SuccessConsole Output

Skipping 67 KB.. Full Log
-RC2:test (test) @ rice-cli ---
Discovery starting.
Discovery completed in 90 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 160 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ rice-cli ---
[INFO] Building jar: /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/rice-cli-0.0.1-SNAPSHOT.jar
[INFO] 
[INFO] --- appassembler-maven-plugin:1.10:assemble (default) @ rice-cli ---
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.7.0/parquet-avro-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.7.0/parquet-avro-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-column/1.7.0/parquet-column-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.7.0/parquet-column-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-common/1.7.0/parquet-common-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.7.0/parquet-common-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-encoding/1.7.0/parquet-encoding-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.7.0/parquet-encoding-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-generator/1.7.0/parquet-generator-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-generator/1.7.0/parquet-generator-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-codec/commons-codec/1.5/commons-codec-1.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-codec/commons-codec/1.5/commons-codec-1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-hadoop/1.7.0/parquet-hadoop-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.7.0/parquet-hadoop-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-jackson/1.7.0/parquet-jackson-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.7.0/parquet-jackson-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.11/jackson-mapper-asl-1.9.11.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.11/jackson-mapper-asl-1.9.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.11/jackson-core-asl-1.9.11.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.11/jackson-core-asl-1.9.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro/1.7.6/avro-1.7.6.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/avro/avro/1.7.6/avro-1.7.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/thoughtworks/paranamer/paranamer/2.3/paranamer-2.3.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.3/paranamer-2.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/tukaani/xz/1.0/xz-1.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/tukaani/xz/1.0/xz-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/args4j/args4j/2.0.23/args4j-2.0.23.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/args4j/args4j/2.0.23/args4j-2.0.23.jar
[INFO] Installing artifact /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/target/rice-core-0.0.1-SNAPSHOT.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/rice/rice-core/0.0.1-SNAPSHOT/rice-core-0.0.1-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-metrics_2.10/0.2.2/utils-metrics_2.10-0.2.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics_2.10/0.2.2/utils-metrics_2.10-0.2.2.jar
[INFO] Installing artifact /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/rice-schemas-0.0.1-SNAPSHOT.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/rice/rice-schemas/0.0.1-SNAPSHOT/rice-schemas-0.0.1-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io_2.10/0.2.2/utils-io_2.10-0.2.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io_2.10/0.2.2/utils-io_2.10-0.2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc_2.10/0.2.2/utils-misc_2.10-0.2.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc_2.10/0.2.2/utils-misc_2.10-0.2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/amazonaws/aws-java-sdk/1.7.5/aws-java-sdk-1.7.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/amazonaws/aws-java-sdk/1.7.5/aws-java-sdk-1.7.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-core/2.1.1/jackson-core-2.1.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-core/2.1.1/jackson-core-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-databind/2.1.1/jackson-databind-2.1.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-databind/2.1.1/jackson-databind-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-annotations/2.1.1/jackson-annotations-2.1.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-annotations/2.1.1/jackson-annotations-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/joda-time/joda-time/2.9.4/joda-time-2.9.4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/joda-time/joda-time/2.9.4/joda-time-2.9.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli_2.10/0.2.2/utils-cli_2.10-0.2.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli_2.10/0.2.2/utils-cli_2.10-0.2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-cli/commons-cli/1.2/commons-cli-1.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-cli/commons-cli/1.2/commons-cli-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-core_2.10/0.17.0/adam-core_2.10-0.17.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core_2.10/0.17.0/adam-core_2.10-0.17.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/ow2/asm/asm/4.0/asm-4.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/ow2/asm/asm/4.0/asm-4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/objenesis/objenesis/1.2/objenesis-1.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/objenesis/objenesis/1.2/objenesis-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-avro/1.6.0rc4/parquet-avro-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-avro/1.6.0rc4/parquet-avro-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-column/1.6.0rc4/parquet-column-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-column/1.6.0rc4/parquet-column-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-common/1.6.0rc4/parquet-common-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-common/1.6.0rc4/parquet-common-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-encoding/1.6.0rc4/parquet-encoding-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-encoding/1.6.0rc4/parquet-encoding-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-generator/1.6.0rc4/parquet-generator-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-generator/1.6.0rc4/parquet-generator-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-hadoop/1.6.0rc4/parquet-hadoop-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-hadoop/1.6.0rc4/parquet-hadoop-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-jackson/1.6.0rc4/parquet-jackson-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-jackson/1.6.0rc4/parquet-jackson-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-format/2.2.0-rc1/parquet-format-2.2.0-rc1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-format/2.2.0-rc1/parquet-format-2.2.0-rc1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-scala_2.10/1.6.0rc4/parquet-scala_2.10-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-scala_2.10/1.6.0rc4/parquet-scala_2.10-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/samtools/htsjdk/1.129/htsjdk-1.129.