7/jars/aircompressor-0.8.jar spark-2.3.3-bin-hadoop2.7/jars/antlr-2.7.7.jar spark-2.3.3-bin-hadoop2.7/jars/antlr-runtime-3.4.jar spark-2.3.3-bin-hadoop2.7/jars/antlr4-runtime-4.7.jar spark-2.3.3-bin-hadoop2.7/jars/aopalliance-1.0.jar spark-2.3.3-bin-hadoop2.7/jars/aopalliance-repackaged-2.4.0-b34.jar spark-2.3.3-bin-hadoop2.7/jars/apache-log4j-extras-1.2.17.jar spark-2.3.3-bin-hadoop2.7/jars/apacheds-i18n-2.0.0-M15.jar spark-2.3.3-bin-hadoop2.7/jars/apacheds-kerberos-codec-2.0.0-M15.jar spark-2.3.3-bin-hadoop2.7/jars/api-asn1-api-1.0.0-M20.jar spark-2.3.3-bin-hadoop2.7/jars/api-util-1.0.0-M20.jar spark-2.3.3-bin-hadoop2.7/jars/arpack_combined_all-0.1.jar spark-2.3.3-bin-hadoop2.7/jars/arrow-format-0.8.0.jar spark-2.3.3-bin-hadoop2.7/jars/arrow-memory-0.8.0.jar spark-2.3.3-bin-hadoop2.7/jars/arrow-vector-0.8.0.jar spark-2.3.3-bin-hadoop2.7/jars/automaton-1.11-8.jar spark-2.3.3-bin-hadoop2.7/jars/avro-1.7.7.jar spark-2.3.3-bin-hadoop2.7/jars/avro-ipc-1.7.7.jar spark-2.3.3-bin-hadoop2.7/jars/avro-mapred-1.7.7-hadoop2.jar spark-2.3.3-bin-hadoop2.7/jars/base64-2.3.8.jar spark-2.3.3-bin-hadoop2.7/jars/bcprov-jdk15on-1.58.jar spark-2.3.3-bin-hadoop2.7/jars/bonecp-0.8.0.RELEASE.jar spark-2.3.3-bin-hadoop2.7/jars/breeze-macros_2.11-0.13.2.jar spark-2.3.3-bin-hadoop2.7/jars/breeze_2.11-0.13.2.jar spark-2.3.3-bin-hadoop2.7/jars/calcite-avatica-1.2.0-incubating.jar spark-2.3.3-bin-hadoop2.7/jars/calcite-core-1.2.0-incubating.jar spark-2.3.3-bin-hadoop2.7/jars/calcite-linq4j-1.2.0-incubating.jar spark-2.3.3-bin-hadoop2.7/jars/chill-java-0.8.4.jar spark-2.3.3-bin-hadoop2.7/jars/chill_2.11-0.8.4.jar spark-2.3.3-bin-hadoop2.7/jars/commons-beanutils-1.7.0.jar spark-2.3.3-bin-hadoop2.7/jars/commons-beanutils-core-1.8.0.jar spark-2.3.3-bin-hadoop2.7/jars/commons-cli-1.2.jar spark-2.3.3-bin-hadoop2.7/jars/commons-codec-1.10.jar spark-2.3.3-bin-hadoop2.7/jars/commons-collections-3.2.2.jar spark-2.3.3-bin-hadoop2.7/jars/commons-compiler-3.0.8.jar spark-2.3.3-bin-hadoop2.7/jars/commons-compress-1.4.1.jar spark-2.3.3-bin-hadoop2.7/jars/commons-configuration-1.6.jar spark-2.3.3-bin-hadoop2.7/jars/commons-crypto-1.0.0.jar spark-2.3.3-bin-hadoop2.7/jars/commons-dbcp-1.4.jar spark-2.3.3-bin-hadoop2.7/jars/commons-digester-1.8.jar spark-2.3.3-bin-hadoop2.7/jars/commons-httpclient-3.1.jar spark-2.3.3-bin-hadoop2.7/jars/commons-io-2.4.jar spark-2.3.3-bin-hadoop2.7/jars/commons-lang-2.6.jar spark-2.3.3-bin-hadoop2.7/jars/commons-lang3-3.5.jar spark-2.3.3-bin-hadoop2.7/jars/commons-logging-1.1.3.jar spark-2.3.3-bin-hadoop2.7/jars/commons-math3-3.4.1.jar spark-2.3.3-bin-hadoop2.7/jars/commons-net-2.2.jar spark-2.3.3-bin-hadoop2.7/jars/commons-pool-1.5.4.jar spark-2.3.3-bin-hadoop2.7/jars/compress-lzf-1.0.3.jar spark-2.3.3-bin-hadoop2.7/jars/core-1.1.2.jar spark-2.3.3-bin-hadoop2.7/jars/curator-client-2.7.1.jar spark-2.3.3-bin-hadoop2.7/jars/curator-framework-2.7.1.jar spark-2.3.3-bin-hadoop2.7/jars/curator-recipes-2.7.1.jar spark-2.3.3-bin-hadoop2.7/jars/datanucleus-api-jdo-3.2.6.jar spark-2.3.3-bin-hadoop2.7/jars/datanucleus-core-3.2.10.jar spark-2.3.3-bin-hadoop2.7/jars/datanucleus-rdbms-3.2.9.jar spark-2.3.3-bin-hadoop2.7/jars/derby-10.12.1.1.jar spark-2.3.3-bin-hadoop2.7/jars/eigenbase-properties-1.1.5.jar spark-2.3.3-bin-hadoop2.7/jars/flatbuffers-1.2.0-3f79e055.jar spark-2.3.3-bin-hadoop2.7/jars/generex-1.0.1.jar spark-2.3.3-bin-hadoop2.7/jars/gson-2.2.4.jar spark-2.3.3-bin-hadoop2.7/jars/guava-14.0.1.jar spark-2.3.3-bin-hadoop2.7/jars/guice-3.0.jar spark-2.3.3-bin-hadoop2.7/jars/guice-servlet-3.0.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-annotations-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-auth-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-client-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-common-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-hdfs-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-app-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-common-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-core-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-jobclient-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-mapreduce-client-shuffle-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-api-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-client-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-common-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-server-common-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hadoop-yarn-server-web-proxy-2.7.3.jar spark-2.3.3-bin-hadoop2.7/jars/hive-beeline-1.2.1.spark2.jar spark-2.3.3-bin-hadoop2.7/jars/hive-cli-1.2.1.spark2.jar spark-2.3.3-bin-hadoop2.7/jars/hive-exec-1.2.1.spark2.jar spark-2.3.3-bin-hadoop2.7/jars/hive-jdbc-1.2.1.spark2.jar spark-2.3.3-bin-hadoop2.7/jars/hive-metastore-1.2.1.spark2.jar spark-2.3.3-bin-hadoop2.7/jars/hk2-api-2.4.0-b34.jar spark-2.3.3-bin-hadoop2.7/jars/hk2-locator-2.4.0-b34.jar spark-2.3.3-bin-hadoop2.7/jars/hk2-utils-2.4.0-b34.jar spark-2.3.3-bin-hadoop2.7/jars/hppc-0.7.2.jar spark-2.3.3-bin-hadoop2.7/jars/htrace-core-3.1.0-incubating.jar spark-2.3.3-bin-hadoop2.7/jars/httpclient-4.5.4.jar spark-2.3.3-bin-hadoop2.7/jars/httpcore-4.4.8.jar spark-2.3.3-bin-hadoop2.7/jars/ivy-2.4.0.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-annotations-2.6.7.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-core-2.6.7.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-core-asl-1.9.13.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-databind-2.6.7.1.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-dataformat-yaml-2.6.7.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-jaxrs-1.9.13.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-mapper-asl-1.9.13.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-module-jaxb-annotations-2.6.7.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-module-paranamer-2.7.9.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-module-scala_2.11-2.6.7.1.jar spark-2.3.3-bin-hadoop2.7/jars/jackson-xc-1.9.13.jar spark-2.3.3-bin-hadoop2.7/jars/janino-3.0.8.jar spark-2.3.3-bin-hadoop2.7/jars/java-xmlbuilder-1.1.jar spark-2.3.3-bin-hadoop2.7/jars/JavaEWAH-0.3.2.jar spark-2.3.3-bin-hadoop2.7/jars/javassist-3.18.1-GA.jar spark-2.3.3-bin-hadoop2.7/jars/javax.annotation-api-1.2.jar spark-2.3.3-bin-hadoop2.7/jars/javax.inject-1.jar spark-2.3.3-bin-hadoop2.7/jars/javax.inject-2.4.0-b34.jar spark-2.3.3-bin-hadoop2.7/jars/javax.servlet-api-3.1.0.jar spark-2.3.3-bin-hadoop2.7/jars/javax.ws.rs-api-2.0.1.jar spark-2.3.3-bin-hadoop2.7/jars/javolution-5.5.1.jar spark-2.3.3-bin-hadoop2.7/jars/jaxb-api-2.2.2.jar spark-2.3.3-bin-hadoop2.7/jars/jcl-over-slf4j-1.7.16.jar spark-2.3.3-bin-hadoop2.7/jars/jdo-api-3.0.1.jar spark-2.3.3-bin-hadoop2.7/jars/jersey-client-2.22.2.jar spark-2.3.3-bin-hadoop2.7/jars/jersey-common-2.22.2.jar spark-2.3.3-bin-hadoop2.7/jars/jersey-container-servlet-2.22.2.jar spark-2.3.3-bin-hadoop2.7/jars/jersey-container-servlet-core-2.22.2.jar spark-2.3.3-bin-hadoop2.7/jars/jersey-guava-2.22.2.jar spark-2.3.3-bin-hadoop2.7/jars/jersey-media-jaxb-2.22.2.jar spark-2.3.3-bin-hadoop2.7/jars/jersey-server-2.22.2.jar spark-2.3.3-bin-hadoop2.7/jars/jets3t-0.9.4.jar spark-2.3.3-bin-hadoop2.7/jars/jetty-6.1.26.jar spark-2.3.3-bin-hadoop2.7/jars/jetty-util-6.1.26.jar spark-2.3.3-bin-hadoop2.7/jars/jline-2.12.1.jar spark-2.3.3-bin-hadoop2.7/jars/joda-time-2.9.3.jar spark-2.3.3-bin-hadoop2.7/jars/jodd-core-3.5.2.jar spark-2.3.3-bin-hadoop2.7/jars/jpam-1.1.jar spark-2.3.3-bin-hadoop2.7/jars/json4s-ast_2.11-3.2.11.jar spark-2.3.3-bin-hadoop2.7/jars/json4s-core_2.11-3.2.11.jar spark-2.3.3-bin-hadoop2.7/jars/json4s-jackson_2.11-3.2.11.jar spark-2.3.3-bin-hadoop2.7/jars/jsp-api-2.1.jar spark-2.3.3-bin-hadoop2.7/jars/jsr305-1.3.9.jar spark-2.3.3-bin-hadoop2.7/jars/jta-1.1.jar spark-2.3.3-bin-hadoop2.7/jars/jtransforms-2.4.0.jar spark-2.3.3-bin-hadoop2.7/jars/jul-to-slf4j-1.7.16.jar spark-2.3.3-bin-hadoop2.7/jars/kryo-shaded-3.0.3.jar spark-2.3.3-bin-hadoop2.7/jars/kubernetes-client-3.0.0.jar spark-2.3.3-bin-hadoop2.7/jars/kubernetes-model-2.0.0.jar spark-2.3.3-bin-hadoop2.7/jars/leveldbjni-all-1.8.jar spark-2.3.3-bin-hadoop2.7/jars/libfb303-0.9.3.jar spark-2.3.3-bin-hadoop2.7/jars/libthrift-0.9.3.jar spark-2.3.3-bin-hadoop2.7/jars/log4j-1.2.17.jar spark-2.3.3-bin-hadoop2.7/jars/logging-interceptor-3.8.1.jar spark-2.3.3-bin-hadoop2.7/jars/lz4-java-1.4.0.jar spark-2.3.3-bin-hadoop2.7/jars/machinist_2.11-0.6.1.jar spark-2.3.3-bin-hadoop2.7/jars/macro-compat_2.11-1.1.1.jar spark-2.3.3-bin-hadoop2.7/jars/mesos-1.4.0-shaded-protobuf.jar spark-2.3.3-bin-hadoop2.7/jars/metrics-core-3.1.5.jar spark-2.3.3-bin-hadoop2.7/jars/metrics-graphite-3.1.5.jar spark-2.3.3-bin-hadoop2.7/jars/metrics-json-3.1.5.jar spark-2.3.3-bin-hadoop2.7/jars/metrics-jvm-3.1.5.jar spark-2.3.3-bin-hadoop2.7/jars/minlog-1.3.0.jar spark-2.3.3-bin-hadoop2.7/jars/netty-3.9.9.Final.jar spark-2.3.3-bin-hadoop2.7/jars/netty-all-4.1.17.Final.jar spark-2.3.3-bin-hadoop2.7/jars/objenesis-2.1.jar spark-2.3.3-bin-hadoop2.7/jars/okhttp-3.8.1.jar spark-2.3.3-bin-hadoop2.7/jars/okio-1.13.0.jar spark-2.3.3-bin-hadoop2.7/jars/opencsv-2.3.jar spark-2.3.3-bin-hadoop2.7/jars/orc-core-1.4.4-nohive.jar spark-2.3.3-bin-hadoop2.7/jars/orc-mapreduce-1.4.4-nohive.jar spark-2.3.3-bin-hadoop2.7/jars/oro-2.0.8.jar spark-2.3.3-bin-hadoop2.7/jars/osgi-resource-locator-1.0.1.jar spark-2.3.3-bin-hadoop2.7/jars/paranamer-2.8.jar spark-2.3.3-bin-hadoop2.7/jars/parquet-column-1.8.3.jar spark-2.3.3-bin-hadoop2.7/jars/parquet-common-1.8.3.jar spark-2.3.3-bin-hadoop2.7/jars/parquet-encoding-1.8.3.jar spark-2.3.3-bin-hadoop2.7/jars/parquet-format-2.3.1.jar spark-2.3.3-bin-hadoop2.7/jars/parquet-hadoop-1.8.3.jar spark-2.3.3-bin-hadoop2.7/jars/parquet-hadoop-bundle-1.6.0.jar spark-2.3.3-bin-hadoop2.7/jars/parquet-jackson-1.8.3.jar spark-2.3.3-bin-hadoop2.7/jars/protobuf-java-2.5.0.jar spark-2.3.3-bin-hadoop2.7/jars/py4j-0.10.7.jar spark-2.3.3-bin-hadoop2.7/jars/pyrolite-4.13.jar spark-2.3.3-bin-hadoop2.7/jars/RoaringBitmap-0.5.11.jar spark-2.3.3-bin-hadoop2.7/jars/scala-compiler-2.11.8.jar spark-2.3.3-bin-hadoop2.7/jars/scala-library-2.11.8.jar spark-2.3.3-bin-hadoop2.7/jars/scala-parser-combinators_2.11-1.0.4.jar spark-2.3.3-bin-hadoop2.7/jars/scala-reflect-2.11.8.jar spark-2.3.3-bin-hadoop2.7/jars/scala-xml_2.11-1.0.5.jar spark-2.3.3-bin-hadoop2.7/jars/scalap-2.11.8.jar spark-2.3.3-bin-hadoop2.7/jars/shapeless_2.11-2.3.2.jar spark-2.3.3-bin-hadoop2.7/jars/slf4j-api-1.7.16.jar spark-2.3.3-bin-hadoop2.7/jars/slf4j-log4j12-1.7.16.jar spark-2.3.3-bin-hadoop2.7/jars/snakeyaml-1.15.jar spark-2.3.3-bin-hadoop2.7/jars/snappy-0.2.jar spark-2.3.3-bin-hadoop2.7/jars/snappy-java-1.1.2.6.jar spark-2.3.3-bin-hadoop2.7/jars/spark-catalyst_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-core_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-graphx_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-hive-thriftserver_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-hive_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-kubernetes_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-kvstore_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-launcher_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-mesos_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-mllib-local_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-mllib_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-network-common_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-network-shuffle_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-repl_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-sketch_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-sql_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-streaming_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-tags_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-unsafe_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spark-yarn_2.11-2.3.3.jar spark-2.3.3-bin-hadoop2.7/jars/spire-macros_2.11-0.13.0.jar spark-2.3.3-bin-hadoop2.7/jars/spire_2.11-0.13.0.jar spark-2.3.3-bin-hadoop2.7/jars/ST4-4.0.4.jar spark-2.3.3-bin-hadoop2.7/jars/stax-api-1.0-2.jar spark-2.3.3-bin-hadoop2.7/jars/stax-api-1.0.1.jar spark-2.3.3-bin-hadoop2.7/jars/stream-2.7.0.jar spark-2.3.3-bin-hadoop2.7/jars/stringtemplate-3.2.1.jar spark-2.3.3-bin-hadoop2.7/jars/super-csv-2.2.0.jar spark-2.3.3-bin-hadoop2.7/jars/univocity-parsers-2.5.9.jar spark-2.3.3-bin-hadoop2.7/jars/validation-api-1.1.0.Final.jar spark-2.3.3-bin-hadoop2.7/jars/xbean-asm5-shaded-4.4.jar spark-2.3.3-bin-hadoop2.7/jars/xercesImpl-2.9.1.jar spark-2.3.3-bin-hadoop2.7/jars/xmlenc-0.52.jar spark-2.3.3-bin-hadoop2.7/jars/xz-1.0.jar spark-2.3.3-bin-hadoop2.7/jars/zjsonpatch-0.3.0.jar spark-2.3.3-bin-hadoop2.7/jars/zookeeper-3.4.6.jar spark-2.3.3-bin-hadoop2.7/jars/zstd-jni-1.3.2-2.jar spark-2.3.3-bin-hadoop2.7/kubernetes/ spark-2.3.3-bin-hadoop2.7/kubernetes/dockerfiles/ spark-2.3.3-bin-hadoop2.7/kubernetes/dockerfiles/spark/ spark-2.3.3-bin-hadoop2.7/kubernetes/dockerfiles/spark/Dockerfile spark-2.3.3-bin-hadoop2.7/kubernetes/dockerfiles/spark/entrypoint.sh spark-2.3.3-bin-hadoop2.7/LICENSE spark-2.3.3-bin-hadoop2.7/licenses/ spark-2.3.3-bin-hadoop2.7/licenses/LICENSE-AnchorJS.txt 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spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/ spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/ spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/.part-r-00007.gz.parquet.crc spark-2.3.3-bin-hadoop2.7/python/test_support/sql/parquet_partitioned/year=2015/month=9/day=1/part-r-00007.gz.parquet spark-2.3.3-bin-hadoop2.7/python/test_support/sql/people.json spark-2.3.3-bin-hadoop2.7/python/test_support/sql/people1.json spark-2.3.3-bin-hadoop2.7/python/test_support/sql/people_array.json spark-2.3.3-bin-hadoop2.7/python/test_support/sql/streaming/ spark-2.3.3-bin-hadoop2.7/python/test_support/sql/streaming/text-test.txt spark-2.3.3-bin-hadoop2.7/python/test_support/sql/text-test.txt spark-2.3.3-bin-hadoop2.7/python/test_support/userlib-0.1.zip spark-2.3.3-bin-hadoop2.7/python/test_support/userlibrary.py spark-2.3.3-bin-hadoop2.7/R/ spark-2.3.3-bin-hadoop2.7/R/lib/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/DESCRIPTION spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/index.html spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/sparkr-vignettes.html spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/sparkr-vignettes.R spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/doc/sparkr-vignettes.Rmd spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/aliases.rds spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/AnIndex spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/paths.rds spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdb spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/help/SparkR.rdx spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/html/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/html/00Index.html spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/html/R.css spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/INDEX spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/features.rds spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/hsearch.rds spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/links.rds spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/nsInfo.rds spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/package.rds spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/Rd.rds spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/Meta/vignette.rds spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/NAMESPACE spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/profile/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/profile/general.R spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/profile/shell.R spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/SparkR spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdb spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/R/SparkR.rdx spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/tests/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/tests/testthat/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/tests/testthat/test_basic.R spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/worker/ spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/worker/daemon.R spark-2.3.3-bin-hadoop2.7/R/lib/SparkR/worker/worker.R spark-2.3.3-bin-hadoop2.7/R/lib/sparkr.zip spark-2.3.3-bin-hadoop2.7/README.md spark-2.3.3-bin-hadoop2.7/RELEASE spark-2.3.3-bin-hadoop2.7/sbin/ spark-2.3.3-bin-hadoop2.7/sbin/slaves.sh spark-2.3.3-bin-hadoop2.7/sbin/spark-config.sh spark-2.3.3-bin-hadoop2.7/sbin/spark-daemon.sh spark-2.3.3-bin-hadoop2.7/sbin/spark-daemons.sh spark-2.3.3-bin-hadoop2.7/sbin/start-all.sh spark-2.3.3-bin-hadoop2.7/sbin/start-history-server.sh spark-2.3.3-bin-hadoop2.7/sbin/start-master.sh spark-2.3.3-bin-hadoop2.7/sbin/start-mesos-dispatcher.sh spark-2.3.3-bin-hadoop2.7/sbin/start-mesos-shuffle-service.sh spark-2.3.3-bin-hadoop2.7/sbin/start-shuffle-service.sh spark-2.3.3-bin-hadoop2.7/sbin/start-slave.sh spark-2.3.3-bin-hadoop2.7/sbin/start-slaves.sh spark-2.3.3-bin-hadoop2.7/sbin/start-thriftserver.sh spark-2.3.3-bin-hadoop2.7/sbin/stop-all.sh spark-2.3.3-bin-hadoop2.7/sbin/stop-history-server.sh spark-2.3.3-bin-hadoop2.7/sbin/stop-master.sh spark-2.3.3-bin-hadoop2.7/sbin/stop-mesos-dispatcher.sh spark-2.3.3-bin-hadoop2.7/sbin/stop-mesos-shuffle-service.sh spark-2.3.3-bin-hadoop2.7/sbin/stop-shuffle-service.sh spark-2.3.3-bin-hadoop2.7/sbin/stop-slave.sh spark-2.3.3-bin-hadoop2.7/sbin/stop-slaves.sh spark-2.3.3-bin-hadoop2.7/sbin/stop-thriftserver.sh spark-2.3.3-bin-hadoop2.7/yarn/ spark-2.3.3-bin-hadoop2.7/yarn/spark-2.3.3-yarn-shuffle.jar + export SPARK_HOME=/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7 + SPARK_HOME=/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7 ls -1 "${SPARK_HOME}/python/lib" | grep py4j ++ ls -1 /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python/lib ++ grep py4j + PY4J_ZIP=py4j-0.10.7-src.zip + export PYTHONPATH=/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python:/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip: + PYTHONPATH=/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python:/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python/lib/py4j-0.10.7-src.zip: + ASSEMBLY_DIR=/tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target ls -1 "$ASSEMBLY_DIR" | grep "^mango-assembly[0-9A-Za-z\_\.-]*\.jar$" | grep -v javadoc | grep -v sources || true ++ ls -1 /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target ++ grep '^mango-assembly[0-9A-Za-z\_\.-]*\.jar$' ++ grep -v sources ++ grep -v javadoc + ASSEMBLY_JAR=mango-assembly-0.0.3-SNAPSHOT.jar + export 'PYSPARK_SUBMIT_ARGS=--jars /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar --driver-class-path /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar pyspark-shell' + PYSPARK_SUBMIT_ARGS='--jars /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar --driver-class-path /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-assembly/target/mango-assembly-0.0.3-SNAPSHOT.jar pyspark-shell' + pythons=(2.7 3.6) + for python in '${pythons[*]}' uuidgen ++ uuidgen + uuid=5f6c0abc-d93e-417a-aa48-1bc33829d006 + conda create -y -q -n mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006 python=2.7 Package plan for installation in environment /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006: The following NEW packages will be INSTALLED: ca-certificates: 2019.1.23-0 certifi: 2019.3.9-py27_0 libedit: 3.1.20181209-hc058e9b_0 libffi: 3.2.1-hd88cf55_4 libgcc-ng: 8.2.0-hdf63c60_1 libstdcxx-ng: 8.2.0-hdf63c60_1 ncurses: 6.1-he6710b0_1 openssl: 1.1.1b-h7b6447c_1 pip: 19.1.1-py27_0 python: 2.7.16-h9bab390_0 readline: 7.0-h7b6447c_5 setuptools: 41.0.1-py27_0 sqlite: 3.28.0-h7b6447c_0 tk: 8.6.8-hbc83047_0 wheel: 0.33.2-py27_0 zlib: 1.2.11-h7b6447c_3 + source activate mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006 #!/bin/bash # Determine the directory containing this script if [[ -n $BASH_VERSION ]]; then _SCRIPT_LOCATION=${BASH_SOURCE[0]} _SHELL="bash" elif [[ -n $ZSH_VERSION ]]; then _SCRIPT_LOCATION=${funcstack[1]} _SHELL="zsh" else echo "Only bash and zsh are supported" return 1 fi ++ [[ -n 4.3.48(1)-release ]] ++ _SCRIPT_LOCATION=/home/anaconda/bin/activate ++ _SHELL=bash _CONDA_DIR=$(dirname "$_SCRIPT_LOCATION") dirname "$_SCRIPT_LOCATION" +++ dirname /home/anaconda/bin/activate ++ _CONDA_DIR=/home/anaconda/bin if [ $# -gt 1 ]; then (>&2 echo "Error: did not expect more than one argument.") (>&2 echo " (Got $@)") return 1 fi ++ '[' 1 -gt 1 ']' case "$(uname -s)" in CYGWIN*|MINGW*|MSYS*) EXT=".exe" export MSYS2_ENV_CONV_EXCL=CONDA_PATH # ignore any windows backup paths from bat-based activation if [ "${CONDA_PATH_BACKUP:0:1}" != "/" ]; then unset CONDA_PATH_BACKUP fi export _CONDA_PYTHON="$_CONDA_DIR/../python" ;; *) EXT="" export _CONDA_PYTHON="$_CONDA_DIR/python" ;; esac ++ case "$(uname -s)" in uname -s +++ uname -s ++ EXT= ++ export _CONDA_PYTHON=/home/anaconda/bin/python ++ _CONDA_PYTHON=/home/anaconda/bin/python # Ensure that this script is sourced, not executed # Also note that errors are ignored as `activate foo` doesn't generate a bad # value for $0 which would cause errors. if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "activate" ]]; then (>&2 echo "Error: activate must be sourced. Run 'source activate envname' instead of 'activate envname'. ") "$_CONDA_DIR/conda" ..activate $_SHELL$EXT -h exit 1 fi ++ [[ -n 4.3.48(1)-release ]] basename "$0" 2> /dev/null +++ basename /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test ++ [[ jenkins-test == \a\c\t\i\v\a\t\e ]] if [ "$#" -eq "0" ]; then args=('root') else args=$@ fi ++ '[' 1 -eq 0 ']' ++ args=mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006 "$_CONDA_DIR/conda" ..checkenv $_SHELL$EXT "$args" ++ /home/anaconda/bin/conda ..checkenv bash mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006 if (( $? != 0 )); then return 1 fi ++ (( 0 != 0 )) # Ensure we deactivate any scripts from the old env _CONDA_HOLD=true ++ _CONDA_HOLD=true source "$_CONDA_DIR/deactivate" ++ source /home/anaconda/bin/deactivate #!