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Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core-spark2_2.11/0.27.0/adam-core-spark2_2.11-0.27.0.jar (3986 KB at 1065.5 KB/sec)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 22 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/scala-2.11.12/classes at 1558626299171
[WARNING] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure
[WARNING]       case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector)
[WARNING]               ^
[WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 9 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/test/scala:-1: info: compiling
[INFO] Compiling 5 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/scala-2.11.12/test-classes at 1558626309075
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.1:jar (default-jar) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/deca-core_2.11-0.2.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-jar-plugin:3.1.1:test-jar (default) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/deca-core_2.11-0.2.1-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-cli-spark2_2.11/0.27.0/adam-cli-spark2_2.11-0.27.0.pom
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Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-cli-spark2_2.11/0.27.0/adam-cli-spark2_2.11-0.27.0.pom (7 KB at 423.3 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-apis-spark2_2.11/0.27.0/adam-apis-spark2_2.11-0.27.0.pom
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Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-apis-spark2_2.11/0.27.0/adam-apis-spark2_2.11-0.27.0.pom (5 KB at 345.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-cli-spark2_2.11/0.27.0/adam-cli-spark2_2.11-0.27.0.jar
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-apis-spark2_2.11/0.27.0/adam-apis-spark2_2.11-0.27.0.jar
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Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-apis-spark2_2.11/0.27.0/adam-apis-spark2_2.11-0.27.0.jar (187 KB at 1102.3 KB/sec)
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  net.codingwell:scala-guice_2.11:4.2.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.12 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/classes at 1558626318617
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  net.codingwell:scala-guice_2.11:4.2.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.12 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/test-classes at 1558626323756
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.1:jar (default-jar) @ deca-cli_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/deca-cli_2.11-0.2.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ deca-cli_2.11 ---
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-shade-spark2_2.11/0.27.0/adam-shade-spark2_2.11-0.27.0.pom
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Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-shade-spark2_2.11/0.27.0/adam-shade-spark2_2.11-0.27.0.pom (2 KB at 85.5 KB/sec)
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-shade-spark2_2.11/0.27.0/adam-shade-spark2_2.11-0.27.0.jar
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[INFO] Including net.fnothaft:jsr203-s3a:jar:0.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
[INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.12 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-serialization-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.deca:deca-core_2.11:jar:0.2.1-SNAPSHOT in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.27.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including 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 org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.18.2 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:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.27.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.27.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.27.0 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.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:slf4j-api:jar:1.7.16 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.2.6 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including org.scalanlp:breeze_2.11:jar:0.12 in the shaded jar.
[INFO] Including org.scalanlp:breeze-macros_2.11:jar:0.12 in the shaded jar.
[INFO] Including com.github.fommil.netlib:core:jar:1.1.2 in the shaded jar.
[INFO] Including net.sourceforge.f2j:arpack_combined_all:jar:0.1 in the shaded jar.
[INFO] Including net.sf.opencsv:opencsv:jar:2.3 in the shaded jar.
[INFO] Including com.github.rwl:jtransforms:jar:2.4.0 in the shaded jar.
[INFO] Including junit:junit:jar:4.8.2 in the shaded jar.
[INFO] Including org.spire-math:spire_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including org.spire-math:spire-macros_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including com.chuusai:shapeless_2.11:jar:2.0.0 in the shaded jar.
[INFO] Including org.scalanlp:breeze-natives_2.11:jar:0.12 in the shaded jar.
[INFO] Skipping pom dependency com.github.fommil.netlib:all:pom:1.1.2 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-osx-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:native_ref-java:jar:1.1 in the shaded jar.