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/github/samtools/htsjdk/1.129/htsjdk-1.129.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/guava/14.0.1/guava-14.0.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/google/guava/guava/14.0.1/guava-14.0.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.7.5/slf4j-api-1.7.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.5/slf4j-api-1.7.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/log4j/log4j/1.2.17/log4j-1.2.17.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/xerial/snappy/snappy-java/1.1.1.6/snappy-java-1.1.1.6.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.1.1.6/snappy-java-1.1.1.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/jblas/jblas/1.2.3/jblas-1.2.3.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/jblas/jblas/1.2.3/jblas-1.2.3.jar
[INFO] Installing artifact /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/rice-cli-0.0.1-SNAPSHOT.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/rice/rice-cli/0.0.1-SNAPSHOT/rice-cli-0.0.1-SNAPSHOT.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] rice: an ADAM-based RNA-seq quantification pipeline  SUCCESS [4.616s]
[INFO] rice-schemas: Avro formats for quantification indices  SUCCESS [4.578s]
[INFO] rice-core: ADAM based RNA-seq quantification ...... SUCCESS [1:39.413s]
[INFO] rice-cli: Command line for ADAM based RNA-seq quantification  SUCCESS [9.594s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:58.456s
[INFO] Finished at: Thu Oct 13 08:11:54 PDT 2016
[INFO] Final Memory: 37M/1931M
[INFO] ------------------------------------------------------------------------
[centos] $ /home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/mvn -Dhadoop.version=2.2.0 -Dlabel=centos --settings=/home/jenkins/workspace/settings.xml deploy
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.rice:rice-schemas:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: args4j:args4j:jar -> duplicate declaration of version 2.0.23 @ org.bdgenomics.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 325, column 19
[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.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 290, 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.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 294, 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.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 298, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.rice:rice-core:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: args4j:args4j:jar -> duplicate declaration of version 2.0.23 @ org.bdgenomics.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 325, column 19
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 290, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 294, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 298, 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.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 290, 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.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 294, 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.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 298, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.rice:rice-cli:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: args4j:args4j:jar -> duplicate declaration of version 2.0.23 @ org.bdgenomics.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 325, column 19
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:appassembler-maven-plugin is missing. @ line 20, column 15
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 290, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 294, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 298, 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.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 290, 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.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 294, 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.rice:rice-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml, line 298, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.rice:rice-parent:pom:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: args4j:args4j:jar -> duplicate declaration of version 2.0.23 @ line 325, column 19
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 290, 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 294, 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 298, 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] rice: an ADAM-based RNA-seq quantification pipeline
[INFO] rice-schemas: Avro formats for quantification indices
[INFO] rice-core: ADAM based RNA-seq quantification
[INFO] rice-cli: Command line for ADAM based RNA-seq quantification
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building rice: an ADAM-based RNA-seq quantification pipeline 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ rice-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ rice-parent ---
[ERROR] Error formatting /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/src/main/scala/org/bdgenomics/rice/algorithms/Quantify.scala: java.nio.charset.MalformedInputException: Input length = 1
[ERROR] Error formatting /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/src/main/scala/org/bdgenomics/rice/Timers.scala: java.nio.charset.MalformedInputException: Input length = 1
[INFO] Modified 0 of 14 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ rice-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ rice-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ rice-parent ---
[INFO] Checking licenses...