/bin/bash # Determine the directory containing this script if [[ -n $BASH_VERSION ]]; then _SCRIPT_LOCATION=${BASH_SOURCE[0]} _SHELL="bash" elif [[ -n $ZSH_VERSION ]]; then _SCRIPT_LOCATION=${funcstack[1]} _SHELL="zsh" else echo "Only bash and zsh are supported" return 1 fi +++ [[ -n 4.3.48(1)-release ]] +++ _SCRIPT_LOCATION=/home/anaconda/bin/deactivate +++ _SHELL=bash _CONDA_DIR=$(dirname "$_SCRIPT_LOCATION") dirname "$_SCRIPT_LOCATION" ++++ dirname /home/anaconda/bin/deactivate +++ _CONDA_DIR=/home/anaconda/bin case "$(uname -s)" in CYGWIN*|MINGW*|MSYS*) EXT=".exe" export MSYS2_ENV_CONV_EXCL=CONDA_PATH ;; *) EXT="" ;; esac +++ case "$(uname -s)" in uname -s ++++ uname -s +++ EXT= # shift over all args. We don't accept any, so it's OK that we ignore them all here. while [[ $# > 0 ]] do key="$1" case $key in -h|--help) "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then exit 0 else return 0 fi ;; esac shift # past argument or value done +++ [[ 1 > 0 ]] +++ key=mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006 +++ case $key in +++ shift +++ [[ 0 > 0 ]] # Ensure that this script is sourced, not executed # Note that if the script was executed, we're running inside bash! # Also note that errors are ignored as `activate foo` doesn't generate a bad # value for $0 which would cause errors. if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then (>&2 echo "Error: deactivate must be sourced. Run 'source deactivate' instead of 'deactivate'. ") "$_CONDA_DIR/conda" ..deactivate $_SHELL$EXT -h exit 1 fi +++ [[ -n 4.3.48(1)-release ]] basename "$0" 2> /dev/null ++++ basename /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test +++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]] if [[ -z "$CONDA_PATH_BACKUP" ]]; then if [[ -n $BASH_VERSION ]] && [[ "$(basename "$0" 2> /dev/null)" == "deactivate" ]]; then exit 0 else return 0 fi fi +++ [[ -z '' ]] +++ [[ -n 4.3.48(1)-release ]] basename "$0" 2> /dev/null ++++ basename /home/jenkins/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu/scripts/jenkins-test +++ [[ jenkins-test == \d\e\a\c\t\i\v\a\t\e ]] +++ return 0 unset _CONDA_HOLD ++ unset _CONDA_HOLD _NEW_PART=$("$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$args") "$_CONDA_DIR/conda" ..activate $_SHELL$EXT "$args" +++ /home/anaconda/bin/conda ..activate bash mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006 ++ _NEW_PART=/home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/bin if (( $? == 0 )); then export CONDA_PATH_BACKUP="$PATH" # export this to restore it upon deactivation export CONDA_PS1_BACKUP="$PS1" # look if the deactivate script left a placeholder for us if [[ $PATH == *"CONDA_PATH_PLACEHOLDER"* ]]; then # If it did, replace it with our _NEW_PART export PATH="$($_CONDA_PYTHON -c "import re; print(re.sub(r'CONDA_PATH_PLACEHOLDER', r'$_NEW_PART', '$PATH', 1))")" else export PATH="$_NEW_PART:$PATH" fi # CONDA_DEFAULT_ENV is the shortest representation of how conda recognizes your env. # It can be an env name, or a full path. # Last date of change: 2016-06-21 # If the string contains / it's a path if [[ "$@" == */* ]]; then export CONDA_DEFAULT_ENV=$(get_abs_filename "$args") else export CONDA_DEFAULT_ENV="$args" fi # CONDA_PREFIX is always the full path to the activated environment. It is not set # when no environment is active. # Legacy support: CONDA_DEFAULT_ENV is either env name or full path if given as path. # CONDA_PREFIX is always the full path, for consistency. # Last date of change: 2016-06-21 firstpath=${_NEW_PART%%:*} export CONDA_PREFIX="$(echo ${firstpath} | sed "s|/bin$||")" &>/dev/null # if CONDA_DEFAULT_ENV not in PS1, prepend it with parentheses if [ $("$_CONDA_DIR/conda" ..changeps1) = "1" ]; then if ! $(grep -q CONDA_DEFAULT_ENV <<<$PS1); then if ! $(grep -q "POWERLINE" <<<$PS1); then export PS1="(${CONDA_DEFAULT_ENV}) $PS1" fi fi fi # Load any of the scripts found $PREFIX/etc/conda/activate.d AFTER activation _CONDA_D="${CONDA_PREFIX}/etc/conda/activate.d" if [[ -d "$_CONDA_D" ]]; then eval $(find "$_CONDA_D" -iname "*.sh" -exec echo source \'{}\'';' \;) fi unset _CONDA_PYTHON else unset _CONDA_PYTHON return $? fi ++ (( 0 == 0 )) ++ export CONDA_PATH_BACKUP=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ++ CONDA_PATH_BACKUP=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ++ export CONDA_PS1_BACKUP= ++ CONDA_PS1_BACKUP= ++ [[ /usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games == *\C\O\N\D\A\_\P\A\T\H\_\P\L\A\C\E\H\O\L\D\E\R* ]] ++ export PATH=/home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ++ PATH=/home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/bin:/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/::/home/anaconda/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games ++ [[ '' == */* ]] ++ export CONDA_DEFAULT_ENV=mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006 ++ CONDA_DEFAULT_ENV=mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006 ++ firstpath=/home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/bin echo ${firstpath} | sed "s|/bin$||" +++ echo /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/bin +++ sed 's|/bin$||' ++ export CONDA_PREFIX=/home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006 "$_CONDA_DIR/conda" ..changeps1 +++ /home/anaconda/bin/conda ..changeps1 ++ '[' 1 = 1 ']' grep -q CONDA_DEFAULT_ENV <<<$PS1 +++ grep -q CONDA_DEFAULT_ENV grep -q "POWERLINE" <<<$PS1 +++ grep -q POWERLINE ++ export 'PS1=(mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006) ' ++ PS1='(mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006) ' ++ _CONDA_D=/home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/etc/conda/activate.d ++ [[ -d /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/etc/conda/activate.d ]] ++ unset _CONDA_PYTHON unset CONDA_PATH ++ unset CONDA_PATH if [[ -n $BASH_VERSION ]]; then hash -r elif [[ -n $ZSH_VERSION ]]; then rehash else echo "Only bash and zsh are supported" return 1 fi ++ [[ -n 4.3.48(1)-release ]] ++ hash -r + conda install -y nodejs Fetching package metadata ........... Solving package specifications: . Package plan for installation in environment /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006: The following NEW packages will be INSTALLED: nodejs: 10.13.0-he6710b0_0 + pushd mango-python /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu + make prepare pip install pytest==3.9.1 DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Collecting pytest==3.9.1 Using cached https://files.pythonhosted.org/packages/bf/14/a16e1ac03aeb9776d98374bb76495a6623d56dff0f7b815ed5a1e04d893e/pytest-3.9.1-py2.py3-none-any.whl Collecting atomicwrites>=1.0 (from pytest==3.9.1) Using cached https://files.pythonhosted.org/packages/52/90/6155aa926f43f2b2a22b01be7241be3bfd1ceaf7d0b3267213e8127d41f4/atomicwrites-1.3.0-py2.py3-none-any.whl Collecting more-itertools>=4.0.0 (from pytest==3.9.1) Using cached https://files.pythonhosted.org/packages/2f/9d/dcfe59e213093695f108508af1214cf9cd95cc5489e46877ec5cb56369e5/more_itertools-5.0.0-py2-none-any.whl Collecting pluggy>=0.7 (from pytest==3.9.1) Using cached https://files.pythonhosted.org/packages/cc/e4/2003a5e4e445424602c8f06a436eeed9e78bcae4947128f64741c66c7216/pluggy-0.11.0-py2.py3-none-any.whl Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from pytest==3.9.1) (41.0.1) Collecting attrs>=17.4.0 (from pytest==3.9.1) Using cached https://files.pythonhosted.org/packages/23/96/d828354fa2dbdf216eaa7b7de0db692f12c234f7ef888cc14980ef40d1d2/attrs-19.1.0-py2.py3-none-any.whl Collecting pathlib2>=2.2.0; python_version < "3.6" (from pytest==3.9.1) Using cached https://files.pythonhosted.org/packages/2a/46/c696dcf1c7aad917b39b875acdc5451975e3a9b4890dca8329983201c97a/pathlib2-2.3.3-py2.py3-none-any.whl Collecting py>=1.5.0 (from pytest==3.9.1) Using cached https://files.pythonhosted.org/packages/76/bc/394ad449851729244a97857ee14d7cba61ddb268dce3db538ba2f2ba1f0f/py-1.8.0-py2.py3-none-any.whl Requirement already satisfied: six>=1.10.0 in /home/jenkins/.local/lib/python2.7/site-packages (from pytest==3.9.1) (1.11.0) Collecting funcsigs; python_version < "3.0" (from pytest==3.9.1) Using cached https://files.pythonhosted.org/packages/69/cb/f5be453359271714c01b9bd06126eaf2e368f1fddfff30818754b5ac2328/funcsigs-1.0.2-py2.py3-none-any.whl Collecting scandir; python_version < "3.5" (from pathlib2>=2.2.0; python_version < "3.6"->pytest==3.9.1) Installing collected packages: atomicwrites, more-itertools, pluggy, attrs, scandir, pathlib2, py, funcsigs, pytest Successfully installed atomicwrites-1.3.0 attrs-19.1.0 funcsigs-1.0.2 more-itertools-5.0.0 pathlib2-2.3.3 pluggy-0.11.0 py-1.8.0 pytest-3.9.1 scandir-1.10.0 # ipython version required for python 2.7 pip install jupyter_contrib_nbextensions DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Collecting jupyter_contrib_nbextensions Using cached https://files.pythonhosted.org/packages/33/f0/6e2c00afda860f655fbf0f795f7310bdbf12122846344dfdc803fc7455d5/jupyter_contrib_nbextensions-0.5.1-py2.py3-none-any.whl Collecting jupyter-contrib-core>=0.3.3 (from jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/e6/8f/04a752a8b66a66e7092c035e5d87d2502ac7ec07f9fb6059059b6c0dc272/jupyter_contrib_core-0.3.3-py2.py3-none-any.whl Collecting traitlets>=4.1 (from jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/93/d6/abcb22de61d78e2fc3959c964628a5771e47e7cc60d53e9342e21ed6cc9a/traitlets-4.3.2-py2.py3-none-any.whl Collecting ipython-genutils (from jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl Collecting nbconvert>=4.2 (from jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/35/e7/f46c9d65f149271e47fca6ab084ef5c6e4cb1870f4c5cce6690feac55231/nbconvert-5.5.0-py2.py3-none-any.whl Collecting notebook>=4.0 (from jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/f6/36/89ebfffc9dd8c8dbd81c1ffb53e3d4233ee666414c143959477cb07cc5f5/notebook-5.7.8-py2.py3-none-any.whl Collecting jupyter-latex-envs>=1.3.8 (from jupyter_contrib_nbextensions) Collecting jupyter-core (from jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/1d/44/065d2d7bae7bebc06f1dd70d23c36da8c50c0f08b4236716743d706762a8/jupyter_core-4.4.0-py2.py3-none-any.whl Collecting lxml (from jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/89/51/a8a6cdb8a084d32dbc9bda94623dc35310ae2002be57de8702a1703c0026/lxml-4.3.3-cp27-cp27mu-manylinux1_x86_64.whl Collecting tornado (from jupyter_contrib_nbextensions) Collecting jupyter-nbextensions-configurator>=0.4.0 (from jupyter_contrib_nbextensions) Collecting jupyter-highlight-selected-word>=0.1.1 (from jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/50/d7/19ab7cfd60bf268d2abbacc52d4295a40f52d74dfc0d938e4761ee5e598b/jupyter_highlight_selected_word-0.2.0-py2.py3-none-any.whl Collecting pyyaml (from jupyter_contrib_nbextensions) Requirement already satisfied: setuptools in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jupyter-contrib-core>=0.3.3->jupyter_contrib_nbextensions) (41.0.1) Collecting enum34; python_version == "2.7" (from traitlets>=4.1->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/c5/db/e56e6b4bbac7c4a06de1c50de6fe1ef3810018ae11732a50f15f62c7d050/enum34-1.1.6-py2-none-any.whl Requirement already satisfied: six in /home/jenkins/.local/lib/python2.7/site-packages (from traitlets>=4.1->jupyter_contrib_nbextensions) (1.11.0) Collecting decorator (from traitlets>=4.1->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/5f/88/0075e461560a1e750a0dcbf77f1d9de775028c37a19a346a6c565a257399/decorator-4.4.0-py2.py3-none-any.whl Collecting entrypoints>=0.2.2 (from nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl Collecting nbformat>=4.4 (from nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/da/27/9a654d2b6cc1eaa517d1c5a4405166c7f6d72f04f6e7eea41855fe808a46/nbformat-4.4.0-py2.py3-none-any.whl Collecting jinja2>=2.4 (from nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl Collecting pygments (from nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/6e/00/c5cb5fc7c047da4af049005d0146b3a961b1a25d9cefbbe24bf0882a11ad/Pygments-2.4.0-py2.py3-none-any.whl Collecting bleach (from nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/ab/05/27e1466475e816d3001efb6e0a85a819be17411420494a1e602c36f8299d/bleach-3.1.0-py2.py3-none-any.whl Collecting pandocfilters>=1.4.1 (from nbconvert>=4.2->jupyter_contrib_nbextensions) Collecting testpath (from nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/be/a4/162f9ebb6489421fe46dcca2ae420369edfee4b563c668d93cb4605d12ba/testpath-0.4.2-py2.py3-none-any.whl Collecting defusedxml (from nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/06/74/9b387472866358ebc08732de3da6dc48e44b0aacd2ddaa5cb85ab7e986a2/defusedxml-0.6.0-py2.py3-none-any.whl Collecting mistune>=0.8.1 (from nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl Collecting jupyter-client>=5.2.0 (from notebook>=4.0->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/3b/c3/3043fe9ffd140d03c9d091a056794ccdc427c56ec19b8eea74f9ea0a498f/jupyter_client-5.2.4-py2.py3-none-any.whl Collecting terminado>=0.8.1 (from notebook>=4.0->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/a7/56/80ea7fa66565fa75ae21ce0c16bc90067530e5d15e48854afcc86585a391/terminado-0.8.2-py2.py3-none-any.whl Collecting Send2Trash (from notebook>=4.0->jupyter_contrib_nbextensions) Collecting pyzmq>=17 (from notebook>=4.0->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/91/f5/c9bef3768d6f8d71aae8f44f1ddbee90162dad909560fa6c13e4872e28c9/pyzmq-18.0.1-cp27-cp27mu-manylinux1_x86_64.whl Collecting prometheus-client (from notebook>=4.0->jupyter_contrib_nbextensions) Collecting ipykernel (from notebook>=4.0->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/00/47/764e4fa1b1b89598426b8d79b1c4fbe8042432621b0f8e1991aeb3c24806/ipykernel-4.10.0-py2-none-any.whl Collecting ipaddress; python_version == "2.7" (from notebook>=4.0->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/fc/d0/7fc3a811e011d4b388be48a0e381db8d990042df54aa4ef4599a31d39853/ipaddress-1.0.22-py2.py3-none-any.whl Collecting ipython (from jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/b0/88/d996ab8be22cea1eaa18baee3678a11265e18cf09974728d683c51102148/ipython-5.8.0-py2-none-any.whl Requirement already satisfied: futures in /home/jenkins/.local/lib/python2.7/site-packages (from tornado->jupyter_contrib_nbextensions) (3.2.0) Collecting singledispatch (from tornado->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/c5/10/369f50bcd4621b263927b0a1519987a04383d4a98fb10438042ad410cf88/singledispatch-3.4.0.3-py2.py3-none-any.whl Collecting backports-abc>=0.4 (from tornado->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/7d/56/6f3ac1b816d0cd8994e83d0c4e55bc64567532f7dc543378bd87f81cebc7/backports_abc-0.5-py2.py3-none-any.whl Collecting configparser>=3.5; python_version == "2.7" (from entrypoints>=0.2.2->nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/ba/05/6c96328e92e625fc31445d24d75a2c92ef9ba34fc5b037fe69693c362a0d/configparser-3.7.4-py2.py3-none-any.whl Collecting jsonschema!=2.5.0,>=2.4 (from nbformat>=4.4->nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/aa/69/df679dfbdd051568b53c38ec8152a3ab6bc533434fc7ed11ab034bf5e82f/jsonschema-3.0.1-py2.py3-none-any.whl Collecting MarkupSafe>=0.23 (from jinja2>=2.4->nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/fb/40/f3adb7cf24a8012813c5edb20329eb22d5d8e2a0ecf73d21d6b85865da11/MarkupSafe-1.1.1-cp27-cp27mu-manylinux1_x86_64.whl Collecting webencodings (from bleach->nbconvert>=4.2->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl Requirement already satisfied: python-dateutil>=2.1 in /home/jenkins/.local/lib/python2.7/site-packages (from jupyter-client>=5.2.0->notebook>=4.0->jupyter_contrib_nbextensions) (2.7.4) Collecting ptyprocess; os_name != "nt" (from terminado>=0.8.1->notebook>=4.0->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (2.3.3) Collecting backports.shutil-get-terminal-size; python_version == "2.7" (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/7d/cd/1750d6c35fe86d35f8562091737907f234b78fdffab42b29c72b1dd861f4/backports.shutil_get_terminal_size-1.0.0-py2.py3-none-any.whl Collecting simplegeneric>0.8 (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) Collecting pexpect; sys_platform != "win32" (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/0e/3e/377007e3f36ec42f1b84ec322ee12141a9e10d808312e5738f52f80a232c/pexpect-4.7.0-py2.py3-none-any.whl Collecting prompt-toolkit<2.0.0,>=1.0.4 (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/4e/4e/e5545e8bebf89790455b31112a0f886580c7b3624a05abec416efa5c3a08/prompt_toolkit-1.0.16-py2-none-any.whl Collecting pickleshare (from ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl Collecting functools32; python_version < "3" (from jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert>=4.2->jupyter_contrib_nbextensions) Collecting pyrsistent>=0.14.0 (from jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert>=4.2->jupyter_contrib_nbextensions) Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert>=4.2->jupyter_contrib_nbextensions) (19.1.0) Requirement already satisfied: scandir; python_version < "3.5" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) (1.10.0) Collecting wcwidth (from prompt-toolkit<2.0.0,>=1.0.4->ipython->jupyter-latex-envs>=1.3.8->jupyter_contrib_nbextensions) Using cached https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl Installing collected packages: enum34, ipython-genutils, decorator, traitlets, pyzmq, jupyter-core, singledispatch, backports-abc, tornado, jupyter-client, functools32, pyrsistent, jsonschema, nbformat, ptyprocess, terminado, Send2Trash, prometheus-client, MarkupSafe, jinja2, backports.shutil-get-terminal-size, simplegeneric, pygments, pexpect, wcwidth, prompt-toolkit, pickleshare, ipython, ipykernel, configparser, entrypoints, webencodings, bleach, pandocfilters, testpath, defusedxml, mistune, nbconvert, ipaddress, notebook, jupyter-contrib-core, jupyter-latex-envs, lxml, pyyaml, jupyter-nbextensions-configurator, jupyter-highlight-selected-word, jupyter-contrib-nbextensions Successfully installed MarkupSafe-1.1.1 Send2Trash-1.5.0 backports-abc-0.5 backports.shutil-get-terminal-size-1.0.0 bleach-3.1.0 configparser-3.7.4 decorator-4.4.0 defusedxml-0.6.0 entrypoints-0.3 enum34-1.1.6 functools32-3.2.3.post2 ipaddress-1.0.22 ipykernel-4.10.0 ipython-5.8.0 ipython-genutils-0.2.0 jinja2-2.10.1 jsonschema-3.0.1 jupyter-client-5.2.4 jupyter-contrib-core-0.3.3 jupyter-contrib-nbextensions-0.5.1 jupyter-core-4.4.0 jupyter-highlight-selected-word-0.2.0 jupyter-latex-envs-1.4.6 jupyter-nbextensions-configurator-0.4.1 lxml-4.3.3 mistune-0.8.4 nbconvert-5.5.0 nbformat-4.4.0 notebook-5.7.8 pandocfilters-1.4.2 pexpect-4.7.0 pickleshare-0.7.5 prometheus-client-0.6.0 prompt-toolkit-1.0.16 ptyprocess-0.6.0 pygments-2.4.0 pyrsistent-0.15.2 pyyaml-5.1 pyzmq-18.0.1 simplegeneric-0.8.1 singledispatch-3.4.0.3 terminado-0.8.2 testpath-0.4.2 tornado-5.1.1 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1 pip install -r requirements.txt DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Collecting cigar==0.1.3 (from -r requirements.txt (line 1)) Collecting matplotlib==2.0.2 (from -r requirements.txt (line 2)) Using cached https://files.pythonhosted.org/packages/2c/69/362c0a5eca37225c7d451e6c57f07c4fee85a5b6cb3aedf16fe649f411ea/matplotlib-2.0.2-cp27-cp27mu-manylinux1_x86_64.whl Collecting ipython==5.5.0 (from -r requirements.txt (line 3)) Using cached https://files.pythonhosted.org/packages/08/2c/6285504003b4eadce5540f3ee3adc081468b26723f3eef07d9d5d7d97ed8/ipython-5.5.0-py2-none-any.whl Collecting jupyter==1.0.0 (from -r requirements.txt (line 4)) Using cached https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl Collecting bdgenomics.mango.pileup==0.0.2a0 (from -r requirements.txt (line 5)) Collecting bdgenomics.adam==0.26.0 (from -r requirements.txt (line 6)) Collecting ipywidgets==7.0.0 (from -r requirements.txt (line 7)) Using cached https://files.pythonhosted.org/packages/14/ea/793f6588d5be295d103fb868e26ba8671686b70bd855a21d02302f8dcd37/ipywidgets-7.0.0-py2.py3-none-any.whl Collecting psutil (from -r requirements.txt (line 8)) Collecting subprocess32 (from matplotlib==2.0.2->-r requirements.txt (line 2)) Collecting cycler>=0.10 (from matplotlib==2.0.2->-r requirements.txt (line 2)) Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl Requirement already satisfied: functools32 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (3.2.3.post2) Requirement already satisfied: six>=1.10 in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.11.0) Requirement already satisfied: pytz in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2018.9) Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 (from matplotlib==2.0.2->-r requirements.txt (line 2)) Using cached https://files.pythonhosted.org/packages/dd/d9/3ec19e966301a6e25769976999bd7bbe552016f0d32b577dc9d63d2e0c49/pyparsing-2.4.0-py2.py3-none-any.whl Requirement already satisfied: numpy>=1.7.1 in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (1.15.3) Requirement already satisfied: python-dateutil in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->-r requirements.txt (line 2)) (2.7.4) Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (2.3.3) Requirement already satisfied: backports.shutil-get-terminal-size; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (1.0.0) Requirement already satisfied: simplegeneric>0.8 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (0.8.1) Requirement already satisfied: traitlets>=4.2 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (4.3.2) Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (2.4.0) Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (4.7.0) Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (41.0.1) Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (1.0.16) Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (0.7.5) Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->-r requirements.txt (line 3)) (4.4.0) Collecting qtconsole (from jupyter==1.0.0->-r requirements.txt (line 4)) Using cached https://files.pythonhosted.org/packages/c7/45/1a50288305797fbca7c2039f9baefff1a9df603322874743fbb8408d8ec2/qtconsole-4.4.4-py2.py3-none-any.whl Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.7.8) Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (5.5.0) Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jupyter==1.0.0->-r requirements.txt (line 4)) (4.10.0) Collecting jupyter-console (from jupyter==1.0.0->-r requirements.txt (line 4)) Using cached https://files.pythonhosted.org/packages/77/82/6469cd7fccf7958cbe5dce2e623f1e3c5e27f1bb1ad36d90519bc2d5d370/jupyter_console-5.2.0-py2.py3-none-any.whl Requirement already satisfied: pyspark>=1.6.0 in /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python (from bdgenomics.adam==0.26.0->-r requirements.txt (line 6)) (2.3.3) Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipywidgets==7.0.0->-r requirements.txt (line 7)) (4.4.0) Collecting widgetsnbextension~=3.0.0 (from ipywidgets==7.0.0->-r requirements.txt (line 7)) Using cached https://files.pythonhosted.org/packages/8d/f2/c8bcccccbed39d51d3e237fb0c0f0c9bbc845d12afc41f5ca5f5728fffc7/widgetsnbextension-3.0.8-py2.py3-none-any.whl Requirement already satisfied: scandir; python_version < "3.5" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython==5.5.0->-r requirements.txt (line 3)) (1.10.0) Requirement already satisfied: enum34; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->-r requirements.txt (line 3)) (1.1.6) Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->-r requirements.txt (line 3)) (0.2.0) Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from pexpect; sys_platform != "win32"->ipython==5.5.0->-r requirements.txt (line 3)) (0.6.0) Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython==5.5.0->-r requirements.txt (line 3)) (0.1.7) Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (4.4.0) Requirement already satisfied: jupyter-client>=4.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->-r requirements.txt (line 4)) (5.2.4) Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.6.0) Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.5.0) Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (18.0.1) Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (2.10.1) Requirement already satisfied: tornado<7,>=4.