FailedConsole Output

Started by upstream project "RNAdam" build number 2337
originally caused by:
 Started by timer
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-01 (spark-packaging spark-experimental-docker centos spark-docs spark-release spark-compile) in workspace /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/RNAdam.git
 > git init /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/RNAdam.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/bigdatagenomics/RNAdam.git +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url https://github.com/bigdatagenomics/RNAdam.git # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/bigdatagenomics/RNAdam.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/RNAdam.git
 > git fetch --tags --progress https://github.com/bigdatagenomics/RNAdam.git +refs/heads/*:refs/remotes/origin/*
Checking out Revision 5e2afeeb8cf666c3c32a422be4614cd2ff2e8419 (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 5e2afeeb8cf666c3c32a422be4614cd2ff2e8419
 > git rev-list 5e2afeeb8cf666c3c32a422be4614cd2ff2e8419 # timeout=10
[centos] $ /home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/mvn -Dhadoop.version=2.2.0 -Dlabel=centos clean package
[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-clean-plugin:2.5:clean (default-clean) @ rice-parent ---
[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] ------------------------------------------------------------------------
[INFO] Building rice-schemas: Avro formats for quantification indices 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ 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] --- 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 1476265749291
[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] ------------------------------------------------------------------------
[INFO] Building rice-core: ADAM based RNA-seq quantification 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://oss.sonatype.org/content/repositories/snapshots/joda-time/joda-time/maven-metadata.xml
Downloading: http://oss.sonatype.org/content/repositories/snapshots/joda-time/joda-time/maven-metadata.xml
Downloading: http://repo.maven.apache.org/maven2/joda-time/joda-time/maven-metadata.xml
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[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ rice-core ---
[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 ---
[INFO] artifact joda-time:joda-time: checking for updates from Sonatype
[INFO] artifact joda-time:joda-time: checking for updates from Apache
[INFO] artifact joda-time:joda-time: checking for updates from central
[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] /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/src/main/scala:-1: info: compiling
[INFO] Compiling 4 source files to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/target/scala-2.10.4/classes at 1476265755797
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[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] /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/src/test/scala:-1: info: compiling
[INFO] Compiling 7 source files to /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/target/scala-2.10.4/test-classes at 1476265764647
[INFO] prepare-compile in 0 s
[INFO] compile in 15 s
[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 229 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
2016-10-12 02:49:42 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2016-10-12 02:49:44 WARN  LinearRegressionWithSGD:71 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2016-10-12 02:49:44 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2016-10-12 02:49:44 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2016-10-12 02:49:50 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
2016-10-12 02:50:04 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
2016-10-12 02:50:12 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
2016-10-12 02:50:22 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
2016-10-12 02:50:26 WARN  TaskSetManager:71 - Stage 1 contains a task of very large size (342 KB). The maximum recommended task size is 100 KB.
2016-10-12 02:50:26 WARN  LinearRegressionWithSGD:71 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2016-10-12 02:50:30 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
2016-10-12 02:50:34 WARN  TaskSetManager:71 - Stage 1 contains a task of very large size (342 KB). The maximum recommended task size is 100 KB.
2016-10-12 02:50:34 WARN  LinearRegressionWithSGD:71 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2016-10-12 02:50:38 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 1 minute, 2 seconds.
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] Building jar: /home/jenkins/workspace/RNAdam/hadoop.version/2.2.0/label/centos/rice-core/target/rice-core-0.0.1-SNAPSHOT.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building rice-cli: Command line for ADAM based RNA-seq quantification 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] rice: an ADAM-based RNA-seq quantification pipeline  SUCCESS [2.992s]
[INFO] rice-schemas: Avro formats for quantification indices  SUCCESS [3.032s]
[INFO] rice-core: ADAM based RNA-seq quantification ...... SUCCESS [1:31.282s]
[INFO] rice-cli: Command line for ADAM based RNA-seq quantification  FAILURE [0.091s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:37.566s
[INFO] Finished at: Wed Oct 12 02:50:42 PDT 2016
[INFO] Final Memory: 35M/1931M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project rice-cli: Could not resolve dependencies for project org.bdgenomics.rice:rice-cli:jar:0.0.1-SNAPSHOT: Failed to collect dependencies at org.bdgenomics.rice:rice-core:jar:0.0.1-SNAPSHOT -> org.bdgenomics.adam:adam-core_2.10:jar:0.17.0 -> org.bdgenomics.utils:utils-io_2.10:jar:0.2.2 -> com.amazonaws:aws-java-sdk:jar:1.7.5 -> joda-time:joda-time:jar:[2.2,): No versions available for joda-time:joda-time:jar:[2.2,) within specified range -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :rice-cli
Build step 'Invoke top-level Maven targets' marked build as failure
Recording test results
Sending e-mails to: fnothaft@berkeley.edu
Finished: FAILURE