[INFO] 
[INFO] >>> scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-parent >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ rice-parent ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-parent <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-parent ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ rice-parent ---
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-parent/0.0.1-SNAPSHOT/rice-parent-0.0.1-SNAPSHOT.pom
[INFO] 
[INFO] --- maven-deploy-plugin:2.7:deploy (default-deploy) @ rice-parent ---
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[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building rice-schemas: Avro formats for quantification indices 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ rice-schemas ---
[INFO] 
[INFO] --- avro-maven-plugin:1.7.6:schema (schemas) @ rice-schemas ---
[INFO] 
[INFO] --- avro-maven-plugin:1.7.6:protocol (schemas) @ rice-schemas ---
[INFO] 
[INFO] --- avro-maven-plugin:1.7.6:idl-protocol (schemas) @ rice-schemas ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ rice-schemas ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ rice-schemas ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ rice-schemas ---
[INFO] /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/generated-sources/avro:-1: info: compiling
[INFO] Compiling 3 source files to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/scala-2.10.4/classes at 1476371548265
[INFO] prepare-compile in 0 s
[INFO] compile in 1 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ rice-schemas ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 3 source files to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/scala-2.10.4/classes
[WARNING] /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/generated-sources/avro/org/bdgenomics/rice/avro/ClassContents.java: /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/generated-sources/avro/org/bdgenomics/rice/avro/ClassContents.java uses unchecked or unsafe operations.
[WARNING] /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/generated-sources/avro/org/bdgenomics/rice/avro/ClassContents.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ rice-schemas ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ rice-schemas ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ rice-schemas ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ rice-schemas ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ rice-schemas ---
[INFO] Building jar: /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/rice-schemas-0.0.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ rice-schemas ---
[INFO] Checking licenses...
[INFO] 
[INFO] >>> scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-schemas >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ rice-schemas ---
[INFO] 
[INFO] --- avro-maven-plugin:1.7.6:schema (schemas) @ rice-schemas ---
[INFO] 
[INFO] --- avro-maven-plugin:1.7.6:protocol (schemas) @ rice-schemas ---
[INFO] 
[INFO] --- avro-maven-plugin:1.7.6:idl-protocol (schemas) @ rice-schemas ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-schemas <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-schemas ---
model contains 8 documentable templates
[INFO] Building jar: /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/rice-schemas-0.0.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ rice-schemas ---
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/rice-schemas-0.0.1-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-schemas/0.0.1-SNAPSHOT/rice-schemas-0.0.1-SNAPSHOT.jar
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-schemas/0.0.1-SNAPSHOT/rice-schemas-0.0.1-SNAPSHOT.pom
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/rice-schemas-0.0.1-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-schemas/0.0.1-SNAPSHOT/rice-schemas-0.0.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-deploy-plugin:2.7:deploy (default-deploy) @ rice-schemas ---
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[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building rice-core: ADAM based RNA-seq quantification 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ rice-core ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ rice-core ---
[ERROR] Error formatting /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/src/main/scala/org/bdgenomics/rice/algorithms/Quantify.scala: java.nio.charset.MalformedInputException: Input length = 1
[ERROR] Error formatting /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/src/main/scala/org/bdgenomics/rice/Timers.scala: java.nio.charset.MalformedInputException: Input length = 1
[INFO] Modified 0 of 11 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ rice-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ rice-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ rice-core ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ rice-core ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ rice-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ rice-core ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ rice-core ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ rice-core ---
Discovery starting.
Discovery completed in 212 milliseconds.
Run starting. Expected test count is: 27
TranscriptGeneratorSuite:
- transcript repetitive check should look for dupe k-mers
- string length and content are correct
- transcripts are independent if there are no shared k-mers
- transcript generator should generate independent, correct length transcripts
TareSuite:
- can't process illegal k-mers
- chop a 2-mer into a feature
- chop an 5-mer with a bad base into a feature
2016-10-13 08:12:44 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2016-10-13 08:12:46 WARN  LinearRegressionWithSGD:71 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2016-10-13 08:12:46 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2016-10-13 08:12:46 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2016-10-13 08:12:51 WARN  LinearRegressionWithSGD:71 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- generate biased kmers and try correcting their counts
- test of Tare.calibrateTxLenBias for 4 hand-picked values
- randomized test of Tare.calibrateTxLenBias for small data size
- randomize test of Tare.calibrateTxLenBias for larger data size
ReadGeneratorSuite:
- generate 100 reads, all 4 bp long
- generate reads from independent transcripts
QuantifySuite:
- test of mapKmersToClasses
- test of initializeEM
- test of e
- test of m
- extract lengths from transcripts
- dummy transcript correctly initialized
- transcripts correctly matched with coverage
2016-10-13 08:13:05 WARN  TaskSetManager:71 - Stage 1 contains a task of very large size (342 KB). The maximum recommended task size is 100 KB.