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (5.1.1) Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.2) Requirement already satisfied: ipaddress; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.0.22) Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.3) Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.1.0) Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.4.2) Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.6.0) Requirement already satisfied: mistune>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.8.4) Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (1.4.2) Collecting py4j==0.10.7 (from pyspark>=1.6.0->bdgenomics.adam==0.26.0->-r requirements.txt (line 6)) Using cached https://files.pythonhosted.org/packages/e3/53/c737818eb9a7dc32a7cd4f1396e787bd94200c3997c72c1dbe028587bd76/py4j-0.10.7-py2.py3-none-any.whl Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (3.0.1) Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jinja2->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (1.1.1) Requirement already satisfied: futures in /home/jenkins/.local/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (3.2.0) Requirement already satisfied: singledispatch in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (3.4.0.3) Requirement already satisfied: backports-abc>=0.4 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5) Requirement already satisfied: configparser>=3.5; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from entrypoints>=0.2.2->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (3.7.4) Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bleach->nbconvert->jupyter==1.0.0->-r requirements.txt (line 4)) (0.5.1) Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (0.15.2) Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->-r requirements.txt (line 7)) (19.1.0) Installing collected packages: cigar, subprocess32, cycler, pyparsing, matplotlib, ipython, qtconsole, widgetsnbextension, ipywidgets, jupyter-console, jupyter, bdgenomics.mango.pileup, bdgenomics.adam, psutil, py4j Found existing installation: ipython 5.8.0 Uninstalling ipython-5.8.0: Successfully uninstalled ipython-5.8.0 Successfully installed bdgenomics.adam-0.26.0 bdgenomics.mango.pileup-0.0.2a0 cigar-0.1.3 cycler-0.10.0 ipython-5.5.0 ipywidgets-7.0.0 jupyter-1.0.0 jupyter-console-5.2.0 matplotlib-2.0.2 psutil-5.6.2 py4j-0.10.7 pyparsing-2.4.0 qtconsole-4.4.4 subprocess32-3.5.3 widgetsnbextension-3.0.8 + popd /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded ~/workspace/mango-prb/HADOOP_VERSION/2.7.5/SCALAVER/2.11/SPARK_VERSION/2.3.3/label/ubuntu + mvn -U -P python,distribution package -DskipTests -Dhadoop.version=2.7.5 -Dspark.version=2.3.3 Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-python:jar:0.0.3-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-python:[unknown-version], /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python/pom.xml, line 21, column 15 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.mango:mango-cli:jar:0.0.3-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:exec-maven-plugin is missing. @ org.bdgenomics.mango:mango-cli:[unknown-version], /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/pom.xml, line 39, column 15 [WARNING] [WARNING] It is highly recommended to fix these problems because they threaten the stability of your build. [WARNING] [WARNING] For this reason, future Maven versions might no longer support building such malformed projects. [WARNING] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] mango [INFO] mango: CORE [INFO] Mango: Python APIs [INFO] mango: CLI [INFO] Mango: Assembly [INFO] mango: Distribution [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-parent --- [INFO] Modified 144 of 226 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-parent --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-parent --- [INFO] No sources to compile [INFO] [INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-parent --- [INFO] Replacing original artifact with shaded artifact. [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-parent --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-parent --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-parent >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-parent --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-parent --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-parent <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-parent --- [INFO] No source files found [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango: CORE 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repository.apache.org/snapshots/commons-codec/commons-codec/maven-metadata.xml Downloading: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml Downloading: https://oss.sonatype.org/content/repositories/snapshots/commons-codec/commons-codec/maven-metadata.xml 537/672 B 672/672 B Downloaded: https://repo.maven.apache.org/maven2/commons-codec/commons-codec/maven-metadata.xml (672 B at 2.2 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core --- [INFO] Source directory: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-core --- [INFO] Modified 0 of 30 .scala files [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala:-1: info: compiling [INFO] Compiling 17 source files to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/scala-2.11.12/classes at 1557796841160 [WARNING] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class AlignmentRecordMaterialization(@transient sc: SparkContext, [WARNING] ^ [WARNING] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class FeatureMaterialization(@transient sc: SparkContext, [WARNING] ^ [WARNING] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] @transient sc: SparkContext, [WARNING] ^ [WARNING] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class VariantContextMaterialization(@transient sc: SparkContext, [WARNING] ^ [WARNING] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled. [WARNING] try { [WARNING] ^ [WARNING] warning: there was one deprecation warning; re-run with -deprecation for details [WARNING] warning: there were four feature warnings; re-run with -feature for details [WARNING] 7 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-core --- [INFO] Test Source directory: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-core --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 24 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala:-1: info: compiling [INFO] Compiling 13 source files to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/scala-2.11.12/test-classes at 1557796851963 [WARNING] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/test/scala/org/bdgenomics/mango/models/LazyMaterializationSuite.scala:77: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class LazyDummy(@transient sc: SparkContext, [WARNING] ^ [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 9 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-core --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-core --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-core --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-core --- [INFO] Building jar: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar [INFO] [INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-core --- [INFO] Including com.github.samtools:htsjdk:jar:2.16.1 in the shaded jar. [INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:2.9.0 in the shaded jar. [INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar. [INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar. [INFO] Including org.scala-lang:scala-compiler:jar:2.11.11 in the shaded jar. [INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar. [INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar. [INFO] Including org.apache.curator:curator-client:jar:2.7.1 in the shaded jar. [INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar. [INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar. [INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar. [INFO] Including it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar. [INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar. [INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar. [INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar. [INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar. [INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar. [INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar. [INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar. [INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar. [INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar. [INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar. [INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar. [INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar. [INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar. [INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar. [INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar. [INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar. [INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar. [INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar. [INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar. [INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar. [INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar. [INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar. [INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar. [INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar. [INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar. [INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar. [INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar. [INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar. [INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar. [INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar. [INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar. [INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar. [INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar. [INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar. [INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar. [INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar. [INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar. [INFO] Including oro:oro:jar:2.0.8 in the shaded jar. [INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar. [INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar. [INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar. [INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar. [INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar. [INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar. [INFO] Including org.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 org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar. [INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar. [INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar. [INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar. [INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar. [INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar. [INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar. [INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar. [INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.2 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including com.google.code.gson:gson:jar:2.3 in the shaded jar. [INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.2.1 in the shaded jar. [INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar. [INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar. [WARNING] minlog-1.3.0.jar, minlog-1.2.jar define 2 overlapping classes: [WARNING] - com.esotericsoftware.minlog.Log [WARNING] - com.esotericsoftware.minlog.Log$Logger [WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: [WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess [WARNING] - com.google.common.util.concurrent.internal.InternalFutures [WARNING] aopalliance-1.0.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: [WARNING] - org.aopalliance.intercept.ConstructorInterceptor [WARNING] - org.aopalliance.intercept.MethodInvocation [WARNING] - org.aopalliance.intercept.MethodInterceptor [WARNING] - org.aopalliance.intercept.Invocation [WARNING] - org.aopalliance.aop.AspectException [WARNING] - org.aopalliance.intercept.Interceptor [WARNING] - org.aopalliance.intercept.Joinpoint [WARNING] - org.aopalliance.aop.Advice [WARNING] - org.aopalliance.intercept.ConstructorInvocation [WARNING] javax.inject-2.4.0-b34.jar, javax.inject-1.jar define 6 overlapping classes: [WARNING] - javax.inject.Inject [WARNING] - javax.inject.Singleton [WARNING] - javax.inject.Named [WARNING] - javax.inject.Scope [WARNING] - javax.inject.Provider [WARNING] - javax.inject.Qualifier [WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, spark-tags_2.11-2.3.3.jar, spark-launcher_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, spark-kvstore_2.11-2.3.3.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: [WARNING] - org.apache.spark.unused.UnusedStubClass [WARNING] commons-logging-1.1.1.jar, jcl-over-slf4j-1.7.16.jar define 6 overlapping classes: [WARNING] - org.apache.commons.logging.impl.SimpleLog$1 [WARNING] - org.apache.commons.logging.Log [WARNING] - org.apache.commons.logging.impl.SimpleLog [WARNING] - org.apache.commons.logging.LogConfigurationException [WARNING] - org.apache.commons.logging.impl.NoOpLog [WARNING] - org.apache.commons.logging.LogFactory [WARNING] kryo-shaded-3.0.3.jar, kryo-2.24.0.jar define 193 overlapping classes: [WARNING] - com.esotericsoftware.kryo.serializers.BeanSerializer$1 [WARNING] - com.esotericsoftware.kryo.Registration [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor [WARNING] - com.esotericsoftware.kryo.util.IntMap$Values [WARNING] - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer [WARNING] - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl [WARNING] - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField [WARNING] - com.esotericsoftware.kryo.serializers.JavaSerializer [WARNING] - 183 more... [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT.jar with /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT-shaded.jar [INFO] Dependency-reduced POM written at: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/dependency-reduced-pom.xml [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-core --- [INFO] Building jar: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-core --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-core >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-core --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-core --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-core --- [INFO] Source directory: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-core <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-core --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/AlignmentRecordMaterialization.scala:57: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) class AlignmentRecordMaterialization(@transient sc: SparkContext, ^ /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/FeatureMaterialization.scala:43: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) class FeatureMaterialization(@transient sc: SparkContext, ^ /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/LazyMaterialization.scala:51: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) @transient sc: SparkContext, ^ /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/models/VariantContextMaterialization.scala:40: warning: no valid targets for annotation on value sc - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) class VariantContextMaterialization(@transient sc: SparkContext, ^ /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:89: warning: A try without a catch or finally is equivalent to putting its body in a block; no exceptions are handled. try { ^ warning: there were four feature warnings; re-run with -feature for details model contains 42 documentable templates /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/RefSeq.scala:29: warning: Variable GENOME undefined in comment for object RefSeqFile in object RefSeqFile * Processes refSeq file, downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz ^ /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes ^ /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:50: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig * - chrom.sizes file: downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/${GENOME}/bigZips/${GENOME}.chrom.sizes ^ /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:51: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig * - cytoBand.txt file: downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/${GENOME}/database/cytoBand.txt.gz ^ /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/src/main/scala/org/bdgenomics/mango/util/GenomeConfig.scala:52: warning: Variable GENOME undefined in comment for object GenomeConfig in object GenomeConfig * - refSeq.txt file: downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/${GENOME}/database/refGene.txt.gz ^ 11 warnings found [INFO] Building jar: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-core/target/mango-core-0.0.3-SNAPSHOT-javadoc.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building Mango: Python APIs 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml 741/741 B Downloaded: https://repo.maven.apache.org/maven2/org/codehaus/mojo/exec-maven-plugin/maven-metadata.xml (741 B at 55.7 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-python --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-python --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-python --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-python --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-python --- [INFO] No sources to compile [INFO] [INFO] --- exec-maven-plugin:1.6.0:exec (dev-python) @ mango-python --- pip install -e . DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Obtaining file:///tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python Requirement already satisfied: cigar==0.1.3 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (0.1.3) Requirement already satisfied: matplotlib==2.0.2 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (2.0.2) Requirement already satisfied: ipython==5.5.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (5.5.0) Requirement already satisfied: jupyter==1.0.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (1.0.0) Requirement already satisfied: bdgenomics.mango.pileup==0.0.2a0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (0.0.2a0) Requirement already satisfied: bdgenomics.adam==0.26.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (0.26.0) Requirement already satisfied: ipywidgets==7.0.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (7.0.0) Requirement already satisfied: psutil in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bdgenomics.mango==0.0.3a0) (5.6.2) Requirement already satisfied: subprocess32 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (3.5.3) Requirement already satisfied: cycler>=0.10 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (0.10.0) Requirement already satisfied: functools32 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (3.2.3.post2) Requirement already satisfied: six>=1.10 in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (1.11.0) Requirement already satisfied: pytz in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (2018.9) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (2.4.0) Requirement already satisfied: numpy>=1.7.1 in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (1.15.3) Requirement already satisfied: python-dateutil in /home/jenkins/.local/lib/python2.7/site-packages (from matplotlib==2.0.2->bdgenomics.mango==0.0.3a0) (2.7.4) Requirement already satisfied: pathlib2; python_version == "2.7" or python_version == "3.3" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (2.3.3) Requirement already satisfied: backports.shutil-get-terminal-size; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.0.0) Requirement already satisfied: simplegeneric>0.8 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.8.1) Requirement already satisfied: traitlets>=4.2 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (4.3.2) Requirement already satisfied: pygments in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (2.4.0) Requirement already satisfied: pexpect; sys_platform != "win32" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (4.7.0) Requirement already satisfied: decorator in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (4.4.0) Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.0.16) Requirement already satisfied: pickleshare in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.7.5) Requirement already satisfied: setuptools>=18.5 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipython==5.5.0->bdgenomics.mango==0.0.3a0) (41.0.1) Requirement already satisfied: qtconsole in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (4.4.4) Requirement already satisfied: notebook in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.7.8) Requirement already satisfied: nbconvert in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.5.0) Requirement already satisfied: ipykernel in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (4.10.0) Requirement already satisfied: jupyter-console in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.2.0) Requirement already satisfied: pyspark>=1.6.0 in /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/spark-2.3.3-bin-hadoop2.7/python (from bdgenomics.adam==0.26.0->bdgenomics.mango==0.0.3a0) (2.3.3) Requirement already satisfied: nbformat>=4.2.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (4.4.0) Requirement already satisfied: widgetsnbextension~=3.0.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (3.0.8) Requirement already satisfied: scandir; python_version < "3.5" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from pathlib2; python_version == "2.7" or python_version == "3.3"->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.10.0) Requirement already satisfied: enum34; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (1.1.6) Requirement already satisfied: ipython-genutils in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from traitlets>=4.2->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.2.0) Requirement already satisfied: ptyprocess>=0.5 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from pexpect; sys_platform != "win32"->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.6.0) Requirement already satisfied: wcwidth in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython==5.5.0->bdgenomics.mango==0.0.3a0) (0.1.7) Requirement already satisfied: jupyter-core in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (4.4.0) Requirement already satisfied: jupyter-client>=4.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from qtconsole->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.2.4) Requirement already satisfied: prometheus-client in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.6.0) Requirement already satisfied: Send2Trash in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (1.5.0) Requirement already satisfied: pyzmq>=17 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (18.0.1) Requirement already satisfied: jinja2 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (2.10.1) Requirement already satisfied: tornado<7,>=4.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (5.1.1) Requirement already satisfied: terminado>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.8.2) Requirement already satisfied: ipaddress; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (1.0.22) Requirement already satisfied: entrypoints>=0.2.2 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.3) Requirement already satisfied: bleach in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (3.1.0) Requirement already satisfied: testpath in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.4.2) Requirement already satisfied: defusedxml in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.6.0) Requirement already satisfied: mistune>=0.8.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.8.4) Requirement already satisfied: pandocfilters>=1.4.1 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (1.4.2) Requirement already satisfied: py4j==0.10.7 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from pyspark>=1.6.0->bdgenomics.adam==0.26.0->bdgenomics.mango==0.0.3a0) (0.10.7) Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (3.0.1) Requirement already satisfied: MarkupSafe>=0.23 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jinja2->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (1.1.1) Requirement already satisfied: futures in /home/jenkins/.local/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (3.2.0) Requirement already satisfied: singledispatch in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (3.4.0.3) Requirement already satisfied: backports-abc>=0.4 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from tornado<7,>=4.1->notebook->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.5) Requirement already satisfied: configparser>=3.5; python_version == "2.7" in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from entrypoints>=0.2.2->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (3.7.4) Requirement already satisfied: webencodings in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from bleach->nbconvert->jupyter==1.0.0->bdgenomics.mango==0.0.3a0) (0.5.1) Requirement already satisfied: pyrsistent>=0.14.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (0.15.2) Requirement already satisfied: attrs>=17.4.0 in /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2.0->ipywidgets==7.0.0->bdgenomics.mango==0.0.3a0) (19.1.0) Installing collected packages: bdgenomics.mango Found existing installation: bdgenomics.mango 0.0.3a0 Can't uninstall 'bdgenomics.mango'. No files were found to uninstall. Running setup.py develop for bdgenomics.mango Successfully installed bdgenomics.mango python setup.py sdist bdist_egg Could not import pypandoc - required to package bdgenomics.mango running sdist running egg_info writing requirements to bdgenomics.mango.egg-info/requires.txt writing bdgenomics.mango.egg-info/PKG-INFO writing top-level names to bdgenomics.mango.egg-info/top_level.txt writing dependency_links to bdgenomics.mango.egg-info/dependency_links.txt reading manifest file 'bdgenomics.mango.