[INFO] Including com.github.fommil:jniloader:jar:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-i686:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-win-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-win-i686:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-armhf:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-osx-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:native_system-java:jar:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-linux-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-linux-i686:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-linux-armhf:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-win-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-win-i686:jar:natives:1.1 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/deca-cli_2.11-0.2.1-SNAPSHOT.jar with /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/deca-cli_2.11-0.2.1-SNAPSHOT-shaded.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.023s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [24.401s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [21.710s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 48.256s
[INFO] Finished at: Thu May 23 08:45:38 PDT 2019
[INFO] Final Memory: 101M/1404M
[INFO] ------------------------------------------------------------------------

# if those pass, build the distribution package and the integration tests
mvn -U \
    clean \
    test \
    -P coverage scoverage:report
+ mvn -U clean test -P coverage scoverage:report
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.deca:deca-core_2.11:jar:0.2.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 416, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.2.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 188, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 416, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.2.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 416, column 25
[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] deca: Distributed Exome CNV Analyzer
[INFO] deca-core: Core variant calling algorithms
[INFO] deca-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: Distributed Exome CNV Analyzer 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 ---
[INFO] Modified 0 of 32 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 ---
[INFO] Modified 0 of 32 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-parent_2.11 ---
[INFO] Skipping SCoverage execution for project with packaging type 'pom'
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ deca-core_2.11 ---
[INFO] Deleting /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 22 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.3 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/scala-2.11.12/classes at 1558626345162
[WARNING] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure
[WARNING]       case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector)
[WARNING]               ^
[WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 9 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.3 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/test/scala:-1: info: compiling
[INFO] Compiling 5 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/scala-2.11.12/test-classes at 1558626354653
[INFO] prepare-compile in 0 s
[INFO] compile in 7 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ deca-core_2.11 ---
Discovery starting.
Discovery completed in 475 milliseconds.
Run starting. Expected test count is: 16
NormalizationSuite:
2019-05-23 08:46:03 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- mean centers data by columns
- zScores data by rows
2019-05-23 08:46:07 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2019-05-23 08:46:07 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2019-05-23 08:46:07 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
2019-05-23 08:46:07 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
- removes top k components of data
2019-05-23 08:46:08 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-05-23 08:46:08 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
2019-05-23 08:46:08 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
2019-05-23 08:46:08 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- produces same results with fixed k
- filters and centers SVD results
2019-05-23 08:46:10 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-05-23 08:46:11 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-05-23 08:46:11 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-05-23 08:46:12 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- filters and normalizes read depth data
HMMSuite:
- Generates transition matrix for array of distances
- Handles contig boundaries in computing transition matrix
- Discovers CNVs
DecaSuite:
- read XHMM matrix
- write XHMM matrix
CoverageSuite:
- Finds correct first target
- computes coverage for targets
- counts fragments not just reads
- counts imperfectly paired fragments
- incorporates CIGAR into fragment analysis
Run completed in 16 seconds, 125 milliseconds.
Total number of tests run: 16
Suites: completed 5, aborted 0
Tests: succeeded 16, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 22 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-core_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.3 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala:-1: info: compiling
[INFO] Compiling 17 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/scala-2.11.12/scoverage-classes at 1558626379527
[WARNING] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure
[WARNING]       case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector)
[WARNING]               ^
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-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.
[INFO] [info] Instrumentation completed [1976 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/scoverage-data]
[WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 10 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.3 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ deca-core_2.11 ---
Discovery starting.
Discovery completed in 481 milliseconds.
Run starting. Expected test count is: 16
NormalizationSuite:
2019-05-23 08:46:31 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- mean centers data by columns
- zScores data by rows
2019-05-23 08:46:35 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2019-05-23 08:46:35 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2019-05-23 08:46:35 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
2019-05-23 08:46:35 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
- removes top k components of data
2019-05-23 08:46:36 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-05-23 08:46:36 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
2019-05-23 08:46:36 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
2019-05-23 08:46:37 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- produces same results with fixed k
- filters and centers SVD results
2019-05-23 08:46:39 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-05-23 08:46:39 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-05-23 08:46:39 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2019-05-23 08:46:40 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- filters and normalizes read depth data
HMMSuite:
- Generates transition matrix for array of distances
- Handles contig boundaries in computing transition matrix
- Discovers CNVs
DecaSuite:
- read XHMM matrix
- write XHMM matrix
CoverageSuite:
- Finds correct first target
- computes coverage for targets
- counts fragments not just reads
- counts imperfectly paired fragments
- incorporates CIGAR into fragment analysis
Run completed in 16 seconds, 501 milliseconds.
Total number of tests run: 16
Suites: completed 5, aborted 0
Tests: succeeded 16, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ deca-cli_2.11 ---
[INFO] Deleting /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  net.codingwell:scala-guice_2.11:4.2.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.12 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.3 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/classes at 1558626409815
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  net.codingwell:scala-guice_2.11:4.2.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.12 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.3 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/test-classes at 1558626415133
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ deca-cli_2.11 ---
Discovery starting.
Discovery completed in 115 milliseconds.
Run starting. Expected test count is: 0
DecaMainSuite:
- no op to test setup !!! IGNORED !!!
Run completed in 171 milliseconds.