- quantify unique transcripts
- Test of TestingTwoBitFile
- Test of Index
2016-10-13 08:13:13 WARN  TaskSetManager:71 - Stage 1 contains a task of very large size (1706 KB). The maximum recommended task size is 100 KB.
- quantify a small set of more realistic but unbiased transcripts
2016-10-13 08:13:22 WARN  TaskSetManager:71 - Stage 1 contains a task of very large size (342 KB). The maximum recommended task size is 100 KB.
- quantify unique transcripts without bias removal
2016-10-13 08:13:26 WARN  TaskSetManager:71 - Stage 1 contains a task of very large size (342 KB). The maximum recommended task size is 100 KB.
2016-10-13 08:13:26 WARN  LinearRegressionWithSGD:71 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2016-10-13 08:13:29 WARN  LinearRegressionWithSGD:71 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- quantify unique transcripts where length bias is so strong that all variation in transcript abundance is due to length
2016-10-13 08:13:32 WARN  TaskSetManager:71 - Stage 1 contains a task of very large size (342 KB). The maximum recommended task size is 100 KB.
2016-10-13 08:13:33 WARN  LinearRegressionWithSGD:71 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2016-10-13 08:13:35 WARN  LinearRegressionWithSGD:71 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
- quantify unique transcripts with a weaker length bias
Run completed in 56 seconds, 105 milliseconds.
Total number of tests run: 27
Suites: completed 5, aborted 0
Tests: succeeded 27, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ rice-core ---
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ rice-core ---
[INFO] Checking licenses...
[INFO] 
[INFO] >>> scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-core >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ rice-core ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-core <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
model contains 8 documentable templates
[INFO] Building jar: /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/target/rice-core-0.0.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ rice-core ---
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/target/rice-core-0.0.1-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-core/0.0.1-SNAPSHOT/rice-core-0.0.1-SNAPSHOT.jar
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-core/0.0.1-SNAPSHOT/rice-core-0.0.1-SNAPSHOT.pom
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/target/rice-core-0.0.1-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-core/0.0.1-SNAPSHOT/rice-core-0.0.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-deploy-plugin:2.7:deploy (default-deploy) @ rice-core ---
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[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building rice-cli: Command line for ADAM based RNA-seq quantification 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ rice-cli ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ rice-cli ---
[INFO] Modified 0 of 3 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ rice-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ rice-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:compile (default-compile) @ rice-cli ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ rice-cli ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ rice-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-compiler-plugin:3.1:testCompile (default-testCompile) @ rice-cli ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ rice-cli ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ rice-cli ---
Discovery starting.
Discovery completed in 82 milliseconds.
Run starting. Expected test count is: 0
DiscoverySuite:
Run completed in 149 milliseconds.
Total number of tests run: 0
Suites: completed 1, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0
No tests were executed.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ rice-cli ---
[INFO] 
[INFO] --- appassembler-maven-plugin:1.10:assemble (default) @ rice-cli ---
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.7.0/parquet-avro-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-avro/1.7.0/parquet-avro-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-column/1.7.0/parquet-column-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-column/1.7.0/parquet-column-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-common/1.7.0/parquet-common-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-common/1.7.0/parquet-common-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-encoding/1.7.0/parquet-encoding-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-encoding/1.7.0/parquet-encoding-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-generator/1.7.0/parquet-generator-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-generator/1.7.0/parquet-generator-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-codec/commons-codec/1.5/commons-codec-1.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-codec/commons-codec/1.5/commons-codec-1.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-hadoop/1.7.0/parquet-hadoop-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-hadoop/1.7.0/parquet-hadoop-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-jackson/1.7.0/parquet-jackson-1.7.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-jackson/1.7.0/parquet-jackson-1.7.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.11/jackson-mapper-asl-1.9.11.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/codehaus/jackson/jackson-mapper-asl/1.9.11/jackson-mapper-asl-1.9.