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '*.py[cod]' found anywhere in distribution warning: no previously-included files matching '__pycache__' found anywhere in distribution warning: no previously-included files matching '.DS_Store' found anywhere in distribution warning: no files found matching '*.jar' under directory 'deps/jars' writing manifest file 'bdgenomics.mango.egg-info/SOURCES.txt' running check creating bdgenomics.mango-0.0.3a0 creating bdgenomics.mango-0.0.3a0/bdgenomics creating bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info creating bdgenomics.mango-0.0.3a0/bdgenomics/mango creating bdgenomics.mango-0.0.3a0/bdgenomics/mango/test copying files to bdgenomics.mango-0.0.3a0... copying MANIFEST.in -> bdgenomics.mango-0.0.3a0 copying README.md -> bdgenomics.mango-0.0.3a0 copying requirements.txt -> bdgenomics.mango-0.0.3a0 copying setup.py -> bdgenomics.mango-0.0.3a0 copying version.py -> bdgenomics.mango-0.0.3a0 copying bdgenomics/__init__.py -> bdgenomics.mango-0.0.3a0/bdgenomics copying bdgenomics.mango.egg-info/PKG-INFO -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info copying bdgenomics.mango.egg-info/SOURCES.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info copying bdgenomics.mango.egg-info/dependency_links.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info copying bdgenomics.mango.egg-info/requires.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info copying bdgenomics.mango.egg-info/top_level.txt -> bdgenomics.mango-0.0.3a0/bdgenomics.mango.egg-info copying bdgenomics/mango/__init__.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango copying bdgenomics/mango/alignments.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango copying bdgenomics/mango/coverage.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango copying bdgenomics/mango/distribution.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango copying bdgenomics/mango/features.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango copying bdgenomics/mango/genotypes.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango copying bdgenomics/mango/utils.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango copying bdgenomics/mango/variants.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango copying bdgenomics/mango/test/__init__.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test copying bdgenomics/mango/test/alignment_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test copying bdgenomics/mango/test/coverage_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test copying bdgenomics/mango/test/distribution_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test copying bdgenomics/mango/test/feature_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test copying bdgenomics/mango/test/genotypes_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test copying bdgenomics/mango/test/notebook_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test copying bdgenomics/mango/test/variant_test.py -> bdgenomics.mango-0.0.3a0/bdgenomics/mango/test Writing bdgenomics.mango-0.0.3a0/setup.cfg creating dist Creating tar archive removing 'bdgenomics.mango-0.0.3a0' (and everything under it) running bdist_egg installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/bdgenomics copying bdgenomics/__init__.py -> build/lib/bdgenomics creating build/lib/bdgenomics/mango copying bdgenomics/mango/variants.py -> build/lib/bdgenomics/mango copying bdgenomics/mango/utils.py -> build/lib/bdgenomics/mango copying bdgenomics/mango/distribution.py -> build/lib/bdgenomics/mango copying bdgenomics/mango/coverage.py -> build/lib/bdgenomics/mango copying bdgenomics/mango/features.py -> build/lib/bdgenomics/mango copying bdgenomics/mango/alignments.py -> build/lib/bdgenomics/mango copying bdgenomics/mango/genotypes.py -> build/lib/bdgenomics/mango copying bdgenomics/mango/__init__.py -> build/lib/bdgenomics/mango creating build/lib/bdgenomics/mango/test copying bdgenomics/mango/test/coverage_test.py -> build/lib/bdgenomics/mango/test copying bdgenomics/mango/test/distribution_test.py -> build/lib/bdgenomics/mango/test copying bdgenomics/mango/test/variant_test.py -> build/lib/bdgenomics/mango/test copying bdgenomics/mango/test/feature_test.py -> build/lib/bdgenomics/mango/test copying bdgenomics/mango/test/notebook_test.py -> build/lib/bdgenomics/mango/test copying bdgenomics/mango/test/genotypes_test.py -> build/lib/bdgenomics/mango/test copying bdgenomics/mango/test/alignment_test.py -> build/lib/bdgenomics/mango/test copying bdgenomics/mango/test/__init__.py -> build/lib/bdgenomics/mango/test creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/bdgenomics creating build/bdist.linux-x86_64/egg/bdgenomics/mango copying build/lib/bdgenomics/mango/variants.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango copying build/lib/bdgenomics/mango/utils.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango copying build/lib/bdgenomics/mango/distribution.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango copying build/lib/bdgenomics/mango/coverage.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango copying build/lib/bdgenomics/mango/features.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango copying build/lib/bdgenomics/mango/alignments.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango copying build/lib/bdgenomics/mango/genotypes.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango copying build/lib/bdgenomics/mango/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango creating build/bdist.linux-x86_64/egg/bdgenomics/mango/test copying build/lib/bdgenomics/mango/test/coverage_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test copying build/lib/bdgenomics/mango/test/distribution_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test copying build/lib/bdgenomics/mango/test/variant_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test copying build/lib/bdgenomics/mango/test/feature_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test copying build/lib/bdgenomics/mango/test/notebook_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test copying build/lib/bdgenomics/mango/test/genotypes_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test copying build/lib/bdgenomics/mango/test/alignment_test.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test copying build/lib/bdgenomics/mango/test/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics/mango/test copying build/lib/bdgenomics/__init__.py -> build/bdist.linux-x86_64/egg/bdgenomics byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/variants.py to variants.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/utils.py to utils.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/distribution.py to distribution.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/coverage.py to coverage.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/features.py to features.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/alignments.py to alignments.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/genotypes.py to genotypes.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/coverage_test.py to coverage_test.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/distribution_test.py to distribution_test.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/variant_test.py to variant_test.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/feature_test.py to feature_test.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/notebook_test.py to notebook_test.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/genotypes_test.py to genotypes_test.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/alignment_test.py to alignment_test.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/mango/test/__init__.py to __init__.pyc byte-compiling build/bdist.linux-x86_64/egg/bdgenomics/__init__.py to __init__.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying bdgenomics.mango.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying bdgenomics.mango.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bdgenomics.mango.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bdgenomics.mango.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying bdgenomics.mango.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO zip_safe flag not set; analyzing archive contents... bdgenomics.__init__: module references __path__ bdgenomics.mango.__init__: module references __path__ creating 'dist/bdgenomics.mango-0.0.3a0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-python --- [INFO] No sources to compile [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-python --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-python --- [INFO] No sources to compile [INFO] [INFO] --- exec-maven-plugin:1.6.0:exec (test-python) @ mango-python --- pushd ../example-files/notebooks \ && jupyter nbconvert --to python mango-python-coverage.ipynb \ && jupyter nbconvert --to python mango-python-alignment.ipynb \ && jupyter nbconvert --to python mango-viz.ipynb \ && jupyter nbconvert --to python mango-python-variants.ipynb /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/example-files/notebooks /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python [NbConvertApp] Converting notebook mango-python-coverage.ipynb to python [NbConvertApp] Writing 1051 bytes to mango-python-coverage.py [NbConvertApp] Converting notebook mango-python-alignment.ipynb to python [NbConvertApp] Writing 2194 bytes to mango-python-alignment.py [NbConvertApp] Converting notebook mango-viz.ipynb to python [NbConvertApp] Writing 1661 bytes to mango-viz.py [NbConvertApp] Converting notebook mango-python-variants.ipynb to python [NbConvertApp] Writing 1941 bytes to mango-python-variants.py mkdir -p target python -m pytest -vv --junitxml target/pytest-reports/tests.xml bdgenomics ============================= test session starts ============================== platform linux2 -- Python 2.7.16, pytest-3.9.1, py-1.8.0, pluggy-0.11.0 -- /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/bin/python cachedir: .pytest_cache rootdir: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python, inifile: collecting ... collected 24 items bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_coverage_distribution PASSED [ 4%] bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_fragment_distribution PASSED [ 8%] bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution PASSED [ 12%] bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_maximal_bin_size PASSED [ 16%] bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_indel_distribution_no_elements PASSED [ 20%] bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_mapq_distribution PASSED [ 25%] bdgenomics/mango/test/alignment_test.py::AlignmentTest::test_visualize_alignments PASSED [ 29%] bdgenomics/mango/test/coverage_test.py::CoverageTest::test_coverage_distribution PASSED [ 33%] bdgenomics/mango/test/coverage_test.py::CoverageTest::test_example_coverage PASSED [ 37%] bdgenomics/mango/test/distribution_test.py::DistributionTest::test_cumulative_count_distribution PASSED [ 41%] bdgenomics/mango/test/distribution_test.py::DistributionTest::test_fail_on_invalid_sample PASSED [ 45%] bdgenomics/mango/test/distribution_test.py::DistributionTest::test_normalized_count_distribution PASSED [ 50%] bdgenomics/mango/test/distribution_test.py::DistributionTest::test_sampling PASSED [ 54%] bdgenomics/mango/test/feature_test.py::FeatureTest::test_visualize_features PASSED [ 58%] bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeCallRatesDistribution PASSED [ 62%] bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_GenotypeSummary PASSED [ 66%] bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_HetHomRatioDistribution PASSED [ 70%] bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistribution PASSED [ 75%] bdgenomics/mango/test/genotypes_test.py::GenotypesTest::test_VariantsPerSampleDistributionSampling PASSED [ 79%] bdgenomics/mango/test/notebook_test.py::NotebookTest::test_alignment_example PASSED [ 83%] bdgenomics/mango/test/notebook_test.py::NotebookTest::test_coverage_example PASSED [ 87%] bdgenomics/mango/test/notebook_test.py::NotebookTest::test_example PASSED [ 91%] bdgenomics/mango/test/notebook_test.py::NotebookTest::test_variants_example PASSED [ 95%] bdgenomics/mango/test/variant_test.py::VariantTest::test_visualize_variants PASSED [100%] - generated xml file: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python/target/pytest-reports/tests.xml - =============================== warnings summary =============================== /home/jenkins/anaconda2/envs/mango-build-5f6c0abc-d93e-417a-aa48-1bc33829d006/lib/python2.7/site-packages/ipywidgets/widgets/widget.py:287: DeprecationWarning: Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator. warnings.warn("Widget registration using a string name has been deprecated. Widget registration now uses a plain `@register` decorator.", DeprecationWarning) -- Docs: https://docs.pytest.org/en/latest/warnings.html =================== 24 passed, 1 warnings in 102.35 seconds ==================== pushd ../example-files/notebooks \ && rm mango-python-coverage.py \ && rm mango-python-alignment.py \ && rm mango-viz.py \ && rm mango-python-variants.py /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/example-files/notebooks /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python exit [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-python --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-python --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-python --- [WARNING] JAR will be empty - no content was marked for inclusion! [INFO] Building jar: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python/target/mango-python-0.0.3-SNAPSHOT.jar [INFO] [INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-python --- [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python/target/mango-python-0.0.3-SNAPSHOT.jar with /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-python/target/mango-python-0.0.3-SNAPSHOT-shaded.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-python --- [INFO] No sources in project. Archive not created. [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-python --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-python >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-python --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-python --- [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-python <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-python --- [INFO] No source files found [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building mango: CLI 0.0.3-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli --- [INFO] Source directory: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ mango-cli --- [INFO] Modified 0 of 8 .scala files [INFO] [INFO] --- maven-resources-plugin:3.0.1:resources (default-resources) @ mango-cli --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 2855 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/scala-2.11.12/classes at 1557797013115 [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- exec-maven-plugin:1.6.0:exec (Run `npm install`) @ mango-cli --- npm notice created a lockfile as package-lock.json. You should commit this file. npm WARN mango-cli@0.0.2 No repository field. audited 125 packages in 0.97s found 0 vulnerabilities [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ mango-cli --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ mango-cli --- [INFO] Test Source directory: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.0.1:testResources (default-testResources) @ mango-cli --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 8 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/test/scala:-1: info: compiling [INFO] Compiling 4 source files to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/scala-2.11.12/test-classes at 1557797023812 [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ mango-cli --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.19.1:test (default-test) @ mango-cli --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ mango-cli --- [INFO] Tests are skipped. [INFO] [INFO] --- sass-maven-plugin:3.7.1:update-stylesheets (default) @ mango-cli --- [INFO] Checked 0 files for /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/sass [INFO] Checked 0 filtered (**/*.css) files for /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.3-SNAPSHOT/css [INFO] Compiling Sass templates [INFO] Queueing Sass template for compile: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets => /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets Ignoring eventmachine-1.2.7 because its extensions are not built. Try: gem pristine eventmachine --version 1.2.7 Ignoring ffi-1.9.23 because its extensions are not built. Try: gem pristine ffi --version 1.9.23 Ignoring http_parser.rb-0.6.0 because its extensions are not built. Try: gem pristine http_parser.rb --version 0.6.0 [INFO] >> /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets/main.scss => /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/../src/main/webapp/stylesheets/main.css [INFO] [INFO] --- maven-jar-plugin:3.0.0:jar (default-jar) @ mango-cli --- [INFO] Building jar: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.3-SNAPSHOT.jar [INFO] [INFO] --- maven-shade-plugin:3.1.0:shade (default) @ mango-cli --- [INFO] Including net.liftweb:lift-json_2.11:jar:3.3.0 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.11.11 in the shaded jar. [INFO] Including org.scala-lang:scalap:jar:2.11.11 in the shaded jar. [INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.8 in the shaded jar. [INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.0.5 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.7 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar. [INFO] Including com.google.code.gson:gson:jar:2.2.4 in the shaded jar. [INFO] Including org.apache.curator:curator-client:jar:2.7.1 in the shaded jar. [INFO] Including org.apache.zookeeper:zookeeper:jar:3.4.6 in the shaded jar. [INFO] Including org.fusesource.leveldbjni:leveldbjni-all:jar:1.8 in the shaded jar. [INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar. [INFO] Including it.unimi.dsi:fastutil:jar:6.5.7 in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.10 in the shaded jar. [INFO] Including org.apache.spark:spark-tags_2.11:jar:2.3.3 in the shaded jar. [INFO] Including com.esotericsoftware:kryo-shaded:jar:3.0.3 in the shaded jar. [INFO] Including com.esotericsoftware:minlog:jar:1.3.0 in the shaded jar. [INFO] Including org.apache.parquet:parquet-column:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-common:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.3 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-databind:jar:2.6.7.1 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-annotations:jar:2.6.0 in the shaded jar. [INFO] Including com.fasterxml.jackson.core:jackson-core:jar:2.6.7 in the shaded jar. [INFO] Including org.apache.xbean:xbean-asm5-shaded:jar:4.4 in the shaded jar. [INFO] Including org.spark-project.spark:unused:jar:1.0.0 in the shaded jar. [INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.3 in the shaded jar. [INFO] Including org.apache.spark:spark-core_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.avro:avro-mapred:jar:hadoop2:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:1.7.7 in the shaded jar. [INFO] Including org.apache.avro:avro-ipc:jar:tests:1.7.7 in the shaded jar. [INFO] Including com.twitter:chill_2.11:jar:0.8.4 in the shaded jar. [INFO] Including com.twitter:chill-java:jar:0.8.4 in the shaded jar. [INFO] Including org.apache.spark:spark-launcher_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-kvstore_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-network-common_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-network-shuffle_2.11:jar:2.3.3 in the shaded jar. [INFO] Including org.apache.spark:spark-unsafe_2.11:jar:2.3.3 in the shaded jar. [INFO] Including net.java.dev.jets3t:jets3t:jar:0.9.4 in the shaded jar. [INFO] Including javax.activation:activation:jar:1.1.1 in the shaded jar. [INFO] Including org.bouncycastle:bcprov-jdk15on:jar:1.52 in the shaded jar. [INFO] Including com.jamesmurty.utils:java-xmlbuilder:jar:1.1 in the shaded jar. [INFO] Including net.iharder:base64:jar:2.3.8 in the shaded jar. [INFO] Including org.apache.curator:curator-recipes:jar:2.6.0 in the shaded jar. [INFO] Including org.apache.curator:curator-framework:jar:2.6.0 in the shaded jar. [INFO] Including javax.servlet:javax.servlet-api:jar:3.1.0 in the shaded jar. [INFO] Including org.apache.commons:commons-lang3:jar:3.5 in the shaded jar. [INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar. [INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar. [INFO] Including org.slf4j:jul-to-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including org.slf4j:jcl-over-slf4j:jar:1.7.16 in the shaded jar. [INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar. [INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.16 in the shaded jar. [INFO] Including com.ning:compress-lzf:jar:1.0.3 in the shaded jar. [INFO] Including org.lz4:lz4-java:jar:1.4.0 in the shaded jar. [INFO] Including com.github.luben:zstd-jni:jar:1.3.2-2 in the shaded jar. [INFO] Including org.roaringbitmap:RoaringBitmap:jar:0.5.11 in the shaded jar. [INFO] Including commons-net:commons-net:jar:2.2 in the shaded jar. [INFO] Including org.json4s:json4s-jackson_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-core_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.json4s:json4s-ast_2.11:jar:3.2.11 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-client:jar:2.22.2 in the shaded jar. [INFO] Including javax.ws.rs:javax.ws.rs-api:jar:2.0.1 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-api:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-utils:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:aopalliance-repackaged:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2.external:javax.inject:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.glassfish.hk2:hk2-locator:jar:2.4.0-b34 in the shaded jar. [INFO] Including org.javassist:javassist:jar:3.18.1-GA in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-common:jar:2.22.2 in the shaded jar. [INFO] Including javax.annotation:javax.annotation-api:jar:1.2 in the shaded jar. [INFO] Including org.glassfish.jersey.bundles.repackaged:jersey-guava:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.hk2:osgi-resource-locator:jar:1.0.1 in the shaded jar. [INFO] Including org.glassfish.jersey.core:jersey-server:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.media:jersey-media-jaxb:jar:2.22.2 in the shaded jar. [INFO] Including javax.validation:validation-api:jar:1.1.0.Final in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet:jar:2.22.2 in the shaded jar. [INFO] Including org.glassfish.jersey.containers:jersey-container-servlet-core:jar:2.22.2 in the shaded jar. [INFO] Including io.netty:netty-all:jar:4.1.17.Final in the shaded jar. [INFO] Including io.netty:netty:jar:3.9.9.Final in the shaded jar. [INFO] Including com.clearspring.analytics:stream:jar:2.7.0 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-core:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-jvm:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-json:jar:3.1.5 in the shaded jar. [INFO] Including io.dropwizard.metrics:metrics-graphite:jar:3.1.5 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-scala_2.11:jar:2.6.7.1 in the shaded jar. [INFO] Including com.fasterxml.jackson.module:jackson-module-paranamer:jar:2.7.9 in the shaded jar. [INFO] Including org.apache.ivy:ivy:jar:2.4.0 in the shaded jar. [INFO] Including oro:oro:jar:2.0.8 in the shaded jar. [INFO] Including net.razorvine:pyrolite:jar:4.13 in the shaded jar. [INFO] Including net.sf.py4j:py4j:jar:0.10.7 in the shaded jar. [INFO] Including org.apache.commons:commons-crypto:jar:1.0.