Total number of tests run: 0
Suites: completed 2, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 1, pending 0
No tests were executed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  net.codingwell:scala-guice_2.11:4.2.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.12 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.3 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/annotations:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/scoverage-classes at 1558626419985
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [328 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 5 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/scoverage-classes
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  net.codingwell:scala-guice_2.11:4.2.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.12 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.9.3 requires scala version: 2.11.12
[WARNING]  org.apache.spark:spark-core_2.11:2.4.3 requires scala version: 2.11.12
[WARNING]  org.json4s:json4s-jackson_2.11:3.5.3 requires scala version: 2.11.11
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ deca-cli_2.11 ---
Discovery starting.
Discovery completed in 115 milliseconds.
Run starting. Expected test count is: 0
DecaMainSuite:
- no op to test setup !!! IGNORED !!!
Run completed in 170 milliseconds.
Total number of tests run: 0
Suites: completed 2, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 1, pending 0
No tests were executed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 ---
[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] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.944s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [1:05.567s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [18.931s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:27.644s
[INFO] Finished at: Thu May 23 08:47:07 PDT 2019
[INFO] Final Memory: 69M/1392M
[INFO] ------------------------------------------------------------------------

# if those pass, build the distribution package
mvn -U \
    -P distribution \
    package \
    -DskipTests \
    -Dhadoop.version=${HADOOP_VERSION} \
    -Dspark.version=${SPARK_VERSION} \
    -DargLine=${DECA_MVN_TMP_DIR}
+ mvn -U -P distribution package -DskipTests -Dhadoop.version=2.6.0 -Dspark.version=2.1.0 -DargLine=/tmp/decaTestMvnWFltJaq
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.deca:deca-core_2.11:jar:0.2.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 416, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.2.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 188, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 416, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-distribution_2.11:pom:0.2.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 416, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.2.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 416, column 25
[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] deca: Distributed Exome CNV Analyzer
[INFO] deca-core: Core variant calling algorithms
[INFO] deca-cli: Command line interface for a distributed variant caller
[INFO] deca: distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: Distributed Exome CNV Analyzer 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 ---
[INFO] Modified 0 of 32 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ deca-parent_2.11 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.11 ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 22 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.1:jar (default-jar) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/deca-core_2.11-0.2.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/deca-core_2.11-0.2.1-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ deca-core_2.11 ---
[INFO] 
[INFO] --- maven-jar-plugin:3.1.1:test-jar (default) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/deca-core_2.11-0.2.1-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  net.codingwell:scala-guice_2.11:4.2.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.12 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/classes at 1558626435871
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/scala-2.11.12/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.12
[WARNING]  org.clapper:grizzled-slf4j_2.11:1.3.3 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.15 requires scala version: 2.11.12
[WARNING]  net.codingwell:scala-guice_2.11:4.2.1 requires scala version: 2.11.12
[WARNING]  org.scala-lang:scala-reflect:2.11.12 requires scala version: 2.11.12
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.1.1:jar (default-jar) @ deca-cli_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/deca-cli_2.11-0.2.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-cli_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/deca-cli_2.11-0.2.1-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ deca-cli_2.11 ---
[INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:3.1.0:javadoc' has not been previously called for the module: 'org.bdgenomics.deca:deca-core_2.11:jar:0.2.1-SNAPSHOT'. Trying to invoke it...
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/apidocs
[ERROR] Error fetching link: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-core/target/apidocs. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.deca.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_60
Building tree for all the packages and classes...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/About.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-frame.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-summary.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-tree.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/constant-values.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/class-use/About.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-use.html...
Building index for all the packages and classes...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/overview-tree.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/index-all.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/allclasses-frame.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/allclasses-noframe.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/index.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/deca-cli_2.11-0.2.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:3.2.0:shade (default) @ deca-cli_2.11 ---
[INFO] Including net.fnothaft:jsr203-s3a:jar:0.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.clapper:grizzled-slf4j_2.11:jar:1.3.3 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar.
[INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.25 in the shaded jar.
[INFO] Including com.netflix.spectator:spectator-api:jar:0.67.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.12 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.33 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-serialization-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.deca:deca-core_2.11:jar:0.2.1-SNAPSHOT in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:2.6 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.27.0 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.15 in the shaded jar.
[INFO] Including 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 org.bdgenomics.bdg-formats:bdg-formats:jar:0.12.0 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.2 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.18.2 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:4.5.7 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:27.0-jre in the shaded jar.