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.11/jackson-core-asl-1.9.11.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/codehaus/jackson/jackson-core-asl/1.9.11/jackson-core-asl-1.9.11.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/parquet/parquet-format/2.3.0-incubating/parquet-format-2.3.0-incubating.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/avro/avro/1.7.6/avro-1.7.6.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/avro/avro/1.7.6/avro-1.7.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/thoughtworks/paranamer/paranamer/2.3/paranamer-2.3.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/thoughtworks/paranamer/paranamer/2.3/paranamer-2.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/tukaani/xz/1.0/xz-1.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/tukaani/xz/1.0/xz-1.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/args4j/args4j/2.0.23/args4j-2.0.23.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/args4j/args4j/2.0.23/args4j-2.0.23.jar
[INFO] Installing artifact /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/target/rice-core-0.0.1-SNAPSHOT.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/rice/rice-core/0.0.1-SNAPSHOT/rice-core-0.0.1-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-metrics_2.10/0.2.2/utils-metrics_2.10-0.2.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/utils/utils-metrics_2.10/0.2.2/utils-metrics_2.10-0.2.2.jar
[INFO] Installing artifact /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-schemas/target/rice-schemas-0.0.1-SNAPSHOT.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/rice/rice-schemas/0.0.1-SNAPSHOT/rice-schemas-0.0.1-SNAPSHOT.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-io_2.10/0.2.2/utils-io_2.10-0.2.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/utils/utils-io_2.10/0.2.2/utils-io_2.10-0.2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-misc_2.10/0.2.2/utils-misc_2.10-0.2.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/utils/utils-misc_2.10/0.2.2/utils-misc_2.10-0.2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/scala-lang/scala-library/2.10.4/scala-library-2.10.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/httpcomponents/httpclient/4.3.2/httpclient-4.3.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/httpcomponents/httpcore/4.3.1/httpcore-4.3.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-logging/commons-logging/1.1.3/commons-logging-1.1.3.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/amazonaws/aws-java-sdk/1.7.5/aws-java-sdk-1.7.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/amazonaws/aws-java-sdk/1.7.5/aws-java-sdk-1.7.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-core/2.1.1/jackson-core-2.1.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-core/2.1.1/jackson-core-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-databind/2.1.1/jackson-databind-2.1.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-databind/2.1.1/jackson-databind-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/fasterxml/jackson/core/jackson-annotations/2.1.1/jackson-annotations-2.1.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/fasterxml/jackson/core/jackson-annotations/2.1.1/jackson-annotations-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/joda-time/joda-time/2.9.4/joda-time-2.9.4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/joda-time/joda-time/2.9.4/joda-time-2.9.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/utils/utils-cli_2.10/0.2.2/utils-cli_2.10-0.2.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/utils/utils-cli_2.10/0.2.2/utils-cli_2.10-0.2.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-cli/commons-cli/1.2/commons-cli-1.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-cli/commons-cli/1.2/commons-cli-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/adam/adam-core_2.10/0.17.0/adam-core_2.10-0.17.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/adam/adam-core_2.10/0.17.0/adam-core_2.10-0.17.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/esotericsoftware/kryo/kryo/2.21/kryo-2.21.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/esotericsoftware/reflectasm/reflectasm/1.07/reflectasm-1.07-shaded.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/ow2/asm/asm/4.0/asm-4.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/ow2/asm/asm/4.0/asm-4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/esotericsoftware/minlog/minlog/1.2/minlog-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/objenesis/objenesis/1.2/objenesis-1.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/objenesis/objenesis/1.2/objenesis-1.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/scoverage/scalac-scoverage-plugin_2.10/0.99.2/scalac-scoverage-plugin_2.10-0.99.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/bdg-formats/bdg-formats/0.4.0/bdg-formats-0.4.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/commons-io/commons-io/1.3.2/commons-io-1.3.2.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/it/unimi/dsi/fastutil/6.4.4/fastutil-6.4.4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/slf4j/slf4j-log4j12/1.7.5/slf4j-log4j12-1.7.