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.11:jar:4.2.1 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.2.0 in the shaded jar. [INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar. [INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar. [INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar. [INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar. [INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar. [INFO] Including org.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:2.16.1 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 org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar. [INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar. [INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar. [INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar. [INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar. [INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar. [INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar. [INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.26.0 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-server:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-http:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-util:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-io:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-webapp:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-xml:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-servlet:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.eclipse.jetty:jetty-security:jar:9.4.15.v20190215 in the shaded jar. [INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-xml_2.11:jar:1.0.2 in the shaded jar. [INFO] Including org.scalatra:scalatra_2.11:jar:2.4.1 in the shaded jar. [INFO] Including org.scalatra:scalatra-common_2.11:jar:2.4.1 in the shaded jar. [INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.0.2 in the shaded jar. [INFO] Including org.scalatra.rl:rl_2.11:jar:0.4.10 in the shaded jar. [INFO] Including com.googlecode.juniversalchardet:juniversalchardet:jar:1.0.3 in the shaded jar. [INFO] Including eu.medsea.mimeutil:mime-util:jar:2.1.3 in the shaded jar. [INFO] Including joda-time:joda-time:jar:2.9.1 in the shaded jar. [INFO] Including org.joda:joda-convert:jar:1.8.1 in the shaded jar. [INFO] Including org.scala-lang.modules:scala-parser-combinators_2.11:jar:1.0.4 in the shaded jar. [INFO] Including org.scalatra.scalate:scalate-core_2.11:jar:1.9.1 in the shaded jar. [INFO] Including org.scala-lang:scala-compiler:jar:2.11.12 in the shaded jar. [INFO] Including org.scalatra.scalate:scalate-util_2.11:jar:1.9.1 in the shaded jar. [INFO] Including org.bdgenomics.mango:mango-core:jar:0.0.3-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including com.google.protobuf:protobuf-java-util:jar:3.0.0-beta-3 in the shaded jar. [INFO] Including org.ga4gh:ga4gh-schemas:jar:0.6.0a10 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-ga4gh:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert-htsjdk:jar:0.6.0 in the shaded jar. [INFO] Including org.bdgenomics.convert:convert:jar:0.6.0 in the shaded jar. [WARNING] jackson-core-2.6.7.jar, mango-core-0.0.3-SNAPSHOT.jar define 93 overlapping classes: [WARNING] - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer$Bucket [WARNING] - com.fasterxml.jackson.core.FormatSchema [WARNING] - com.fasterxml.jackson.core.io.InputDecorator [WARNING] - com.fasterxml.jackson.core.JsonGenerator$Feature [WARNING] - com.fasterxml.jackson.core.sym.BytesToNameCanonicalizer [WARNING] - com.fasterxml.jackson.core.type.ResolvedType [WARNING] - com.fasterxml.jackson.core.io.SegmentedStringWriter [WARNING] - com.fasterxml.jackson.core.TreeNode [WARNING] - com.fasterxml.jackson.core.sym.Name [WARNING] - com.fasterxml.jackson.core.util.JsonGeneratorDelegate [WARNING] - 83 more... [WARNING] curator-client-2.7.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 56 overlapping classes: [WARNING] - org.apache.curator.HandleHolder$Helper [WARNING] - org.apache.curator.utils.PathUtils [WARNING] - org.apache.curator.ensemble.exhibitor.ExhibitorEnsembleProvider$1 [WARNING] - org.apache.curator.utils.CloseableScheduledExecutorService [WARNING] - org.apache.curator.utils.EnsurePath$InitialHelper$1 [WARNING] - org.apache.curator.SessionFailRetryLoop$2 [WARNING] - org.apache.curator.utils.ZKPaths$PathAndNode [WARNING] - org.apache.curator.ensemble.exhibitor.DefaultExhibitorRestClient [WARNING] - org.apache.curator.TimeTrace [WARNING] - org.apache.curator.HandleHolder$1$1 [WARNING] - 46 more... [WARNING] jackson-module-scala_2.11-2.6.7.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 403 overlapping classes: [WARNING] - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializer$$anonfun$2 [WARNING] - com.fasterxml.jackson.module.scala.deser.UnsortedSetDeserializerModule [WARNING] - com.fasterxml.jackson.module.scala.deser.UnsortedMapDeserializerModule$class [WARNING] - com.fasterxml.jackson.module.scala.JacksonModule$$anonfun$1 [WARNING] - com.fasterxml.jackson.module.scala.deser.SortedSetDeserializer$$anonfun$4 [WARNING] - com.fasterxml.jackson.module.scala.util.Options$class [WARNING] - com.fasterxml.jackson.module.scala.util.EnumResolver$ [WARNING] - com.fasterxml.jackson.module.scala.ser.OptionSerializer$$anonfun$serialize$1 [WARNING] - com.fasterxml.jackson.module.scala.ser.OptionSerializerModule [WARNING] - com.fasterxml.jackson.module.scala.modifiers.CollectionLikeTypeModifier$$anonfun$modifyType$3 [WARNING] - 393 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-jvm-3.1.5.jar define 38 overlapping classes: [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$15 [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$3 [WARNING] - com.codahale.metrics.jvm.CachedThreadStatesGaugeSet [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$8 [WARNING] - com.codahale.metrics.jvm.ClassLoadingGaugeSet$1 [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$5 [WARNING] - com.codahale.metrics.jvm.BufferPoolMetricSet [WARNING] - com.codahale.metrics.jvm.ThreadStatesGaugeSet [WARNING] - com.codahale.metrics.jvm.MemoryUsageGaugeSet$10 [WARNING] - 28 more... [WARNING] servo-core-0.12.12.jar, mango-core-0.0.3-SNAPSHOT.jar define 162 overlapping classes: [WARNING] - com.netflix.servo.util.Objects [WARNING] - com.netflix.servo.util.Clock [WARNING] - com.netflix.servo.monitor.MaxGauge [WARNING] - com.netflix.servo.publish.LocalJmxConnector [WARNING] - com.netflix.servo.publish.MonitorRegistryMetricPoller$MonitorValueCallable [WARNING] - com.netflix.servo.util.ExpiringCache$Entry [WARNING] - com.netflix.servo.util.ThreadCpuStats$CpuUsage [WARNING] - com.netflix.servo.tag.SmallTagMap$Builder [WARNING] - com.netflix.servo.stats.StatsConfig [WARNING] - com.netflix.servo.monitor.Monitors$CounterFactory [WARNING] - 152 more... [WARNING] activation-1.1.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 38 overlapping classes: [WARNING] - javax.activation.DataContentHandlerFactory [WARNING] - javax.activation.ObjectDataContentHandler [WARNING] - javax.activation.DataContentHandler [WARNING] - com.sun.activation.registries.MimeTypeEntry [WARNING] - com.sun.activation.viewers.TextViewer [WARNING] - com.sun.activation.registries.LogSupport [WARNING] - javax.activation.CommandObject [WARNING] - javax.activation.SecuritySupport$2 [WARNING] - com.sun.activation.viewers.TextEditor [WARNING] - com.sun.activation.viewers.ImageViewerCanvas [WARNING] - 28 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jackson-databind-2.6.7.1.jar define 563 overlapping classes: [WARNING] - com.fasterxml.jackson.databind.BeanDescription [WARNING] - com.fasterxml.jackson.databind.deser.impl.BeanAsArrayBuilderDeserializer [WARNING] - com.fasterxml.jackson.databind.SerializerProvider [WARNING] - com.fasterxml.jackson.databind.introspect.AnnotatedMethodMap [WARNING] - com.fasterxml.jackson.databind.ser.std.StaticListSerializerBase [WARNING] - com.fasterxml.jackson.databind.ser.std.NumberSerializers$ShortSerializer [WARNING] - com.fasterxml.jackson.databind.ser.BeanSerializerFactory [WARNING] - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonMapFormatVisitor [WARNING] - com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatTypes [WARNING] - com.fasterxml.jackson.databind.deser.impl.MethodProperty [WARNING] - 553 more... [WARNING] fastutil-6.5.7.jar, mango-core-0.0.3-SNAPSHOT.jar define 10653 overlapping classes: [WARNING] - it.unimi.dsi.fastutil.doubles.Double2IntRBTreeMap$Submap$KeySet [WARNING] - it.unimi.dsi.fastutil.longs.Long2CharAVLTreeMap$2$1 [WARNING] - it.unimi.dsi.fastutil.bytes.Byte2ObjectLinkedOpenHashMap$EntryIterator [WARNING] - it.unimi.dsi.fastutil.shorts.Short2FloatOpenCustomHashMap$KeySet [WARNING] - it.unimi.dsi.fastutil.ints.Int2ReferenceRBTreeMap$Submap [WARNING] - it.unimi.dsi.fastutil.bytes.Byte2BooleanRBTreeMap$Submap$1 [WARNING] - it.unimi.dsi.fastutil.floats.AbstractFloat2ShortSortedMap$ValuesCollection [WARNING] - it.unimi.dsi.fastutil.longs.Long2ReferenceRBTreeMap$Submap$2 [WARNING] - it.unimi.dsi.fastutil.chars.AbstractChar2LongSortedMap$ValuesIterator [WARNING] - it.unimi.dsi.fastutil.doubles.DoubleHeaps [WARNING] - 10643 more... [WARNING] bcprov-jdk15on-1.52.jar, mango-core-0.0.3-SNAPSHOT.jar define 2430 overlapping classes: [WARNING] - org.bouncycastle.crypto.modes.gcm.Tables8kGCMMultiplier [WARNING] - org.bouncycastle.crypto.tls.HeartbeatMode [WARNING] - org.bouncycastle.pqc.math.linearalgebra.GF2nPolynomialElement [WARNING] - org.bouncycastle.jcajce.provider.asymmetric.ecgost.KeyFactorySpi [WARNING] - org.bouncycastle.jcajce.provider.symmetric.AES$AlgParamsCCM [WARNING] - org.bouncycastle.asn1.tsp.TimeStampResp [WARNING] - org.bouncycastle.jcajce.provider.digest.SHA384$Mappings [WARNING] - org.bouncycastle.jcajce.provider.asymmetric.elgamal.AlgorithmParameterGeneratorSpi [WARNING] - org.bouncycastle.asn1.x509.CRLNumber [WARNING] - org.bouncycastle.jcajce.provider.digest.SM3 [WARNING] - 2420 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-io-2.6.jar define 127 overlapping classes: [WARNING] - org.apache.commons.io.FileCleaningTracker [WARNING] - org.apache.commons.io.comparator.SizeFileComparator [WARNING] - org.apache.commons.io.input.CloseShieldInputStream [WARNING] - org.apache.commons.io.ByteOrderParser [WARNING] - org.apache.commons.io.filefilter.EmptyFileFilter [WARNING] - org.apache.commons.io.monitor.FileEntry [WARNING] - org.apache.commons.io.output.ThresholdingOutputStream [WARNING] - org.apache.commons.io.input.TailerListener [WARNING] - org.apache.commons.io.IOExceptionWithCause [WARNING] - org.apache.commons.io.filefilter.NotFileFilter [WARNING] - 117 more... [WARNING] guice-4.2.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 572 overlapping classes: [WARNING] - com.google.inject.Scope [WARNING] - com.google.inject.Binding [WARNING] - com.google.inject.internal.cglib.core.$EmitUtils$3 [WARNING] - com.google.inject.spi.TypeConverter [WARNING] - com.google.inject.internal.ConstructionProxy [WARNING] - com.google.inject.spi.InjectionPoint [WARNING] - com.google.inject.spi.StaticInjectionRequest [WARNING] - com.google.inject.internal.cglib.proxy.$FixedValueGenerator [WARNING] - com.google.inject.internal.cglib.proxy.$DispatcherGenerator [WARNING] - com.google.inject.spi.Elements$ElementsAsModule [WARNING] - 562 more... [WARNING] commons-jexl-2.1.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 178 overlapping classes: [WARNING] - org.apache.commons.jexl2.internal.AbstractExecutor$Get [WARNING] - org.apache.commons.jexl2.introspection.JexlPropertyGet [WARNING] - org.apache.commons.jexl2.parser.StringParser [WARNING] - org.apache.commons.jexl2.parser.ASTBitwiseOrNode [WARNING] - org.apache.commons.jexl2.internal.introspection.MethodKey$1 [WARNING] - org.apache.commons.jexl2.Main [WARNING] - org.apache.commons.jexl2.parser.ASTForeachStatement [WARNING] - org.apache.commons.jexl2.introspection.Sandbox [WARNING] - org.apache.commons.jexl2.internal.introspection.ClassMap [WARNING] - org.apache.commons.jexl2.parser.ASTFunctionNode [WARNING] - 168 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-core_2.11-2.3.3.jar define 8350 overlapping classes: [WARNING] - org.apache.spark.shuffle.BaseShuffleHandle [WARNING] - org.apache.spark.SparkContext$$anonfun$11 [WARNING] - org.spark_project.jetty.client.util.MultiPartContentProvider$1 [WARNING] - org.apache.spark.TaskContextImpl$$anonfun$markTaskFailed$1 [WARNING] - org.apache.spark.util.collection.PrimitiveVector$mcI$sp [WARNING] - org.spark_project.jetty.servlets.PushCacheFilter [WARNING] - org.apache.spark.util.Utils$$anonfun$downloadFile$1 [WARNING] - org.apache.spark.util.JsonProtocol$$anonfun$52 [WARNING] - org.apache.spark.ExecutorAllocationManager$$anonfun$org$apache$spark$ExecutorAllocationManager$$onExecutorAdded$2 [WARNING] - org.apache.spark.rdd.util.PeriodicRDDCheckpointer [WARNING] - 8340 more... [WARNING] httpclient-4.5.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 463 overlapping classes: [WARNING] - org.apache.http.impl.cookie.RFC2109Spec [WARNING] - org.apache.http.impl.execchain.MainClientExec [WARNING] - org.apache.http.conn.routing.RouteInfo$TunnelType [WARNING] - org.apache.http.client.methods.HttpGet [WARNING] - org.apache.http.impl.cookie.BrowserCompatSpecFactory [WARNING] - org.apache.http.impl.client.HttpAuthenticator [WARNING] - org.apache.http.conn.ManagedClientConnection [WARNING] - org.apache.http.client.protocol.RequestAuthCache [WARNING] - org.apache.http.conn.params.ConnConnectionParamBean [WARNING] - org.apache.http.impl.client.IdleConnectionEvictor [WARNING] - 453 more... [WARNING] spark-kvstore_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 28 overlapping classes: [WARNING] - org.apache.spark.util.kvstore.LevelDB$TypeAliases [WARNING] - org.apache.spark.util.kvstore.LevelDB$1 [WARNING] - org.apache.spark.util.kvstore.LevelDB$PrefixCache [WARNING] - org.apache.spark.util.kvstore.LevelDBTypeInfo$Index [WARNING] - org.apache.spark.util.kvstore.KVStore [WARNING] - org.apache.spark.util.kvstore.KVTypeInfo [WARNING] - org.apache.spark.util.kvstore.KVIndex [WARNING] - org.apache.spark.util.kvstore.KVStoreIterator [WARNING] - org.apache.spark.util.kvstore.InMemoryStore$InMemoryView [WARNING] - org.apache.spark.util.kvstore.InMemoryStore$1 [WARNING] - 18 more... [WARNING] oro-2.0.8.jar, mango-core-0.0.3-SNAPSHOT.jar define 62 overlapping classes: [WARNING] - org.apache.oro.text.perl.MalformedPerl5PatternException [WARNING] - org.apache.oro.text.regex.Perl5Pattern [WARNING] - org.apache.oro.io.RegexFilenameFilter [WARNING] - org.apache.oro.util.Cache [WARNING] - org.apache.oro.text.GenericPatternCache [WARNING] - org.apache.oro.text.awk.DFAState [WARNING] - org.apache.oro.text.regex.StringSubstitution [WARNING] - org.apache.oro.text.awk.AwkCompiler [WARNING] - org.apache.oro.text.PatternCacheLRU [WARNING] - org.apache.oro.text.regex.Substitution [WARNING] - 52 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-launcher_2.11-2.3.3.jar define 34 overlapping classes: [WARNING] - org.apache.spark.launcher.AbstractAppHandle [WARNING] - org.apache.spark.launcher.SparkAppHandle$State [WARNING] - org.apache.spark.launcher.SparkAppHandle$Listener [WARNING] - org.apache.spark.launcher.ChildProcAppHandle [WARNING] - org.apache.spark.launcher.LauncherProtocol [WARNING] - org.apache.spark.launcher.LauncherProtocol$Stop [WARNING] - org.apache.spark.launcher.SparkSubmitOptionParser [WARNING] - org.apache.spark.launcher.LauncherProtocol$Message [WARNING] - org.apache.spark.launcher.CommandBuilderUtils [WARNING] - org.apache.spark.launcher.SparkSubmitCommandBuilder$OptionParser [WARNING] - 24 more... [WARNING] avro-mapred-1.7.7-hadoop2.jar, mango-core-0.0.3-SNAPSHOT.jar define 126 overlapping classes: [WARNING] - org.apache.avro.mapreduce.AvroMultipleOutputs [WARNING] - org.apache.avro.mapreduce.AvroKeyValueOutputFormat [WARNING] - org.apache.avro.mapred.SequenceFileReader$8 [WARNING] - org.apache.avro.hadoop.file.HadoopCodecFactory [WARNING] - org.apache.avro.mapred.Pair [WARNING] - org.apache.avro.mapred.AvroMultipleOutputs [WARNING] - org.apache.avro.mapred.FsInput [WARNING] - org.apache.avro.mapred.tether.InputProtocol$Callback [WARNING] - org.apache.avro.mapred.AvroOutputFormat$1 [WARNING] - org.apache.avro.hadoop.file.SortedKeyValueFile$Reader$Options [WARNING] - 116 more... [WARNING] utils-cli-spark2_2.11-0.2.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 23 overlapping classes: [WARNING] - org.bdgenomics.utils.cli.Args4j [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$4 [WARNING] - org.bdgenomics.utils.cli.ParquetArgs [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$3 [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$class [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$2 [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$run$1 [WARNING] - org.bdgenomics.utils.cli.ParquetArgs$class [WARNING] - org.bdgenomics.utils.cli.BDGSparkCommand$$anonfun$printMetrics$1 [WARNING] - org.bdgenomics.utils.cli.SaveArgs [WARNING] - 13 more... [WARNING] utils-misc-spark2_2.11-0.2.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 11 overlapping classes: [WARNING] - org.bdgenomics.utils.misc.MathUtils [WARNING] - org.bdgenomics.utils.misc.Logging$ [WARNING] - org.bdgenomics.utils.misc.MathUtils$$anonfun$scalarArrayMultiply$1 [WARNING] - org.bdgenomics.utils.misc.Logging$class [WARNING] - org.bdgenomics.utils.misc.Logging$$anonfun$getContextOrClassLoader$1 [WARNING] - org.bdgenomics.utils.misc.MathUtils$$anonfun$aggregateArray$1 [WARNING] - org.bdgenomics.utils.misc.Logging [WARNING] - org.bdgenomics.utils.misc.HadoopUtil$ [WARNING] - org.bdgenomics.utils.misc.MathUtils$$anonfun$softmax$1 [WARNING] - org.bdgenomics.utils.misc.MathUtils$ [WARNING] - 1 more... [WARNING] utils-intervalrdd-spark2_2.11-0.2.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 51 overlapping classes: [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$ [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$collect$2 [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$4 [WARNING] - org.bdgenomics.utils.interval.array.Interval$class [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$get$1 [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$4 [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$1 [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$ [WARNING] - org.bdgenomics.utils.interval.rdd.IntervalRDD$$anonfun$filter$1 [WARNING] - org.bdgenomics.utils.interval.array.IntervalArray$$anonfun$mapValues$1 [WARNING] - 41 more... [WARNING] stream-2.7.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 78 overlapping classes: [WARNING] - com.clearspring.analytics.stream.cardinality.HyperLogLog [WARNING] - com.clearspring.analytics.stream.membership.DataOutputBuffer [WARNING] - com.clearspring.analytics.stream.quantile.TDigest [WARNING] - com.clearspring.analytics.stream.cardinality.HyperLogLog$SerializationHolder [WARNING] - com.clearspring.analytics.util.ListNode2 [WARNING] - com.clearspring.analytics.stream.frequency.CountMinSketch [WARNING] - com.clearspring.analytics.util.DoublyLinkedList [WARNING] - com.clearspring.analytics.stream.cardinality.CountThenEstimate$CountThenEstimateMergeException [WARNING] - com.clearspring.analytics.stream.quantile.QDigest$1 [WARNING] - com.clearspring.analytics.stream.cardinality.HyperLogLog$HyperLogLogMergeException [WARNING] - 68 more... [WARNING] xz-1.5.jar, mango-core-0.0.3-SNAPSHOT.jar define 105 overlapping classes: [WARNING] - org.tukaani.xz.lzma.LZMADecoder$LengthDecoder [WARNING] - org.tukaani.xz.index.IndexDecoder [WARNING] - org.tukaani.xz.lzma.LZMADecoder [WARNING] - org.tukaani.xz.lzma.LZMAEncoderFast [WARNING] - org.tukaani.xz.lzma.LZMAEncoder$LengthEncoder [WARNING] - org.tukaani.xz.BlockOutputStream [WARNING] - org.tukaani.xz.simple.SimpleFilter [WARNING] - org.tukaani.xz.rangecoder.RangeCoder [WARNING] - org.tukaani.xz.XZOutputStream [WARNING] - org.tukaani.xz.UncompressedLZMA2OutputStream [WARNING] - 95 more... [WARNING] aopalliance-1.0.jar, mango-core-0.0.3-SNAPSHOT.jar, aopalliance-repackaged-2.4.0-b34.jar define 9 overlapping classes: [WARNING] - org.aopalliance.intercept.ConstructorInterceptor [WARNING] - org.aopalliance.intercept.MethodInvocation [WARNING] - org.aopalliance.intercept.MethodInterceptor [WARNING] - org.aopalliance.intercept.Invocation [WARNING] - org.aopalliance.aop.AspectException [WARNING] - org.aopalliance.intercept.Interceptor [WARNING] - org.aopalliance.intercept.Joinpoint [WARNING] - org.aopalliance.aop.Advice [WARNING] - org.aopalliance.intercept.ConstructorInvocation [WARNING] mango-core-0.0.3-SNAPSHOT.jar, slf4j-api-1.7.7.jar define 24 overlapping classes: [WARNING] - org.slf4j.helpers.SubstituteLogger [WARNING] - org.slf4j.ILoggerFactory [WARNING] - org.slf4j.MDC [WARNING] - org.slf4j.helpers.BasicMDCAdapter [WARNING] - org.slf4j.spi.MDCAdapter [WARNING] - org.slf4j.LoggerFactory [WARNING] - org.slf4j.helpers.Util [WARNING] - org.slf4j.helpers.NOPLogger [WARNING] - org.slf4j.helpers.NOPLoggerFactory [WARNING] - org.slf4j.helpers.SubstituteLoggerFactory [WARNING] - 14 more... [WARNING] avro-ipc-1.7.7.jar, mango-core-0.0.3-SNAPSHOT.jar define 114 overlapping classes: [WARNING] - org.apache.avro.ipc.HandshakeRequest$1 [WARNING] - org.apache.avro.ipc.stats.Histogram [WARNING] - org.apache.avro.ipc.stats.Histogram$Entry [WARNING] - org.apache.avro.ipc.trace.Span$Builder [WARNING] - org.apache.avro.ipc.trace.TraceNode [WARNING] - org.apache.avro.ipc.specific.SpecificRequestor [WARNING] - org.apache.avro.ipc.stats.Histogram$SegmenterException [WARNING] - org.apache.avro.ipc.SaslSocketServer$AnonymousServer [WARNING] - org.apache.avro.ipc.stats.Histogram$Segmenter [WARNING] - org.apache.avro.ipc.SaslSocketServer$2 [WARNING] - 104 more... [WARNING] metrics-graphite-3.1.5.jar, mango-core-0.0.3-SNAPSHOT.jar define 10 overlapping classes: [WARNING] - com.codahale.metrics.graphite.PickledGraphite$MetricTuple [WARNING] - com.codahale.metrics.graphite.GraphiteReporter$Builder [WARNING] - com.codahale.metrics.graphite.Graphite [WARNING] - com.codahale.metrics.graphite.GraphiteRabbitMQ$1 [WARNING] - com.codahale.metrics.graphite.GraphiteSender [WARNING] - com.codahale.metrics.graphite.PickledGraphite [WARNING] - com.codahale.metrics.graphite.GraphiteUDP [WARNING] - com.codahale.metrics.graphite.GraphiteReporter [WARNING] - com.codahale.metrics.graphite.GraphiteReporter$1 [WARNING] - com.codahale.metrics.graphite.GraphiteRabbitMQ [WARNING] jersey-client-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 111 overlapping classes: [WARNING] - org.glassfish.jersey.client.ChunkParser [WARNING] - org.glassfish.jersey.client.HttpUrlConnectorProvider [WARNING] - org.glassfish.jersey.client.JerseyInvocation$EntityPresence [WARNING] - org.glassfish.jersey.client.ResponseCallback [WARNING] - org.glassfish.jersey.client.authentication.RequestAuthenticationException [WARNING] - org.glassfish.jersey.client.JerseyInvocation$5 [WARNING] - org.glassfish.jersey.client.ClientConfig$State$4 [WARNING] - org.glassfish.jersey.client.ClientResponse$1 [WARNING] - org.glassfish.jersey.client.InboundJaxrsResponse$2 [WARNING] - org.glassfish.jersey.client.internal.HttpUrlConnector$5 [WARNING] - 101 more... [WARNING] hk2-utils-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar define 80 overlapping classes: [WARNING] - org.glassfish.hk2.utilities.cache.Cache$1 [WARNING] - org.jvnet.hk2.component.MultiMap$1 [WARNING] - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperImpl$4 [WARNING] - org.glassfish.hk2.utilities.cache.internal.WeakCARCacheImpl$1 [WARNING] - org.glassfish.hk2.utilities.cache.LRUHybridCache [WARNING] - org.glassfish.hk2.utilities.cache.LRUCache [WARNING] - org.glassfish.hk2.utilities.reflection.internal.ClassReflectionHelperUtilities [WARNING] - org.glassfish.hk2.utilities.reflection.ClassReflectionHelper [WARNING] - org.glassfish.hk2.utilities.cache.CacheEntry [WARNING] - org.glassfish.hk2.utilities.reflection.ReflectionHelper [WARNING] - 70 more... [WARNING] jsr203hadoop-1.0.