[INFO] Including com.google.guava:failureaccess:jar:1.0 in the shaded jar.
[INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar.
[INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar.
[INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar.
[INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar.
[INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.27.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.27.0 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.27.0 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.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:slf4j-api:jar:1.7.16 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.2.6 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.11.12 in the shaded jar.
[INFO] Including org.scalanlp:breeze_2.11:jar:0.12 in the shaded jar.
[INFO] Including org.scalanlp:breeze-macros_2.11:jar:0.12 in the shaded jar.
[INFO] Including com.github.fommil.netlib:core:jar:1.1.2 in the shaded jar.
[INFO] Including net.sourceforge.f2j:arpack_combined_all:jar:0.1 in the shaded jar.
[INFO] Including net.sf.opencsv:opencsv:jar:2.3 in the shaded jar.
[INFO] Including com.github.rwl:jtransforms:jar:2.4.0 in the shaded jar.
[INFO] Including junit:junit:jar:4.8.2 in the shaded jar.
[INFO] Including org.spire-math:spire_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including org.spire-math:spire-macros_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including com.chuusai:shapeless_2.11:jar:2.0.0 in the shaded jar.
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] WORKAROUND:  refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar
[WARNING] guava-27.0-jre.jar, failureaccess-1.0.jar define 2 overlapping classes: 
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutureFailureAccess
[WARNING]   - com.google.common.util.concurrent.internal.InternalFutures
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/deca-cli_2.11-0.2.1-SNAPSHOT.jar with /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-cli/target/deca-cli_2.11-0.2.1-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: distribution 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-distribution_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-distribution_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-distribution/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-distribution_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-distribution_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-distribution_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-distribution/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-distribution_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-distribution_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ deca-distribution_2.11 ---
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-distribution_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-distribution_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-distribution/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.11 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:3.1.0:single (default) @ deca-distribution_2.11 ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-distribution/target/deca-distribution_2.11-0.2.1-SNAPSHOT-bin.tar.gz
[INFO] Building tar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-distribution/target/deca-distribution_2.11-0.2.1-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/deca-distribution/target/deca-distribution_2.11-0.2.1-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.696s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [2.841s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [19.723s]
[INFO] deca: distribution ................................ SUCCESS [0.593s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 25.980s
[INFO] Finished at: Thu May 23 08:47:34 PDT 2019
[INFO] Final Memory: 65M/1272M
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${DECA_MVN_TMP_DIR}
+ find /tmp/decaTestMvnWFltJaq
/tmp/decaTestMvnWFltJaq
/tmp/decaTestMvnWFltJaq/1558626391022-0
/tmp/decaTestMvnWFltJaq/1558626391022-0/test.txt
/tmp/decaTestMvnWFltJaq/1558626391022-0/.test.txt.crc
/tmp/decaTestMvnWFltJaq/1558626362811-0
/tmp/decaTestMvnWFltJaq/1558626362811-0/test.txt
/tmp/decaTestMvnWFltJaq/1558626362811-0/.test.txt.crc
rm -rf ${DECA_MVN_TMP_DIR}
+ rm -rf /tmp/decaTestMvnWFltJaq

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${DECA_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/decaTestMvnWFltJaq:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

./scripts/format-source
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/scripts
+ pushd /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/scripts/..
~/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos ~/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos
+ mvn org.scalariform:scalariform-maven-plugin:format license:format
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.deca:deca-core_2.11:jar:0.2.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 416, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.2.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 188, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.deca:deca-parent_2.11:0.2.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos/pom.xml, line 416, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.2.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 408, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 412, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 416, column 25
[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] deca: Distributed Exome CNV Analyzer
[INFO] deca-core: Core variant calling algorithms
[INFO] deca-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: Distributed Exome CNV Analyzer 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 ---
[INFO] Modified 0 of 32 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-parent_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 22 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-core_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.2.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-cli_2.11 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [1.639s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.395s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [0.123s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2.475s
[INFO] Finished at: Thu May 23 08:47:38 PDT 2019
[INFO] Final Memory: 18M/1107M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.1.0/label/centos
if test -n "$(git status --porcelain | grep -v -e html -e pdf)"
then
    echo "Please run './scripts/format-source'"
    exit 1
fi
++ git status --porcelain
++ grep -v -e html -e pdf
+ test -n ''

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

Recording test results
Publishing Scoverage XML and HTML report...
Finished: SUCCESS