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-avro/1.6.0rc4/parquet-avro-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-avro/1.6.0rc4/parquet-avro-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-column/1.6.0rc4/parquet-column-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-column/1.6.0rc4/parquet-column-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-common/1.6.0rc4/parquet-common-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-common/1.6.0rc4/parquet-common-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-encoding/1.6.0rc4/parquet-encoding-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-encoding/1.6.0rc4/parquet-encoding-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-generator/1.6.0rc4/parquet-generator-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-generator/1.6.0rc4/parquet-generator-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-hadoop/1.6.0rc4/parquet-hadoop-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-hadoop/1.6.0rc4/parquet-hadoop-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-jackson/1.6.0rc4/parquet-jackson-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-jackson/1.6.0rc4/parquet-jackson-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-format/2.2.0-rc1/parquet-format-2.2.0-rc1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-format/2.2.0-rc1/parquet-format-2.2.0-rc1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/twitter/parquet-scala_2.10/1.6.0rc4/parquet-scala_2.10-1.6.0rc4.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/twitter/parquet-scala_2.10/1.6.0rc4/parquet-scala_2.10-1.6.0rc4.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/seqdoop/hadoop-bam/7.0.0/hadoop-bam-7.0.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/github/samtools/htsjdk/1.129/htsjdk-1.129.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/github/samtools/htsjdk/1.129/htsjdk-1.129.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/netflix/servo/servo-core/0.5.5/servo-core-0.5.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/google/code/findbugs/annotations/2.0.0/annotations-2.0.0.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/com/google/guava/guava/14.0.1/guava-14.0.1.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/com/google/guava/guava/14.0.1/guava-14.0.1.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/slf4j/slf4j-api/1.7.5/slf4j-api-1.7.5.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/slf4j/slf4j-api/1.7.5/slf4j-api-1.7.5.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/log4j/log4j/1.2.17/log4j-1.2.17.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/log4j/log4j/1.2.17/log4j-1.2.17.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/xerial/snappy/snappy-java/1.1.1.6/snappy-java-1.1.1.6.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/xerial/snappy/snappy-java/1.1.1.6/snappy-java-1.1.1.6.jar
[INFO] Installing artifact /home/jenkins/.m2/repository/org/jblas/jblas/1.2.3/jblas-1.2.3.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/jblas/jblas/1.2.3/jblas-1.2.3.jar
[INFO] Installing artifact /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/rice-cli-0.0.1-SNAPSHOT.jar to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/appassembler/repo/org/bdgenomics/rice/rice-cli/0.0.1-SNAPSHOT/rice-cli-0.0.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:check (default) @ rice-cli ---
[INFO] Checking licenses...
[INFO] 
[INFO] >>> scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-cli >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ rice-cli ---
[INFO] 
[INFO] <<< scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-cli <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:doc-jar (attach-scaladocs) @ rice-cli ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.2 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.17.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-remote_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-actor_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.spark-project.akka:akka-slf4j_2.10:2.3.4-spark requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.2.1 requires scala version: 2.10.4
[WARNING]  org.json4s:json4s-jackson_2.10:3.2.10 requires scala version: 2.10.0
[WARNING] Multiple versions of scala libraries detected!
model contains 13 documentable templates
[INFO] Building jar: /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/rice-cli-0.0.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-install-plugin:2.4:install (default-install) @ rice-cli ---
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/rice-cli-0.0.1-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-cli/0.0.1-SNAPSHOT/rice-cli-0.0.1-SNAPSHOT.jar
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-cli/0.0.1-SNAPSHOT/rice-cli-0.0.1-SNAPSHOT.pom
[INFO] Installing /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-cli/target/rice-cli-0.0.1-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/rice/rice-cli/0.0.1-SNAPSHOT/rice-cli-0.0.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-deploy-plugin:2.7:deploy (default-deploy) @ rice-cli ---
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Uploading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/rice/rice-cli/0.0.1-SNAPSHOT/rice-cli-0.0.1-20161013.151358-2823.pom
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[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] rice: an ADAM-based RNA-seq quantification pipeline  SUCCESS [31.740s]
[INFO] rice-schemas: Avro formats for quantification indices  SUCCESS [11.814s]
[INFO] rice-core: ADAM based RNA-seq quantification ...... SUCCESS [1:11.999s]
[INFO] rice-cli: Command line for ADAM based RNA-seq quantification  SUCCESS [13.173s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2:08.908s
[INFO] Finished at: Thu Oct 13 08:14:04 PDT 2016
[INFO] Final Memory: 41M/1931M
[INFO] ------------------------------------------------------------------------
Recording test results
Finished: SUCCESS