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 27 overlapping classes: [WARNING] - hdfs.jsr203.HadoopDirectoryStream [WARNING] - hdfs.jsr203.HadoopPath [WARNING] - hdfs.jsr203.HadoopFileSystem$1 [WARNING] - hdfs.jsr203.HadoopFileOwnerAttributeView [WARNING] - hdfs.jsr203.HadoopUserPrincipal [WARNING] - hdfs.jsr203.IAttributeReader [WARNING] - hdfs.jsr203.HadoopPath$1 [WARNING] - hdfs.jsr203.HadoopBasicFileAttributes [WARNING] - hdfs.jsr203.HadoopDirectoryStream$1 [WARNING] - hdfs.jsr203.package-info [WARNING] - 17 more... [WARNING] animal-sniffer-annotations-1.17.jar, mango-core-0.0.3-SNAPSHOT.jar define 1 overlapping classes: [WARNING] - org.codehaus.mojo.animal_sniffer.IgnoreJRERequirement [WARNING] commons-crypto-1.0.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 46 overlapping classes: [WARNING] - org.apache.commons.crypto.stream.PositionedCryptoInputStream [WARNING] - org.apache.commons.crypto.cipher.OpenSsl [WARNING] - org.apache.commons.crypto.random.CryptoRandomFactory$RandomProvider [WARNING] - org.apache.commons.crypto.cipher.OpenSsl$AlgorithmMode [WARNING] - org.apache.commons.crypto.utils.Utils$DefaultPropertiesHolder [WARNING] - org.apache.commons.crypto.Crypto [WARNING] - org.apache.commons.crypto.cipher.OpenSsl$Transform [WARNING] - org.apache.commons.crypto.OpenSslInfoNative [WARNING] - org.apache.commons.crypto.stream.CtrCryptoOutputStream [WARNING] - org.apache.commons.crypto.jna.OpenSslNativeJna [WARNING] - 36 more... [WARNING] validation-api-1.1.0.Final.jar, mango-core-0.0.3-SNAPSHOT.jar define 106 overlapping classes: [WARNING] - javax.validation.ConstraintDeclarationException [WARNING] - javax.validation.GroupDefinitionException [WARNING] - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder$LeafNodeBuilderDefinedContext [WARNING] - javax.validation.metadata.ParameterDescriptor [WARNING] - javax.validation.Validator [WARNING] - javax.validation.ConstraintValidatorContext$ConstraintViolationBuilder [WARNING] - javax.validation.constraints.AssertTrue$List [WARNING] - javax.validation.constraints.Past [WARNING] - javax.validation.metadata.GroupConversionDescriptor [WARNING] - javax.validation.constraints.Max [WARNING] - 96 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, leveldbjni-all-1.8.jar define 75 overlapping classes: [WARNING] - org.fusesource.leveldbjni.internal.NativeObject [WARNING] - org.fusesource.leveldbjni.internal.NativeDB$DBJNI [WARNING] - org.fusesource.leveldbjni.internal.NativeCache [WARNING] - org.fusesource.leveldbjni.internal.NativeComparator$ComparatorJNI [WARNING] - org.fusesource.leveldbjni.internal.NativeIterator [WARNING] - org.iq80.leveldb.WriteBatch [WARNING] - org.fusesource.hawtjni.runtime.ClassFlag [WARNING] - org.fusesource.leveldbjni.internal.NativeBuffer$1 [WARNING] - org.iq80.leveldb.DBComparator [WARNING] - org.fusesource.leveldbjni.internal.NativeBuffer$Pool [WARNING] - 65 more... [WARNING] osgi-resource-locator-1.0.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 12 overlapping classes: [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$1 [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoader$ProviderFactory [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoader [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$ProvidersPerBundle [WARNING] - org.glassfish.hk2.osgiresourcelocator.ResourceFinderImpl [WARNING] - org.glassfish.hk2.osgiresourcelocator.ResourceFinder [WARNING] - org.glassfish.hk2.osgiresourcelocator.Activator [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$DefaultFactory [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl [WARNING] - org.glassfish.hk2.osgiresourcelocator.ServiceLoaderImpl$BundleTracker [WARNING] - 2 more... [WARNING] commons-lang3-3.5.jar, mango-core-0.0.3-SNAPSHOT.jar define 260 overlapping classes: [WARNING] - org.apache.commons.lang3.time.StopWatch$State$1 [WARNING] - org.apache.commons.lang3.ThreadUtils$1 [WARNING] - org.apache.commons.lang3.ThreadUtils$ThreadGroupPredicate [WARNING] - org.apache.commons.lang3.builder.MultilineRecursiveToStringStyle [WARNING] - org.apache.commons.lang3.concurrent.AbstractCircuitBreaker [WARNING] - org.apache.commons.lang3.SerializationUtils [WARNING] - org.apache.commons.lang3.time.FastDatePrinter$TwentyFourHourField [WARNING] - org.apache.commons.lang3.LocaleUtils [WARNING] - org.apache.commons.lang3.concurrent.ConcurrentException [WARNING] - org.apache.commons.lang3.CharRange [WARNING] - 250 more... [WARNING] jersey-media-jaxb-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 47 overlapping classes: [WARNING] - org.glassfish.jersey.jaxb.internal.XmlRootElementJaxbProvider$App [WARNING] - org.glassfish.jersey.jaxb.internal.XmlJaxbElementProvider$General [WARNING] - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider$General [WARNING] - org.glassfish.jersey.jaxb.internal.JaxbStringReaderProvider$1 [WARNING] - org.glassfish.jersey.jaxb.internal.XmlRootObjectJaxbProvider [WARNING] - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$4 [WARNING] - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$General [WARNING] - org.glassfish.jersey.jaxb.internal.JaxbMessagingBinder [WARNING] - org.glassfish.jersey.jaxb.internal.AbstractJaxbProvider$2 [WARNING] - org.glassfish.jersey.jaxb.internal.XmlCollectionJaxbProvider$Text [WARNING] - 37 more... [WARNING] paranamer-2.8.jar, mango-core-0.0.3-SNAPSHOT.jar define 21 overlapping classes: [WARNING] - com.thoughtworks.paranamer.PositionalParanamer [WARNING] - com.thoughtworks.paranamer.JavadocParanamer [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer$Type [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer$1 [WARNING] - com.thoughtworks.paranamer.JavadocParanamer$DirJavadocProvider [WARNING] - com.thoughtworks.paranamer.AnnotationParanamer$Jsr330Helper [WARNING] - com.thoughtworks.paranamer.BytecodeReadingParanamer$TypeCollector [WARNING] - com.thoughtworks.paranamer.AnnotationParanamer [WARNING] - com.thoughtworks.paranamer.NullParanamer [WARNING] - 11 more... [WARNING] chill_2.11-0.8.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 150 overlapping classes: [WARNING] - com.twitter.chill.Tuple11Serializer [WARNING] - com.twitter.chill.InnerClosureFinder [WARNING] - com.twitter.chill.Instantiators$$anonfun$reflectAsm$1 [WARNING] - com.twitter.chill.RichKryo$$anonfun$fromInputStream$1 [WARNING] - com.twitter.chill.package$$anon$3 [WARNING] - com.twitter.chill.JavaIterableWrapperSerializer [WARNING] - com.twitter.chill.Instantiators$$anonfun$newOrElse$1 [WARNING] - com.twitter.chill.SortedMapSerializer$$anonfun$write$1 [WARNING] - com.twitter.chill.package$$anon$5$$anonfun$apply$2 [WARNING] - com.twitter.chill.Tuple8Serializer [WARNING] - 140 more... [WARNING] convert-ga4gh-0.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 20 overlapping classes: [WARNING] - org.bdgenomics.convert.ga4gh.CigarOperatorToOperation$1 [WARNING] - org.bdgenomics.convert.ga4gh.BdgenomicsVariantToGa4ghVariant [WARNING] - org.bdgenomics.convert.ga4gh.CigarToCigarUnits [WARNING] - org.bdgenomics.convert.ga4gh.BdgenomicsFeatureToGa4ghFeature [WARNING] - org.bdgenomics.convert.ga4gh.StringToOntologyTerm [WARNING] - org.bdgenomics.convert.ga4gh.ProgramToProcessingStep [WARNING] - org.bdgenomics.convert.ga4gh.Ga4ghReadGroupToBdgenomicsReadGroup [WARNING] - org.bdgenomics.convert.ga4gh.Ga4ghOntologyTermToBdgenomicsOntologyTerm [WARNING] - org.bdgenomics.convert.ga4gh.ProcessingStepToProgram [WARNING] - org.bdgenomics.convert.ga4gh.BdgenomicsStrandToGa4ghStrand [WARNING] - 10 more... [WARNING] parquet-encoding-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 184 overlapping classes: [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer14 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingBE$Packer24 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer10 [WARNING] - org.apache.parquet.column.values.bitpacking.LemireBitPackingBE$Packer7 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer20 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer7 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer30 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer13 [WARNING] - org.apache.parquet.column.values.bitpacking.ByteBitPackingLE$Packer23 [WARNING] - org.apache.parquet.column.values.bitpacking.LemireBitPackingLE$Packer19 [WARNING] - 174 more... [WARNING] slf4j-log4j12-1.7.16.jar, mango-core-0.0.3-SNAPSHOT.jar define 6 overlapping classes: [WARNING] - org.slf4j.impl.Log4jLoggerAdapter [WARNING] - org.slf4j.impl.Log4jMDCAdapter [WARNING] - org.slf4j.impl.StaticMarkerBinder [WARNING] - org.slf4j.impl.Log4jLoggerFactory [WARNING] - org.slf4j.impl.StaticLoggerBinder [WARNING] - org.slf4j.impl.StaticMDCBinder [WARNING] mango-core-0.0.3-SNAPSHOT.jar, ga4gh-schemas-0.6.0a10.jar define 541 overlapping classes: [WARNING] - ga4gh.AlleleAnnotations$TranscriptEffectOrBuilder [WARNING] - ga4gh.PeerServiceOuterClass$GetInfoResponse$1 [WARNING] - ga4gh.MetadataServiceOuterClass$GetDatasetRequestOrBuilder [WARNING] - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest [WARNING] - ga4gh.RnaQuantificationServiceOuterClass$SearchExpressionLevelsRequest$Builder [WARNING] - ga4gh.GenotypePhenotypeServiceOuterClass$EvidenceQuery$1 [WARNING] - ga4gh.BioMetadataServiceOuterClass$SearchBiosamplesRequest$1 [WARNING] - ga4gh.ReferenceServiceOuterClass$ListReferenceBasesResponseOrBuilder [WARNING] - ga4gh.VariantServiceOuterClass$SearchCallSetsRequest [WARNING] - ga4gh.RnaQuantificationServiceOuterClass$GetExpressionLevelRequest [WARNING] - 531 more... [WARNING] parquet-avro-1.8.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 83 overlapping classes: [WARNING] - org.apache.parquet.avro.AvroRecordConverter$AvroCollectionConverter$1 [WARNING] - org.apache.parquet.avro.AvroParquetInputFormat [WARNING] - org.apache.parquet.avro.AvroRecordConverter$AvroArrayConverter$7 [WARNING] - org.apache.parquet.avro.AvroConverters$AvroPrimitiveConverter [WARNING] - org.apache.parquet.avro.AvroWriteSupport$TwoLevelListWriter [WARNING] - org.apache.parquet.avro.AvroConverters$FieldIntegerConverter [WARNING] - org.apache.parquet.avro.AvroCompatRecordMaterializer [WARNING] - org.apache.parquet.avro.AvroIndexedRecordConverter$AvroArrayConverter$1 [WARNING] - org.apache.parquet.avro.AvroWriteSupport$ListWriter [WARNING] - org.apache.parquet.avro.AvroConverters$FieldByteBufferConverter [WARNING] - 73 more... [WARNING] javax.annotation-api-1.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 15 overlapping classes: [WARNING] - javax.annotation.ManagedBean [WARNING] - javax.annotation.PreDestroy [WARNING] - javax.annotation.Generated [WARNING] - javax.annotation.Resource$AuthenticationType [WARNING] - javax.annotation.security.DeclareRoles [WARNING] - javax.annotation.Priority [WARNING] - javax.annotation.Resource [WARNING] - javax.annotation.security.DenyAll [WARNING] - javax.annotation.security.RunAs [WARNING] - javax.annotation.sql.DataSourceDefinitions [WARNING] - 5 more... [WARNING] minlog-1.3.0.jar, minlog-1.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 2 overlapping classes: [WARNING] - com.esotericsoftware.minlog.Log [WARNING] - com.esotericsoftware.minlog.Log$Logger [WARNING] jersey-common-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 474 overlapping classes: [WARNING] - org.glassfish.jersey.internal.inject.ContextInjectionResolver$Binder [WARNING] - org.glassfish.jersey.internal.ServiceFinder$ServiceIteratorProvider [WARNING] - org.glassfish.jersey.message.internal.HttpHeaderReader$1 [WARNING] - org.glassfish.jersey.internal.util.collection.KeyComparatorHashMap$1 [WARNING] - org.glassfish.jersey.uri.UriTemplate$1ValuesFromArrayStrategy [WARNING] - org.glassfish.jersey.message.internal.TracingLogger$Level [WARNING] - org.glassfish.jersey.internal.util.PropertyAlias [WARNING] - org.glassfish.jersey.uri.UriTemplate$3 [WARNING] - org.glassfish.jersey.model.internal.ComponentBag$7 [WARNING] - org.glassfish.jersey.spi.AbstractThreadPoolProvider [WARNING] - 464 more... [WARNING] convert-htsjdk-0.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 3 overlapping classes: [WARNING] - org.bdgenomics.convert.htsjdk.HtsjdkModule [WARNING] - org.bdgenomics.convert.htsjdk.ConversionStringencyToValidationStringency [WARNING] - org.bdgenomics.convert.htsjdk.ValidationStringencyToConversionStringency [WARNING] mango-core-0.0.3-SNAPSHOT.jar, py4j-0.10.7.jar define 67 overlapping classes: [WARNING] - py4j.reflection.TypeConverter [WARNING] - py4j.Py4JJavaServer [WARNING] - py4j.Py4JNetworkException [WARNING] - py4j.reflection.PythonProxyHandler [WARNING] - py4j.reflection.MethodInvoker$1 [WARNING] - py4j.commands.JVMViewCommand [WARNING] - py4j.Py4JClientConnection [WARNING] - py4j.model.Py4JClass [WARNING] - py4j.commands.ReflectionCommand [WARNING] - py4j.commands.MemoryCommand [WARNING] - 57 more... [WARNING] curator-framework-2.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 167 overlapping classes: [WARNING] - org.apache.curator.framework.imps.TempGetDataBuilderImpl [WARNING] - org.apache.curator.framework.imps.GetDataBuilderImpl$2 [WARNING] - org.apache.curator.framework.imps.CuratorFrameworkImpl$4 [WARNING] - org.apache.curator.framework.state.ConnectionState [WARNING] - org.apache.curator.framework.api.CreateModable [WARNING] - org.apache.curator.framework.imps.SetDataBuilderImpl$4 [WARNING] - org.apache.curator.framework.imps.PathAndBytes [WARNING] - org.apache.curator.framework.api.ACLVersionBackgroundPathable [WARNING] - org.apache.curator.framework.api.ACLCreateModeBackgroundPathAndBytesable [WARNING] - org.apache.curator.framework.listen.ListenerContainer [WARNING] - 157 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, scalap-2.11.11.jar define 581 overlapping classes: [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigEntryParsers$$anonfun$25$$anonfun$apply$13 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$_pmt$1$1 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigParser$$anonfun$scalaSigFromAnnotation$2 [WARNING] - scala.tools.scalap.scalax.rules.StateRules$$anonfun$anyOf$2 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ConstantType$ [WARNING] - scala.tools.scalap.scalax.rules.scalasig.Symbol$class [WARNING] - scala.tools.scalap.scalax.rules.Rule$$anonfun$flatMap$1 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.ScalaSigPrinter$$anonfun$printSymbolAttributes$1 [WARNING] - scala.tools.scalap.scalax.rules.InRule$$anonfun$unary_$bang$1$$anonfun$apply$1 [WARNING] - scala.tools.scalap.scalax.rules.scalasig.NoType$ [WARNING] - 571 more... [WARNING] jersey-container-servlet-core-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 51 overlapping classes: [WARNING] - org.glassfish.jersey.servlet.WebComponent$3 [WARNING] - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder [WARNING] - org.glassfish.jersey.servlet.internal.LocalizationMessages [WARNING] - org.glassfish.jersey.servlet.WebConfig [WARNING] - org.glassfish.jersey.servlet.spi.FilterUrlMappingsProvider [WARNING] - org.glassfish.jersey.servlet.WebComponent$WebComponentBinder$3 [WARNING] - org.glassfish.jersey.servlet.ServletPropertiesDelegate [WARNING] - org.glassfish.jersey.servlet.WebComponent$7 [WARNING] - org.glassfish.jersey.servlet.internal.ResponseWriter [WARNING] - org.glassfish.jersey.servlet.WebAppResourcesScanner$1 [WARNING] - 41 more... [WARNING] gson-2.2.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 153 overlapping classes: [WARNING] - com.google.gson.internal.bind.JsonTreeWriter [WARNING] - com.google.gson.internal.Excluder [WARNING] - com.google.gson.JsonDeserializationContext [WARNING] - com.google.gson.FieldNamingPolicy$5 [WARNING] - com.google.gson.internal.LinkedTreeMap$KeySet [WARNING] - com.google.gson.internal.$Gson$Types [WARNING] - com.google.gson.internal.UnsafeAllocator$2 [WARNING] - com.google.gson.internal.bind.SqlDateTypeAdapter$1 [WARNING] - com.google.gson.FieldAttributes [WARNING] - com.google.gson.internal.$Gson$Types$ParameterizedTypeImpl [WARNING] - 143 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-json-3.1.5.jar define 11 overlapping classes: [WARNING] - com.codahale.metrics.json.MetricsModule$MetricRegistrySerializer [WARNING] - com.codahale.metrics.json.HealthCheckModule$HealthCheckResultSerializer [WARNING] - com.codahale.metrics.json.HealthCheckModule [WARNING] - com.codahale.metrics.json.MetricsModule$TimerSerializer [WARNING] - com.codahale.metrics.json.MetricsModule$GaugeSerializer [WARNING] - com.codahale.metrics.json.MetricsModule$1 [WARNING] - com.codahale.metrics.json.MetricsModule$MeterSerializer [WARNING] - com.codahale.metrics.json.MetricsModule [WARNING] - com.codahale.metrics.json.MetricsModule$HistogramSerializer [WARNING] - com.codahale.metrics.json.MetricsModule$CounterSerializer [WARNING] - 1 more... [WARNING] hadoop-bam-7.9.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 115 overlapping classes: [WARNING] - org.seqdoop.hadoop_bam.BAMSplitGuesser [WARNING] - org.seqdoop.hadoop_bam.util.SAMHeaderReader [WARNING] - org.seqdoop.hadoop_bam.QseqInputFormat [WARNING] - org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter [WARNING] - org.seqdoop.hadoop_bam.FastaInputFormat$1 [WARNING] - org.seqdoop.hadoop_bam.util.SAMOutputPreparer$1 [WARNING] - org.seqdoop.hadoop_bam.QseqOutputFormat$QseqRecordWriter [WARNING] - org.seqdoop.hadoop_bam.FastaInputFormat [WARNING] - org.seqdoop.hadoop_bam.LineReader [WARNING] - org.seqdoop.hadoop_bam.util.BGZFCodec [WARNING] - 105 more... [WARNING] avro-1.8.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 1172 overlapping classes: [WARNING] - org.apache.avro.message.SchemaStore [WARNING] - avro.shaded.com.google.common.collect.SingletonImmutableList [WARNING] - org.apache.avro.io.EncoderFactory$DefaultEncoderFactory [WARNING] - avro.shaded.com.google.common.collect.Iterables$15 [WARNING] - org.apache.avro.GuavaClasses [WARNING] - avro.shaded.com.google.common.collect.Sets$PowerSet$1$1 [WARNING] - avro.shaded.com.google.common.collect.RegularImmutableMap [WARNING] - org.apache.avro.generic.GenericDatumReader$2 [WARNING] - avro.shaded.com.google.common.collect.Synchronized$SynchronizedSortedSet [WARNING] - org.apache.avro.file.BZip2Codec [WARNING] - 1162 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, spark-tags_2.11-2.3.3.jar define 11 overlapping classes: [WARNING] - org.apache.spark.annotation.Since [WARNING] - org.apache.spark.annotation.InterfaceStability$Stable [WARNING] - org.apache.spark.annotation.package [WARNING] - org.apache.spark.annotation.DeveloperApi [WARNING] - org.apache.spark.annotation.InterfaceStability$Evolving [WARNING] - org.apache.spark.annotation.package$ [WARNING] - org.apache.spark.annotation.Experimental [WARNING] - org.apache.spark.annotation.AlphaComponent [WARNING] - org.apache.spark.annotation.Private [WARNING] - org.apache.spark.annotation.InterfaceStability [WARNING] - 1 more... [WARNING] json4s-jackson_2.11-3.2.11.jar, mango-core-0.0.3-SNAPSHOT.jar define 27 overlapping classes: [WARNING] - org.json4s.jackson.JsonMethods$class [WARNING] - org.json4s.jackson.Json [WARNING] - org.json4s.jackson.Json$ [WARNING] - org.json4s.jackson.JValueSerializerResolver$ [WARNING] - org.json4s.jackson.Json4sModule$ [WARNING] - org.json4s.jackson.JsonMethods$$anonfun$parseOpt$1 [WARNING] - org.json4s.jackson.JValueDeserializerResolver$ [WARNING] - org.json4s.jackson.package [WARNING] - org.json4s.jackson.package$ [WARNING] - org.json4s.jackson.Json4sScalaModule$ [WARNING] - 17 more... [WARNING] parquet-common-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 32 overlapping classes: [WARNING] - org.apache.parquet.SemanticVersion$SemanticVersionParseException [WARNING] - org.apache.parquet.glob.GlobNode$GlobNodeSequence [WARNING] - org.apache.parquet.Ints [WARNING] - org.apache.parquet.Version [WARNING] - org.apache.parquet.glob.GlobNode$Atom [WARNING] - org.apache.parquet.SemanticVersion$NumberOrString [WARNING] - org.apache.parquet.Files [WARNING] - org.apache.parquet.ParquetRuntimeException [WARNING] - org.apache.parquet.glob.GlobNode [WARNING] - org.apache.parquet.io.InputFile [WARNING] - 22 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar, commons-logging-1.1.3.jar define 6 overlapping classes: [WARNING] - org.apache.commons.logging.impl.SimpleLog$1 [WARNING] - org.apache.commons.logging.Log [WARNING] - org.apache.commons.logging.impl.SimpleLog [WARNING] - org.apache.commons.logging.LogConfigurationException [WARNING] - org.apache.commons.logging.impl.NoOpLog [WARNING] - org.apache.commons.logging.LogFactory [WARNING] lz4-java-1.4.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 77 overlapping classes: [WARNING] - net.jpountz.xxhash.AbstractStreamingXXHash32Java [WARNING] - net.jpountz.lz4.LZ4BlockInputStream [WARNING] - net.jpountz.lz4.LZ4FrameOutputStream [WARNING] - net.jpountz.xxhash.XXHash32JNI [WARNING] - net.jpountz.lz4.LZ4BlockOutputStream [WARNING] - net.jpountz.lz4.LZ4JNI [WARNING] - net.jpountz.lz4.LZ4JavaUnsafeFastDecompressor [WARNING] - net.jpountz.lz4.LZ4SafeUtils [WARNING] - net.jpountz.xxhash.StreamingXXHash32JNI$Factory [WARNING] - net.jpountz.util.UnsafeUtils [WARNING] - 67 more... [WARNING] lift-json_2.11-3.3.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 390 overlapping classes: [WARNING] - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$deserialize$2 [WARNING] - net.liftweb.json.TypeInfo$ [WARNING] - net.liftweb.json.JsonAST$JString$ [WARNING] - net.liftweb.json.JsonAST$RenderSettings$ [WARNING] - net.liftweb.json.JsonAST$JDouble$ [WARNING] - net.liftweb.json.TypeHints$CompositeTypeHints$$anonfun$classFor$2 [WARNING] - net.liftweb.json.JsonAST$RenderSpecialDoubleValuesAsIs$ [WARNING] - net.liftweb.json.Meta$$anonfun$net$liftweb$json$Meta$$fieldMapping$1$4 [WARNING] - net.liftweb.json.Meta$DeclaredConstructor [WARNING] - net.liftweb.json.Formats$$anonfun$customSerializer$1 [WARNING] - 380 more... [WARNING] httpcore-4.4.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 254 overlapping classes: [WARNING] - org.apache.http.protocol.HttpRequestHandler [WARNING] - org.apache.http.impl.io.ChunkedOutputStream [WARNING] - org.apache.http.protocol.ChainBuilder [WARNING] - org.apache.http.impl.entity.DisallowIdentityContentLengthStrategy [WARNING] - org.apache.http.impl.ConnSupport [WARNING] - org.apache.http.impl.io.DefaultHttpResponseParserFactory [WARNING] - org.apache.http.HttpClientConnection [WARNING] - org.apache.http.NameValuePair [WARNING] - org.apache.http.protocol.HttpExpectationVerifier [WARNING] - org.apache.http.protocol.UriPatternMatcher [WARNING] - 244 more... [WARNING] jackson-mapper-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 502 overlapping classes: [WARNING] - org.codehaus.jackson.map.ext.DOMSerializer [WARNING] - org.codehaus.jackson.node.POJONode [WARNING] - org.codehaus.jackson.map.ext.JodaDeserializers$LocalDateDeserializer [WARNING] - org.codehaus.jackson.map.ser.StdSerializers$UtilDateSerializer [WARNING] - org.codehaus.jackson.map.deser.std.JsonNodeDeserializer$ArrayDeserializer [WARNING] - org.codehaus.jackson.map.deser.std.PrimitiveArrayDeserializers$StringDeser [WARNING] - org.codehaus.jackson.map.util.Comparators$1 [WARNING] - org.codehaus.jackson.map.util.StdDateFormat [WARNING] - org.codehaus.jackson.map.KeyDeserializer [WARNING] - org.codehaus.jackson.map.MapperConfig$Impl [WARNING] - 492 more... [WARNING] jsr305-1.3.9.jar, mango-core-0.0.3-SNAPSHOT.jar define 35 overlapping classes: [WARNING] - javax.annotation.RegEx [WARNING] - javax.annotation.concurrent.Immutable [WARNING] - javax.annotation.meta.TypeQualifierDefault [WARNING] - javax.annotation.meta.TypeQualifier [WARNING] - javax.annotation.Syntax [WARNING] - javax.annotation.CheckReturnValue [WARNING] - javax.annotation.CheckForNull [WARNING] - javax.annotation.Nonnull [WARNING] - javax.annotation.meta.TypeQualifierNickname [WARNING] - javax.annotation.MatchesPattern [WARNING] - 25 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, args4j-2.0.31.jar define 71 overlapping classes: [WARNING] - org.kohsuke.args4j.spi.DoubleOptionHandler [WARNING] - org.kohsuke.args4j.spi.MethodSetter [WARNING] - org.kohsuke.args4j.spi.StringArrayOptionHandler [WARNING] - org.kohsuke.args4j.spi.MacAddressOptionHandler [WARNING] - org.kohsuke.args4j.spi.SubCommand [WARNING] - org.kohsuke.args4j.spi.PatternOptionHandler [WARNING] - org.kohsuke.args4j.ParserProperties$1 [WARNING] - org.kohsuke.args4j.OptionHandlerFilter$2 [WARNING] - org.kohsuke.args4j.spi.MultiFileOptionHandler [WARNING] - org.kohsuke.args4j.Localizable [WARNING] - 61 more... [WARNING] ngs-java-2.9.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 73 overlapping classes: [WARNING] - ngs.itf.ReadItf [WARNING] - gov.nih.nlm.ncbi.ngs.error.cause.JvmErrorCause [WARNING] - ngs.ReferenceIterator [WARNING] - gov.nih.nlm.ncbi.ngs.Manager$1 [WARNING] - gov.nih.nlm.ncbi.ngs.LMProperties [WARNING] - gov.nih.nlm.ncbi.ngs.error.LibraryLoadError [WARNING] - gov.nih.nlm.ncbi.ngs.LibDependencies [WARNING] - gov.nih.nlm.ncbi.ngs.error.cause.ConnectionProblemCause [WARNING] - ngs.itf.PileupEventItf [WARNING] - gov.nih.nlm.ncbi.ngs.LibManager$Location [WARNING] - 63 more... [WARNING] commons-net-2.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 137 overlapping classes: [WARNING] - org.apache.commons.net.telnet.SimpleOptionHandler [WARNING] - org.apache.commons.net.ftp.parser.FTPFileEntryParserFactory [WARNING] - org.apache.commons.net.DefaultDatagramSocketFactory [WARNING] - org.apache.commons.net.ftp.parser.ConfigurableFTPFileEntryParserImpl [WARNING] - org.apache.commons.net.ntp.NTPUDPClient [WARNING] - org.apache.commons.net.util.SubnetUtils$1 [WARNING] - org.apache.commons.net.tftp.TFTP [WARNING] - org.apache.commons.net.ftp.FTPClient [WARNING] - org.apache.commons.net.echo.EchoTCPClient [WARNING] - org.apache.commons.net.telnet.Telnet [WARNING] - 127 more... [WARNING] parquet-scala_2.10-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 19 overlapping classes: [WARNING] - org.apache.parquet.filter2.dsl.Dsl$SupportsEqNotEq [WARNING] - org.apache.parquet.filter2.dsl.Dsl$FloatColumn$ [WARNING] - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$Column$class [WARNING] - org.apache.parquet.filter2.dsl.Dsl [WARNING] - org.apache.parquet.filter2.dsl.Dsl$FloatColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$LongColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$BinaryColumn [WARNING] - org.apache.parquet.filter2.dsl.Dsl$IntColumn$ [WARNING] - org.apache.parquet.filter2.dsl.Dsl$DoubleColumn$ [WARNING] - 9 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, zstd-jni-1.3.2-2.jar define 8 overlapping classes: [WARNING] - com.github.luben.zstd.ZstdDirectBufferDecompressingStream [WARNING] - com.github.luben.zstd.ZstdOutputStream [WARNING] - com.github.luben.zstd.ZstdDictCompress [WARNING] - com.github.luben.zstd.ZstdDictDecompress [WARNING] - com.github.luben.zstd.ZstdInputStream [WARNING] - com.github.luben.zstd.Zstd [WARNING] - com.github.luben.zstd.util.Native [WARNING] - com.github.luben.zstd.ZstdDirectBufferCompressingStream [WARNING] javax.inject-2.4.0-b34.jar, javax.inject-1.jar, mango-core-0.0.3-SNAPSHOT.jar define 6 overlapping classes: [WARNING] - javax.inject.Inject [WARNING] - javax.inject.Singleton [WARNING] - javax.inject.Named [WARNING] - javax.inject.Scope [WARNING] - javax.inject.Provider [WARNING] - javax.inject.Qualifier [WARNING] ivy-2.4.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 744 overlapping classes: [WARNING] - org.apache.ivy.ant.IvyDeliver [WARNING] - org.apache.ivy.plugins.resolver.util.ApacheHttpURLLister [WARNING] - org.apache.ivy.ant.BuildOBRTask [WARNING] - org.apache.ivy.osgi.p2.P2MetadataParser$UnitsHandler$1 [WARNING] - org.apache.ivy.core.cache.ResolutionCacheManager [WARNING] - org.apache.ivy.osgi.repo.EditableRepoDescriptor [WARNING] - org.apache.ivy.plugins.parser.AbstractModuleDescriptorParser$AbstractParser [WARNING] - org.apache.ivy.plugins.latest.LatestLexicographicStrategy$1 [WARNING] - org.apache.ivy.osgi.repo.FSManifestIterable$3 [WARNING] - org.apache.ivy.util.url.HttpClientHandler [WARNING] - 734 more... [WARNING] jersey-server-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 665 overlapping classes: [WARNING] - org.glassfish.jersey.server.internal.inject.ParamConverters$TypeFromString [WARNING] - org.glassfish.jersey.server.internal.inject.QueryParamValueFactoryProvider [WARNING] - org.glassfish.jersey.server.internal.inject.ParamInjectionResolver [WARNING] - org.glassfish.jersey.server.internal.InternalServerProperties [WARNING] - org.glassfish.jersey.server.internal.inject.ParameterInjectionBinder$5 [WARNING] - jersey.repackaged.org.objectweb.asm.FieldWriter [WARNING] - org.glassfish.jersey.server.internal.RuntimeDelegateImpl [WARNING] - org.glassfish.jersey.server.internal.inject.ParamConverterFactory [WARNING] - org.glassfish.jersey.server.internal.monitoring.RequestEventImpl$Builder [WARNING] - org.glassfish.jersey.server.ContainerRequest [WARNING] - 655 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, javax.ws.rs-api-2.0.1.jar define 125 overlapping classes: [WARNING] - javax.ws.rs.ext.RuntimeDelegate$HeaderDelegate [WARNING] - javax.ws.rs.DefaultValue [WARNING] - javax.ws.rs.core.StreamingOutput [WARNING] - javax.ws.rs.HEAD [WARNING] - javax.ws.rs.ext.WriterInterceptor [WARNING] - javax.ws.rs.core.Request [WARNING] - javax.ws.rs.ext.Providers [WARNING] - javax.ws.rs.container.Suspended [WARNING] - javax.ws.rs.container.ConnectionCallback [WARNING] - javax.ws.rs.client.FactoryFinder [WARNING] - 115 more... [WARNING] jets3t-0.9.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 616 overlapping classes: [WARNING] - org.jets3t.service.acl.GroupGrantee [WARNING] - org.jets3t.service.multithread.CreateObjectsEvent [WARNING] - org.jets3t.service.model.S3BucketLoggingStatus [WARNING] - contribs.com.centerkey.utils.BareBonesBrowserLaunch [WARNING] - org.jets3t.service.impl.rest.CloudFrontXmlResponsesSaxParser$CacheBehaviorHandler [WARNING] - org.jets3t.apps.uploader.XmlGenerator$ObjectAndSignatureRequestDetails [WARNING] - org.jets3t.service.MultipartUploadChunk [WARNING] - org.jets3t.apps.cockpit.Cockpit$27 [WARNING] - org.jets3t.service.model.S3DeleteMarker [WARNING] - org.jets3t.gui.TableSorter$Row [WARNING] - 606 more... [WARNING] error_prone_annotations-2.2.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 22 overlapping classes: [WARNING] - com.google.errorprone.annotations.NoAllocation [WARNING] - com.google.errorprone.annotations.Var [WARNING] - com.google.errorprone.annotations.IncompatibleModifiers [WARNING] - com.google.errorprone.annotations.CompatibleWith [WARNING] - com.google.errorprone.annotations.concurrent.LockMethod [WARNING] - com.google.errorprone.annotations.FormatString [WARNING] - com.google.errorprone.annotations.DoNotCall [WARNING] - com.google.errorprone.annotations.Immutable [WARNING] - com.google.errorprone.annotations.RestrictedApi [WARNING] - com.google.errorprone.annotations.CompileTimeConstant [WARNING] - 12 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-parser-combinators_2.11-1.0.4.jar define 352 overlapping classes: [WARNING] - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$whitespace$1$$anonfun$apply$20$$anonfun$apply$21 [WARNING] - scala.util.parsing.combinator.ImplicitConversions$$anonfun$flatten5$1 [WARNING] - scala.util.parsing.combinator.Parsers$$anonfun$rep$1 [WARNING] - scala.util.parsing.json.Lexer$$anonfun$number$1$$anonfun$apply$16 [WARNING] - scala.util.parsing.combinator.Parsers$NoSuccess$$anonfun$1 [WARNING] - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$3$$anonfun$apply$3$$anonfun$apply$4 [WARNING] - scala.util.parsing.combinator.token.StdTokens$class [WARNING] - scala.util.parsing.json.Lexer$$anonfun$charSeq$10 [WARNING] - scala.util.parsing.combinator.Parsers$Parser$$anonfun$$tilde$greater$1 [WARNING] - scala.util.parsing.combinator.lexical.StdLexical$$anonfun$token$5 [WARNING] - 342 more... [WARNING] hk2-locator-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar define 95 overlapping classes: [WARNING] - org.jvnet.hk2.internal.PerLocatorUtilities$1 [WARNING] - org.jvnet.hk2.internal.Utilities$4 [WARNING] - org.jvnet.hk2.internal.ProxyUtilities$2 [WARNING] - org.jvnet.hk2.internal.ServiceLocatorImpl$12 [WARNING] - org.jvnet.hk2.internal.MethodInterceptorInvocationHandler [WARNING] - org.jvnet.hk2.internal.ClazzCreator [WARNING] - org.jvnet.hk2.internal.ValidationInformationImpl [WARNING] - org.jvnet.hk2.internal.ServiceLocatorImpl$6 [WARNING] - org.jvnet.hk2.internal.ConstructorInterceptorHandler$1 [WARNING] - org.jvnet.hk2.internal.ServiceLocatorImpl$IgdValue [WARNING] - 85 more... [WARNING] base64-2.3.8.jar, mango-core-0.0.3-SNAPSHOT.jar define 4 overlapping classes: [WARNING] - net.iharder.Base64$InputStream [WARNING] - net.iharder.Base64$OutputStream [WARNING] - net.iharder.Base64$1 [WARNING] - net.iharder.Base64 [WARNING] kryo-shaded-3.0.3.jar, mango-core-0.0.3-SNAPSHOT.jar, kryo-2.24.0.jar define 193 overlapping classes: [WARNING] - com.esotericsoftware.kryo.serializers.BeanSerializer$1 [WARNING] - com.esotericsoftware.kryo.Registration [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Handler [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.ByteVector [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.FieldVisitor [WARNING] - com.esotericsoftware.kryo.util.IntMap$Values [WARNING] - com.esotericsoftware.kryo.serializers.DefaultSerializers$IntSerializer [WARNING] - com.esotericsoftware.kryo.serializers.FieldSerializerUnsafeUtilImpl [WARNING] - com.esotericsoftware.kryo.serializers.ObjectField$ObjectIntField [WARNING] - com.esotericsoftware.kryo.serializers.JavaSerializer [WARNING] - 183 more... [WARNING] parquet-column-1.8.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 731 overlapping classes: [WARNING] - org.apache.parquet.it.unimi.dsi.fastutil.longs.LongComparator [WARNING] - org.apache.parquet.filter2.recordlevel.IncrementallyUpdatedFilterPredicateBuilder$25 [WARNING] - org.apache.parquet.column.values.dictionary.DictionaryValuesWriter$PlainIntegerDictionaryValuesWriter [WARNING] - org.apache.parquet.it.unimi.dsi.fastutil.ints.Int2IntLinkedOpenHashMap$MapEntry [WARNING] - org.apache.parquet.io.PrimitiveColumnIO [WARNING] - org.apache.parquet.io.api.Binary$ByteBufferBackedBinary [WARNING] - org.apache.parquet.column.statistics.BooleanStatistics [WARNING] - org.apache.parquet.column.values.boundedint.BoundedIntValuesReader [WARNING] - org.apache.parquet.schema.PrimitiveType$PrimitiveTypeName$3 [WARNING] - org.apache.parquet.it.unimi.dsi.fastutil.doubles.DoubleSortedSet [WARNING] - 721 more... [WARNING] spark-network-shuffle_2.11-2.3.3.jar, unused-1.0.0.jar, mango-core-0.0.3-SNAPSHOT.jar, spark-tags_2.11-2.3.3.jar, spark-launcher_2.11-2.3.3.jar, spark-unsafe_2.11-2.3.3.jar, spark-kvstore_2.11-2.3.3.jar, spark-network-common_2.11-2.3.3.jar, spark-core_2.11-2.3.3.jar define 1 overlapping classes: [WARNING] - org.apache.spark.unused.UnusedStubClass [WARNING] j2objc-annotations-1.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 12 overlapping classes: [WARNING] - com.google.j2objc.annotations.Property [WARNING] - com.google.j2objc.annotations.RetainedWith [WARNING] - com.google.j2objc.annotations.RetainedLocalRef [WARNING] - com.google.j2objc.annotations.J2ObjCIncompatible [WARNING] - com.google.j2objc.annotations.AutoreleasePool [WARNING] - com.google.j2objc.annotations.LoopTranslation$LoopStyle [WARNING] - com.google.j2objc.annotations.ReflectionSupport$Level [WARNING] - com.google.j2objc.annotations.ReflectionSupport [WARNING] - com.google.j2objc.annotations.Weak [WARNING] - com.google.j2objc.annotations.WeakOuter [WARNING] - 2 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, zookeeper-3.4.6.jar define 440 overlapping classes: [WARNING] - org.apache.zookeeper.server.NettyServerCnxn$DumpCommand [WARNING] - org.apache.zookeeper.proto.GetMaxChildrenRequest [WARNING] - org.apache.jute.XmlInputArchive$XMLParser [WARNING] - org.apache.zookeeper.server.NettyServerCnxn$SendBufferWriter [WARNING] - org.apache.jute.CsvInputArchive$1 [WARNING] - org.apache.zookeeper.KeeperException$CodeDeprecated [WARNING] - org.apache.zookeeper.server.ZooKeeperServerMXBean [WARNING] - org.apache.zookeeper.server.NettyServerCnxn$EnvCommand [WARNING] - org.apache.zookeeper.server.quorum.Learner$PacketInFlight [WARNING] - org.apache.zookeeper.Op$Check [WARNING] - 430 more... [WARNING] utils-metrics-spark2_2.11-0.2.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 407 overlapping classes: [WARNING] - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$reduceByKey$2$$anonfun$apply$33 [WARNING] - org.bdgenomics.utils.instrumentation.SimpleMonitorValueExtractor [WARNING] - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$fullOuterJoin$2 [WARNING] - org.bdgenomics.utils.instrumentation.MetricsListener$$anonfun$onTaskEnd$2 [WARNING] - org.bdgenomics.utils.metrics.Histogram$$anonfun$countSubset$1 [WARNING] - org.bdgenomics.utils.instrumentation.Alignment$ [WARNING] - org.apache.spark.rdd.InstrumentedPairRDDFunctions$$anonfun$saveAsHadoopFile$3 [WARNING] - org.bdgenomics.utils.instrumentation.Metrics$TreeNode$$anonfun$6 [WARNING] - org.apache.spark.rdd.InstrumentedRDD$$anonfun$reduce$1$$anonfun$apply$35 [WARNING] - org.apache.spark.rdd.InstrumentedRDD$$anonfun$aggregate$1$$anonfun$apply$39$$anonfun$apply$40 [WARNING] - 397 more... [WARNING] jersey-container-servlet-2.22.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 6 overlapping classes: [WARNING] - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl [WARNING] - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$ExtensionImpl [WARNING] - org.glassfish.jersey.servlet.init.JerseyServletContainerInitializer [WARNING] - org.glassfish.jersey.servlet.init.FilterUrlMappingsProviderImpl [WARNING] - org.glassfish.jersey.servlet.async.AsyncContextDelegateProviderImpl$1 [WARNING] - org.glassfish.jersey.servlet.init.internal.LocalizationMessages [WARNING] json4s-core_2.11-3.2.11.jar, mango-core-0.0.3-SNAPSHOT.jar define 407 overlapping classes: [WARNING] - org.json4s.CustomSerializer [WARNING] - org.json4s.reflect.Reflector$ClassDescriptorBuilder$$anonfun$constructorsAndCompanion$3$$anonfun$13$$anonfun$apply$3 [WARNING] - org.json4s.reflect.package$$anon$2 [WARNING] - org.json4s.DefaultReaders$JValueReader$ [WARNING] - org.json4s.StreamingJsonWriter$$anonfun$addJValue$1 [WARNING] - org.json4s.ParserUtil$RecycledSegment [WARNING] - org.json4s.package [WARNING] - org.json4s.DefaultReaders$ [WARNING] - org.json4s.Xml$$anonfun$directChildren$1$1 [WARNING] - org.json4s.JDoubleJObjectJsonWriter [WARNING] - 397 more... [WARNING] adam-codegen-spark2_2.11-0.26.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 18 overlapping classes: [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$ [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$getters$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$setters$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$apply$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$ [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProduct$$anonfun$fields$1 [WARNING] - org.bdgenomics.adam.codegen.DumpSchemasToProjectionEnums$$anonfun$fields$1 [WARNING] - 8 more... [WARNING] htsjdk-2.16.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 983 overlapping classes: [WARNING] - htsjdk.samtools.cram.ref.ReferenceSource [WARNING] - htsjdk.samtools.HighAccuracyDownsamplingIterator [WARNING] - htsjdk.samtools.util.zip.DeflaterFactory [WARNING] - htsjdk.samtools.filter.DuplicateReadFilter [WARNING] - htsjdk.variant.vcf.VCFEncoder [WARNING] - htsjdk.samtools.util.CloserUtil [WARNING] - htsjdk.tribble.TribbleException$FeatureFileDoesntExist [WARNING] - htsjdk.tribble.index.tabix.TabixIndex [WARNING] - htsjdk.samtools.AbstractBAMFileIndex [WARNING] - htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder$1 [WARNING] - 973 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, metrics-core-3.1.5.jar define 115 overlapping classes: [WARNING] - com.codahale.metrics.JmxReporter$JmxGaugeMBean [WARNING] - com.codahale.metrics.ThreadLocalRandomProxy$InternalProvider [WARNING] - com.codahale.metrics.JmxReporter [WARNING] - com.codahale.metrics.EWMA [WARNING] - com.codahale.metrics.Gauge [WARNING] - com.codahale.metrics.MetricRegistry$MetricBuilder$1 [WARNING] - com.codahale.metrics.MetricFilter$1 [WARNING] - com.codahale.metrics.JmxReporter$JmxCounterMBean [WARNING] - com.codahale.metrics.InstrumentedExecutorService$InstrumentedRunnable [WARNING] - com.codahale.metrics.RatioGauge$Ratio [WARNING] - 105 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, commons-logging-1.1.3.jar define 22 overlapping classes: [WARNING] - org.apache.commons.logging.LogSource [WARNING] - org.apache.commons.logging.impl.ServletContextCleaner [WARNING] - org.apache.commons.logging.LogFactory$4 [WARNING] - org.apache.commons.logging.impl.WeakHashtable$1 [WARNING] - org.apache.commons.logging.LogFactory$3 [WARNING] - org.apache.commons.logging.LogFactory$2 [WARNING] - org.apache.commons.logging.impl.LogFactoryImpl$2 [WARNING] - org.apache.commons.logging.impl.LogKitLogger [WARNING] - org.apache.commons.logging.impl.LogFactoryImpl$3 [WARNING] - org.apache.commons.logging.impl.WeakHashtable$Entry [WARNING] - 12 more... [WARNING] jackson-annotations-2.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 58 overlapping classes: [WARNING] - com.fasterxml.jackson.annotation.JsonAutoDetect [WARNING] - com.fasterxml.jackson.annotation.JsonInclude [WARNING] - com.fasterxml.jackson.annotation.ObjectIdGenerators [WARNING] - com.fasterxml.jackson.annotation.JsonFormat$Features [WARNING] - com.fasterxml.jackson.annotation.JsonFormat$Feature [WARNING] - com.fasterxml.jackson.annotation.JsonIgnore [WARNING] - com.fasterxml.jackson.annotation.JsonSetter [WARNING] - com.fasterxml.jackson.annotation.JsonTypeInfo$None [WARNING] - com.fasterxml.jackson.annotation.JsonSubTypes [WARNING] - com.fasterxml.jackson.annotation.JsonFormat$Shape [WARNING] - 48 more... [WARNING] chill-java-0.8.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 54 overlapping classes: [WARNING] - com.twitter.chill.java.ClosureSerializer [WARNING] - com.twitter.chill.config.JavaMapConfig [WARNING] - com.twitter.chill.java.IterableRegistrar [WARNING] - com.twitter.chill.java.SqlTimeSerializer [WARNING] - com.twitter.chill.KryoInstantiator [WARNING] - com.twitter.chill.java.PackageRegistrar [WARNING] - com.twitter.chill.config.ConfiguredInstantiator [WARNING] - com.twitter.chill.java.SimpleDateFormatSerializer [WARNING] - com.twitter.chill.KryoInstantiator$4 [WARNING] - com.twitter.chill.java.UnmodifiableSetSerializer [WARNING] - 44 more... [WARNING] adam-cli-spark2_2.11-0.26.0.jar, mango-cli-0.0.3-SNAPSHOT.jar define 3 overlapping classes: [WARNING] - org.bdgenomics.adam.cli.CommandGroup [WARNING] - org.bdgenomics.adam.cli.InitArgs [WARNING] - org.bdgenomics.adam.cli.CommandGroup$ [WARNING] mango-core-0.0.3-SNAPSHOT.jar, netty-all-4.1.17.Final.jar define 2501 overlapping classes: [WARNING] - io.netty.handler.codec.http.multipart.InterfaceHttpData$HttpDataType [WARNING] - io.netty.resolver.dns.InflightNameResolver$1 [WARNING] - io.netty.channel.AbstractChannel$AbstractUnsafe$8 [WARNING] - io.netty.handler.codec.smtp.DefaultSmtpRequest [WARNING] - io.netty.handler.codec.redis.RedisMessage [WARNING] - io.netty.handler.codec.memcache.binary.BinaryMemcacheResponse [WARNING] - io.netty.handler.timeout.IdleStateHandler [WARNING] - io.netty.buffer.FixedCompositeByteBuf$Component [WARNING] - io.netty.handler.codec.http.HttpHeaders [WARNING] - io.netty.handler.codec.http2.Http2ClientUpgradeCodec [WARNING] - 2491 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, pyrolite-4.13.jar define 54 overlapping classes: [WARNING] - net.razorvine.pickle.objects.ByteArrayConstructor [WARNING] - net.razorvine.pyro.NameServerProxy [WARNING] - net.razorvine.pyro.serializer.PyroSerializer [WARNING] - net.razorvine.pickle.objects.DateTimeConstructor [WARNING] - net.razorvine.pickle.IObjectConstructor [WARNING] - net.razorvine.pickle.objects.ClassDictConstructor [WARNING] - net.razorvine.pyro.serializer.PyroUriSerpent [WARNING] - net.razorvine.pickle.objects.OperatorAttrGetterForCalendarTz$CalendarLocalizer [WARNING] - net.razorvine.pickle.objects.TimeZoneConstructor [WARNING] - net.razorvine.pyro.Config [WARNING] - 44 more... [WARNING] java-xmlbuilder-1.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 5 overlapping classes: [WARNING] - com.jamesmurty.utils.NamespaceContextImpl [WARNING] - com.jamesmurty.utils.BaseXMLBuilder [WARNING] - com.jamesmurty.utils.XMLBuilder [WARNING] - com.jamesmurty.utils.XMLBuilder2 [WARNING] - com.jamesmurty.utils.XMLBuilderRuntimeException [WARNING] spark-network-shuffle_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 41 overlapping classes: [WARNING] - org.apache.spark.network.shuffle.RetryingBlockFetcher$1 [WARNING] - org.apache.spark.network.shuffle.protocol.BlockTransferMessage$Type [WARNING] - org.apache.spark.network.shuffle.ShuffleIndexRecord [WARNING] - org.apache.spark.network.sasl.ShuffleSecretManager [WARNING] - org.apache.spark.network.shuffle.SimpleDownloadFile [WARNING] - org.apache.spark.network.shuffle.OneForOneBlockFetcher [WARNING] - org.apache.spark.network.shuffle.ExternalShuffleBlockResolver$2 [WARNING] - org.apache.spark.network.shuffle.ExternalShuffleBlockHandler$ManagedBufferIterator [WARNING] - org.apache.spark.network.shuffle.DownloadFileManager [WARNING] - org.apache.spark.network.shuffle.protocol.RegisterExecutor [WARNING] - 31 more... [WARNING] scala-library-2.11.11.jar, mango-core-0.0.3-SNAPSHOT.jar define 3828 overlapping classes: [WARNING] - scala.collection.mutable.SortedSet$class [WARNING] - scala.collection.immutable.IndexedSeq [WARNING] - scala.collection.SeqLike$$anonfun$reverseMap$2 [WARNING] - scala.Function2$mcDID$sp [WARNING] - scala.collection.immutable.IntMapValueIterator [WARNING] - scala.collection.MapLike$DefaultKeySet [WARNING] - scala.collection.parallel.FactoryOps$Otherwise [WARNING] - scala.math.Ordering$String$ [WARNING] - scala.util.Either$ [WARNING] - scala.collection.mutable.SetProxy [WARNING] - 3818 more... [WARNING] RoaringBitmap-0.5.11.jar, mango-core-0.0.3-SNAPSHOT.jar define 69 overlapping classes: [WARNING] - org.roaringbitmap.ReverseRunContainerShortIterator [WARNING] - org.roaringbitmap.ShortIterator [WARNING] - org.roaringbitmap.Util [WARNING] - org.roaringbitmap.buffer.RawMappeableRunContainerShortIterator [WARNING] - org.roaringbitmap.buffer.MappeableBitmapContainer [WARNING] - org.roaringbitmap.buffer.BufferFastAggregation$2 [WARNING] - org.roaringbitmap.buffer.MappeableBitmapContainerShortIterator [WARNING] - org.roaringbitmap.RunContainerShortIterator [WARNING] - org.roaringbitmap.buffer.ReverseMappeableArrayContainerShortIterator [WARNING] - org.roaringbitmap.buffer.MappeableContainerPointer [WARNING] - 59 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, objenesis-2.1.jar define 37 overlapping classes: [WARNING] - org.objenesis.ObjenesisBase [WARNING] - org.objenesis.instantiator.gcj.GCJInstantiator [WARNING] - org.objenesis.strategy.SingleInstantiatorStrategy [WARNING] - org.objenesis.instantiator.sun.SunReflectionFactoryHelper [WARNING] - org.objenesis.ObjenesisHelper [WARNING] - org.objenesis.instantiator.jrockit.JRockitLegacyInstantiator [WARNING] - org.objenesis.instantiator.sun.SunReflectionFactoryInstantiator [WARNING] - org.objenesis.instantiator.basic.NullInstantiator [WARNING] - org.objenesis.instantiator.android.Android17Instantiator [WARNING] - org.objenesis.instantiator.ObjectInstantiator [WARNING] - 27 more... [WARNING] compress-lzf-1.0.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 42 overlapping classes: [WARNING] - com.ning.compress.lzf.LZFUncompressor [WARNING] - com.ning.compress.BufferRecycler [WARNING] - com.ning.compress.lzf.LZFEncoder [WARNING] - com.ning.compress.lzf.impl.UnsafeChunkEncoderBE [WARNING] - com.ning.compress.lzf.impl.UnsafeChunkEncoderLE [WARNING] - com.ning.compress.gzip.OptimizedGZIPInputStream [WARNING] - com.ning.compress.lzf.util.LZFFileOutputStream$Wrapper [WARNING] - com.ning.compress.lzf.util.LZFFileInputStream$1 [WARNING] - com.ning.compress.lzf.ChunkEncoder [WARNING] - com.ning.compress.lzf.impl.UnsafeChunkDecoder [WARNING] - 32 more... [WARNING] bdg-formats-0.12.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 61 overlapping classes: [WARNING] - org.bdgenomics.formats.avro.VariantCallingAnnotations$Builder [WARNING] - org.bdgenomics.formats.avro.VariantAnnotation$Builder [WARNING] - org.bdgenomics.formats.avro.Reference$1 [WARNING] - org.bdgenomics.formats.avro.VariantAnnotationMessage [WARNING] - org.bdgenomics.formats.avro.OntologyTerm$1 [WARNING] - org.bdgenomics.formats.avro.Feature$1 [WARNING] - org.bdgenomics.formats.avro.AlignmentRecord [WARNING] - org.bdgenomics.formats.avro.Sequence$1 [WARNING] - org.bdgenomics.formats.avro.ReadGroup$Builder [WARNING] - org.bdgenomics.formats.avro.ReadGroup [WARNING] - 51 more... [WARNING] netty-3.9.9.Final.jar, mango-core-0.0.3-SNAPSHOT.jar define 879 overlapping classes: [WARNING] - org.jboss.netty.handler.traffic.TrafficCounter$TrafficMonitoringTask [WARNING] - org.jboss.netty.handler.codec.spdy.SpdyGoAwayFrame [WARNING] - org.jboss.netty.util.internal.jzlib.Deflate [WARNING] - org.jboss.netty.channel.socket.ServerSocketChannelConfig [WARNING] - org.jboss.netty.util.internal.ConcurrentHashMap$HashIterator [WARNING] - org.jboss.netty.handler.codec.serialization.ObjectDecoder [WARNING] - org.jboss.netty.util.internal.jzlib.Tree [WARNING] - org.jboss.netty.util.internal.ConcurrentIdentityWeakKeyHashMap$Segment [WARNING] - org.jboss.netty.util.internal.ConcurrentIdentityHashMap$ValueIterator [WARNING] - org.jboss.netty.handler.codec.http.multipart.HttpPostRequestEncoder [WARNING] - 869 more... [WARNING] avro-ipc-1.7.7-tests.jar, mango-core-0.0.3-SNAPSHOT.jar define 248 overlapping classes: [WARNING] - test.StringablesRecord$Builder [WARNING] - org.apache.avro.specific.TestSpecificRecordBuilder [WARNING] - org.apache.avro.test.TestRecordWithUnion$Builder [WARNING] - org.apache.avro.test.TestError [WARNING] - org.apache.avro.test.Kind [WARNING] - org.apache.avro.io.Perf$IntTest [WARNING] - org.apache.avro.Interop$1 [WARNING] - org.apache.avro.test.TestError$Builder [WARNING] - org.apache.avro.TestProtocolReflect$1 [WARNING] - org.apache.avro.ipc.trace.TestFileSpanStorage [WARNING] - 238 more... [WARNING] javax.servlet-api-3.1.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 79 overlapping classes: [WARNING] - javax.servlet.http.Cookie [WARNING] - javax.servlet.ServletContext [WARNING] - javax.servlet.Registration [WARNING] - javax.servlet.http.HttpSessionListener [WARNING] - javax.servlet.http.HttpSessionContext [WARNING] - javax.servlet.FilterChain [WARNING] - javax.servlet.http.WebConnection [WARNING] - javax.servlet.http.HttpServletRequestWrapper [WARNING] - javax.servlet.http.HttpSessionAttributeListener [WARNING] - javax.servlet.annotation.HandlesTypes [WARNING] - 69 more... [WARNING] utils-io-spark2_2.11-0.2.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 23 overlapping classes: [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$3 [WARNING] - org.bdgenomics.utils.io.FileLocator [WARNING] - org.bdgenomics.utils.io.ByteAccess [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$readByteStream$1 [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$1 [WARNING] - org.bdgenomics.utils.io.ByteAccess$$anonfun$readFully$2 [WARNING] - org.bdgenomics.utils.io.LocalFileByteAccess [WARNING] - org.bdgenomics.utils.io.HTTPRangedByteAccess$$anonfun$2 [WARNING] - org.bdgenomics.utils.io.HTTPFileLocator$ [WARNING] - 13 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, json4s-ast_2.11-3.2.11.jar define 68 overlapping classes: [WARNING] - org.json4s.Merge$Mergeable [WARNING] - org.json4s.Merge$Mergeable$MergeSyntax [WARNING] - org.json4s.Merge$$anonfun$mergeRec$2$1 [WARNING] - org.json4s.BigDecimalMode$class [WARNING] - org.json4s.JsonAST$JBool$ [WARNING] - org.json4s.JsonAST$JField$ [WARNING] - org.json4s.DoubleMode$class [WARNING] - org.json4s.JsonAST$JString [WARNING] - org.json4s.LowPriorityMergeDep$class [WARNING] - org.json4s.JsonAST [WARNING] - 58 more... [WARNING] log4j-1.2.17.jar, mango-core-0.0.3-SNAPSHOT.jar define 314 overlapping classes: [WARNING] - org.apache.log4j.or.sax.AttributesRenderer [WARNING] - org.apache.log4j.pattern.MessagePatternConverter [WARNING] - org.apache.log4j.chainsaw.ControlPanel$3 [WARNING] - org.apache.log4j.pattern.NameAbbreviator$DropElementAbbreviator [WARNING] - org.apache.log4j.jmx.MethodUnion [WARNING] - org.apache.log4j.lf5.viewer.LogTable [WARNING] - org.apache.log4j.BasicConfigurator [WARNING] - org.apache.log4j.rewrite.RewriteAppender [WARNING] - org.apache.log4j.lf5.viewer.LogBrokerMonitor$22 [WARNING] - org.apache.log4j.pattern.LoggingEventPatternConverter [WARNING] - 304 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, javassist-3.18.1-GA.jar define 390 overlapping classes: [WARNING] - javassist.util.proxy.ProxyFactory$3 [WARNING] - javassist.bytecode.FieldInfo [WARNING] - javassist.DirClassPath [WARNING] - javassist.ClassPool$1 [WARNING] - javassist.expr.Cast$ProceedForCast [WARNING] - javassist.URLClassPath [WARNING] - javassist.CtMethod$LongConstParameter [WARNING] - javassist.compiler.Javac$2 [WARNING] - javassist.bytecode.annotation.ClassMemberValue [WARNING] - javassist.bytecode.stackmap.TypeData$ClassName [WARNING] - 380 more... [WARNING] commons-compress-1.8.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 127 overlapping classes: [WARNING] - org.apache.commons.compress.archivers.dump.ShortFileException [WARNING] - org.apache.commons.compress.utils.CountingInputStream [WARNING] - org.apache.commons.compress.compressors.bzip2.BZip2CompressorOutputStream [WARNING] - org.apache.commons.compress.compressors.bzip2.CRC [WARNING] - org.apache.commons.compress.archivers.dump.DumpArchiveEntry [WARNING] - org.apache.commons.compress.compressors.bzip2.BlockSort [WARNING] - org.apache.commons.compress.archivers.tar.TarArchiveEntry [WARNING] - org.apache.commons.compress.archivers.dump.UnsupportedCompressionAlgorithmException [WARNING] - org.apache.commons.compress.archivers.zip.AbstractUnicodeExtraField [WARNING] - org.apache.commons.compress.archivers.dump.InvalidFormatException [WARNING] - 117 more... [WARNING] kryo-shaded-3.0.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 14 overlapping classes: [WARNING] - com.esotericsoftware.kryo.serializers.VersionFieldSerializer [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.Context [WARNING] - com.esotericsoftware.kryo.serializers.EnumNameSerializer [WARNING] - com.esotericsoftware.kryo.serializers.ClosureSerializer [WARNING] - com.esotericsoftware.kryo.pool.KryoPool [WARNING] - com.esotericsoftware.kryo.pool.SoftReferenceQueue [WARNING] - com.esotericsoftware.kryo.pool.KryoCallback [WARNING] - com.esotericsoftware.reflectasm.shaded.org.objectweb.asm.TypePath [WARNING] - com.esotericsoftware.reflectasm.PublicConstructorAccess [WARNING] - com.esotericsoftware.kryo.pool.KryoPoolQueueImpl [WARNING] - 4 more... [WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar, failureaccess-1.0.jar define 2 overlapping classes: [WARNING] - com.google.common.util.concurrent.internal.InternalFutureFailureAccess [WARNING] - com.google.common.util.concurrent.internal.InternalFutures [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jersey-guava-2.22.2.jar define 753 overlapping classes: [WARNING] - jersey.repackaged.com.google.common.collect.AbstractNavigableMap$DescendingMap [WARNING] - jersey.repackaged.com.google.common.collect.AbstractMultiset$ElementSet [WARNING] - jersey.repackaged.com.google.common.collect.Collections2$OrderedPermutationCollection [WARNING] - jersey.repackaged.com.google.common.collect.StandardTable$TableSet [WARNING] - jersey.repackaged.com.google.common.base.Splitter [WARNING] - jersey.repackaged.com.google.common.util.concurrent.Futures$1$1 [WARNING] - jersey.repackaged.com.google.common.base.CharMatcher$5 [WARNING] - jersey.repackaged.com.google.common.collect.SortedMapDifference [WARNING] - jersey.repackaged.com.google.common.collect.ImmutableListMultimap [WARNING] - jersey.repackaged.com.google.common.cache.LocalCache$AbstractReferenceEntry [WARNING] - 743 more... [WARNING] hk2-api-2.4.0-b34.jar, mango-core-0.0.3-SNAPSHOT.jar define 165 overlapping classes: [WARNING] - org.glassfish.hk2.api.ActiveDescriptor [WARNING] - org.glassfish.hk2.api.Proxiable [WARNING] - org.glassfish.hk2.utilities.InjecteeImpl [WARNING] - org.glassfish.hk2.api.ProxyCtl [WARNING] - org.glassfish.hk2.api.DynamicConfiguration [WARNING] - org.glassfish.hk2.internal.ImmediateHelper$1 [WARNING] - org.glassfish.hk2.api.InjectionResolver [WARNING] - org.glassfish.hk2.utilities.ServiceLocatorUtilities$3 [WARNING] - org.glassfish.hk2.api.Validator [WARNING] - org.glassfish.hk2.api.PopulatorPostProcessor [WARNING] - 155 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, jcl-over-slf4j-1.7.16.jar define 3 overlapping classes: [WARNING] - org.apache.commons.logging.impl.SLF4JLogFactory [WARNING] - org.apache.commons.logging.impl.SLF4JLocationAwareLog [WARNING] - org.apache.commons.logging.impl.SLF4JLog [WARNING] jul-to-slf4j-1.7.16.jar, mango-core-0.0.3-SNAPSHOT.jar define 1 overlapping classes: [WARNING] - org.slf4j.bridge.SLF4JBridgeHandler [WARNING] spark-network-common_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 1697 overlapping classes: [WARNING] - org.spark_project.guava.annotations.Beta [WARNING] - org.spark_project.guava.util.concurrent.UncaughtExceptionHandlers$Exiter [WARNING] - org.spark_project.guava.eventbus.Subscribe [WARNING] - org.spark_project.guava.collect.TreeRangeMap [WARNING] - org.spark_project.guava.collect.ImmutableList$SubList [WARNING] - org.spark_project.guava.cache.RemovalCause$1 [WARNING] - org.spark_project.guava.collect.ForwardingMultimap [WARNING] - org.spark_project.guava.io.LimitInputStream [WARNING] - org.spark_project.guava.math.BigIntegerMath [WARNING] - org.spark_project.guava.collect.Tables [WARNING] - 1687 more... [WARNING] guava-27.0-jre.jar, mango-core-0.0.3-SNAPSHOT.jar define 1955 overlapping classes: [WARNING] - com.google.common.collect.CompactHashMap$Itr [WARNING] - com.google.common.collect.ImmutableMapValues$1 [WARNING] - com.google.common.util.concurrent.AbstractService$5 [WARNING] - com.google.common.io.LineProcessor [WARNING] - com.google.common.io.BaseEncoding$StandardBaseEncoding$2 [WARNING] - com.google.common.io.ByteProcessor [WARNING] - com.google.common.math.package-info [WARNING] - com.google.common.util.concurrent.SimpleTimeLimiter [WARNING] - com.google.common.cache.AbstractCache$StatsCounter [WARNING] - com.google.common.util.concurrent.CycleDetectingLockFactory$Policies [WARNING] - 1945 more... [WARNING] commons-codec-1.10.jar, mango-core-0.0.3-SNAPSHOT.jar define 92 overlapping classes: [WARNING] - org.apache.commons.codec.language.Nysiis [WARNING] - org.apache.commons.codec.language.bm.Rule$1 [WARNING] - org.apache.commons.codec.language.bm.Rule$RPattern [WARNING] - org.apache.commons.codec.language.ColognePhonetic$CologneInputBuffer [WARNING] - org.apache.commons.codec.digest.HmacUtils [WARNING] - org.apache.commons.codec.language.bm.BeiderMorseEncoder [WARNING] - org.apache.commons.codec.digest.UnixCrypt [WARNING] - org.apache.commons.codec.language.Soundex [WARNING] - org.apache.commons.codec.binary.BinaryCodec [WARNING] - org.apache.commons.codec.language.bm.Languages$1 [WARNING] - 82 more... [WARNING] snappy-java-1.0.5.jar, mango-core-0.0.3-SNAPSHOT.jar define 12 overlapping classes: [WARNING] - org.xerial.snappy.SnappyLoader [WARNING] - org.xerial.snappy.SnappyOutputStream [WARNING] - org.xerial.snappy.SnappyErrorCode [WARNING] - org.xerial.snappy.SnappyBundleActivator [WARNING] - org.xerial.snappy.SnappyError [WARNING] - org.xerial.snappy.SnappyNativeAPI [WARNING] - org.xerial.snappy.SnappyException [WARNING] - org.xerial.snappy.Snappy [WARNING] - org.xerial.snappy.SnappyNative [WARNING] - org.xerial.snappy.OSInfo [WARNING] - 2 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, aopalliance-repackaged-2.4.0-b34.jar define 17 overlapping classes: [WARNING] - org.aopalliance.reflect.ClassLocator [WARNING] - org.aopalliance.reflect.Metadata [WARNING] - org.aopalliance.instrument.Instrumentation [WARNING] - org.aopalliance.reflect.Field [WARNING] - org.aopalliance.intercept.FieldInterceptor [WARNING] - org.aopalliance.reflect.Method [WARNING] - org.aopalliance.reflect.CodeLocator [WARNING] - org.aopalliance.intercept.FieldAccess [WARNING] - org.aopalliance.reflect.ProgramUnit [WARNING] - org.aopalliance.instrument.UndoNotSupportedException [WARNING] - 7 more... [WARNING] scala-xml_2.11-1.0.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 421 overlapping classes: [WARNING] - scala.xml.PrettyPrinter$Para [WARNING] - scala.xml.Group$ [WARNING] - scala.xml.PrettyPrinter$$anonfun$traverse$1 [WARNING] - scala.xml.MetaData [WARNING] - scala.xml.MalformedAttributeException [WARNING] - scala.xml.pull.EvComment [WARNING] - scala.xml.parsing.TokenTests$$anonfun$isSpace$1 [WARNING] - scala.xml.Properties [WARNING] - scala.xml.parsing.MarkupParser$$anonfun$1 [WARNING] - scala.xml.pull.EvEntityRef$ [WARNING] - 411 more... [WARNING] xbean-asm5-shaded-4.4.jar, mango-core-0.0.3-SNAPSHOT.jar define 81 overlapping classes: [WARNING] - org.apache.xbean.asm5.FieldWriter [WARNING] - org.apache.xbean.asm5.commons.GeneratorAdapter [WARNING] - org.apache.xbean.asm5.AnnotationWriter [WARNING] - org.apache.xbean.asm5.tree.IntInsnNode [WARNING] - org.apache.xbean.asm5.Type [WARNING] - org.apache.xbean.asm5.commons.RemappingClassAdapter [WARNING] - org.apache.xbean.asm5.tree.FieldInsnNode [WARNING] - org.apache.xbean.asm5.tree.MultiANewArrayInsnNode [WARNING] - org.apache.xbean.asm5.tree.IincInsnNode [WARNING] - org.apache.xbean.asm5.tree.InsnList$InsnListIterator [WARNING] - 71 more... [WARNING] scala-reflect-2.11.7.jar, mango-core-0.0.3-SNAPSHOT.jar define 2793 overlapping classes: [WARNING] - scala.reflect.runtime.ReflectionUtils [WARNING] - scala.reflect.internal.Types$LazyType [WARNING] - scala.reflect.internal.Scopes$LookupInaccessible$ [WARNING] - scala.reflect.internal.Definitions$DefinitionsClass$$anonfun$newT1NullaryMethod$1 [WARNING] - scala.reflect.internal.SymbolPairs$Cursor [WARNING] - scala.reflect.internal.Types$StaticallyAnnotatedType$ [WARNING] - scala.reflect.runtime.SynchronizedOps$SynchronizedScope$$anonfun$isEmpty$1 [WARNING] - scala.reflect.internal.Kinds$TypeConKind$$anonfun$buildState$3 [WARNING] - scala.reflect.api.StandardLiftables$StandardUnliftableInstances$$anonfun$unliftTuple18$1 [WARNING] - scala.reflect.runtime.SynchronizedSymbols$SynchronizedClassSymbol [WARNING] - 2783 more... [WARNING] checker-qual-2.5.2.jar, mango-core-0.0.3-SNAPSHOT.jar define 302 overlapping classes: [WARNING] - org.checkerframework.checker.formatter.FormatUtil [WARNING] - org.checkerframework.checker.units.qual.MixedUnits [WARNING] - org.checkerframework.checker.units.qual.PolyUnit [WARNING] - org.checkerframework.checker.regex.qual.PolyRegex [WARNING] - org.checkerframework.checker.units.qual.C [WARNING] - org.checkerframework.checker.formatter.FormatUtil$IllegalFormatConversionCategoryException [WARNING] - org.checkerframework.framework.qual.Unqualified [WARNING] - org.checkerframework.common.reflection.qual.UnknownMethod [WARNING] - org.checkerframework.framework.qual.EnsuresQualifierIf [WARNING] - org.checkerframework.checker.signedness.SignednessUtil [WARNING] - 292 more... [WARNING] commons-math3-3.4.1.jar, mango-core-0.0.3-SNAPSHOT.jar define 1215 overlapping classes: [WARNING] - org.apache.commons.math3.optim.linear.LinearOptimizer [WARNING] - org.apache.commons.math3.linear.LUDecomposition$Solver [WARNING] - org.apache.commons.math3.analysis.function.Gaussian$Parametric [WARNING] - org.apache.commons.math3.stat.descriptive.WeightedEvaluation [WARNING] - org.apache.commons.math3.analysis.FunctionUtils$3 [WARNING] - org.apache.commons.math3.stat.descriptive.AbstractStorelessUnivariateStatistic [WARNING] - org.apache.commons.math3.ml.clustering.FuzzyKMeansClusterer [WARNING] - org.apache.commons.math3.analysis.FunctionUtils$3$1 [WARNING] - org.apache.commons.math3.ode.nonstiff.MidpointStepInterpolator [WARNING] - org.apache.commons.math3.ode.ParameterConfiguration [WARNING] - 1205 more... [WARNING] jackson-module-paranamer-2.7.9.jar, mango-core-0.0.3-SNAPSHOT.jar define 26 overlapping classes: [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.NullParanamer [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.ParameterNamesNotFoundException [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$1 [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$MethodCollector [WARNING] - com.fasterxml.jackson.module.paranamer.SerializableParanamer [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.JavadocParanamer$DirJavadocProvider [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.BytecodeReadingParanamer$Type [WARNING] - com.fasterxml.jackson.module.paranamer.ParanamerAnnotationIntrospector [WARNING] - com.fasterxml.jackson.module.paranamer.shaded.CachingParanamer$WithoutWeakReferences [WARNING] - com.fasterxml.jackson.module.paranamer.ParanamerOnJacksonAnnotationIntrospector [WARNING] - 16 more... [WARNING] mango-core-0.0.3-SNAPSHOT.jar, scala-compiler-2.11.12.jar define 9084 overlapping classes: [WARNING] - scala.tools.nsc.doc.base.CommentFactoryBase$SimpleTagKey [WARNING] - scala.tools.jline_embedded.Terminal [WARNING] - scala.tools.nsc.Global$$anonfun$scala$tools$nsc$Global$$writeICode$1 [WARNING] - scala.tools.nsc.backend.opt.ClosureElimination$ClosureElim$$anonfun$analyzeMethod$1$$anonfun$apply$2 [WARNING] - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$typedCase$2$$anonfun$apply$27 [WARNING] - scala.tools.nsc.backend.icode.analysis.TypeFlowAnalysis$MTFAGrowable$$anonfun$scala$tools$nsc$backend$icode$analysis$TypeFlowAnalysis$MTFAGrowable$$putOnRadar$1$$anonfun$3 [WARNING] - scala.tools.nsc.interpreter.ILoop$$anonfun$standardCommands$3 [WARNING] - scala.tools.nsc.typechecker.Typers$Typer$$anonfun$isReferencedFrom$1 [WARNING] - scala.tools.nsc.typechecker.Typers$Typer$dyna$ [WARNING] - scala.tools.nsc.transform.patmat.MatchAnalysis$MatchAnalyzer$NegativeExample$$anonfun$23 [WARNING] - 9074 more... [WARNING] convert-0.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 23 overlapping classes: [WARNING] - org.bdgenomics.convert.bdgenomics.SliceToRead [WARNING] - org.bdgenomics.convert.bdgenomics.SliceToSequence [WARNING] - org.bdgenomics.convert.bdgenomics.BdgenomicsModule [WARNING] - org.bdgenomics.convert.ConversionException [WARNING] - org.bdgenomics.convert.bdgenomics.OntologyTermToString [WARNING] - org.bdgenomics.convert.bdgenomics.StringToVariantAnnotationMessage [WARNING] - org.bdgenomics.convert.ConversionStringency [WARNING] - org.bdgenomics.convert.bdgenomics.ReadToSlice [WARNING] - org.bdgenomics.convert.Converter [WARNING] - org.bdgenomics.convert.bdgenomics.ReadToSequence [WARNING] - 13 more... [WARNING] spark-unsafe_2.11-2.3.3.jar, mango-core-0.0.3-SNAPSHOT.jar define 18 overlapping classes: [WARNING] - org.apache.spark.unsafe.types.UTF8String [WARNING] - org.apache.spark.unsafe.memory.HeapMemoryAllocator [WARNING] - org.apache.spark.unsafe.array.LongArray [WARNING] - org.apache.spark.unsafe.types.UTF8String$LongWrapper [WARNING] - org.apache.spark.unsafe.bitset.BitSetMethods [WARNING] - org.apache.spark.unsafe.memory.UnsafeMemoryAllocator [WARNING] - org.apache.spark.sql.catalyst.expressions.HiveHasher [WARNING] - org.apache.spark.unsafe.KVIterator [WARNING] - org.apache.spark.unsafe.types.CalendarInterval [WARNING] - org.apache.spark.unsafe.memory.MemoryBlock [WARNING] - 8 more... [WARNING] jackson-core-asl-1.9.13.jar, mango-core-0.0.3-SNAPSHOT.jar define 121 overlapping classes: [WARNING] - org.codehaus.jackson.annotate.JsonManagedReference [WARNING] - org.codehaus.jackson.util.DefaultPrettyPrinter$FixedSpaceIndenter [WARNING] - org.codehaus.jackson.JsonGenerationException [WARNING] - org.codehaus.jackson.util.BufferRecycler$CharBufferType [WARNING] - org.codehaus.jackson.io.UTF32Reader [WARNING] - org.codehaus.jackson.sym.Name1 [WARNING] - org.codehaus.jackson.util.MinimalPrettyPrinter [WARNING] - org.codehaus.jackson.impl.JsonParserBase [WARNING] - org.codehaus.jackson.annotate.JsonValue [WARNING] - org.codehaus.jackson.sym.CharsToNameCanonicalizer$Bucket [WARNING] - 111 more... [WARNING] adam-core-spark2_2.11-0.26.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 2708 overlapping classes: [WARNING] - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$74$$anonfun$apply$77 [WARNING] - org.bdgenomics.adam.rdd.feature.FeatureDataset$$anonfun$filterToTranscript$2$$anonfun$apply$9$$anonfun$apply$10 [WARNING] - org.bdgenomics.adam.rdd.read.AlignmentRecordDataset$$typecreator9$1 [WARNING] - org.bdgenomics.adam.sql.VariantCallingAnnotations$$anonfun$toAvro$58 [WARNING] - org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$63 [WARNING] - org.bdgenomics.adam.rdd.feature.DatasetBoundFeatureDataset$$anonfun$filterByAttribute$1 [WARNING] - org.bdgenomics.adam.io.InterleavedFastqInputFormat [WARNING] - org.bdgenomics.adam.util.FileMerger$$anonfun$mergeFilesAcrossFilesystems$4 [WARNING] - org.bdgenomics.adam.rdd.fragment.DatasetBoundFragmentDataset [WARNING] - org.bdgenomics.adam.sql.VariantAnnotation$$anonfun$fromAvro$80 [WARNING] - 2698 more... [WARNING] curator-recipes-2.6.0.jar, mango-core-0.0.3-SNAPSHOT.jar define 190 overlapping classes: [WARNING] - org.apache.curator.framework.recipes.atomic.DistributedAtomicNumber [WARNING] - org.apache.curator.framework.recipes.locks.Reaper$State [WARNING] - org.apache.curator.framework.recipes.locks.InterProcessReadWriteLock [WARNING] - org.apache.curator.framework.recipes.queue.QueueBase [WARNING] - org.apache.curator.framework.recipes.locks.ChildReaper$1 [WARNING] - org.apache.curator.framework.recipes.cache.Operation [WARNING] - org.apache.curator.framework.recipes.shared.SharedValue$1 [WARNING] - org.apache.curator.framework.recipes.locks.Revoker [WARNING] - org.apache.curator.framework.recipes.queue.QueueSharderPolicies [WARNING] - org.apache.curator.framework.recipes.locks.StandardLockInternalsDriver [WARNING] - 180 more... [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.3-SNAPSHOT.jar with /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.3-SNAPSHOT-shaded.jar [INFO] Dependency-reduced POM written at: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/dependency-reduced-pom.xml [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ mango-cli --- [INFO] Building jar: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.3-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ mango-cli --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ mango-cli >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ mango-cli --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ mango-cli --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ mango-cli --- [INFO] Source directory: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ mango-cli <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ mango-cli --- [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [INFO] artifact commons-codec:commons-codec: checking for updates from central [WARNING] Expected all dependencies to require Scala version: 2.11.12 [WARNING] net.liftweb:lift-json_2.11:3.3.0 requires scala version: 2.11.11 [WARNING] Multiple versions of scala libraries detected! model contains 26 documentable templates [INFO] Building jar: /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/mango-cli-0.0.3-SNAPSHOT-javadoc.jar [INFO] [INFO] --- appassembler-maven-plugin:1.10:assemble (default) @ mango-cli --- [INFO] Installing artifact /home/jenkins/.m2/repository/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/net/liftweb/lift-json_2.11/3.3.0/lift-json_2.11-3.3.0.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scala-library/2.11.11/scala-library-2.11.11.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/scala-lang/scalap/2.11.11/scalap-2.11.11.jar [INFO] Installing artifact /home/jenkins/.m2/repository/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.8/paranamer-2.8.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro/1.8.2/avro-1.8.2.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/avro/avro/1.8.2/avro-1.8.2.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.13/jackson-core-asl-1.9.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.13/jackson-mapper-asl-1.9.13.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.0.5/snappy-java-1.0.5.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.8.1/commons-compress-1.8.1.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/tukaani/xz/1.5/xz-1.5.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/tukaani/xz/1.5/xz-1.5.jar [INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar to /tmp/mangoTestcbqUd3G/deleteMePleaseThisIsNoLongerNeeded/mango-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.7/slf4j-api-1.7.7.jar