FailedConsole Output

Started by upstream project "bdg-services-prb" build number 16
originally caused by:
 GitHub pull request #6 of commit 7b1605afc70e5636f97df9512de88e488d575fd4 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on test02.amplab (CentOS 6.5) (test02 centos) in workspace /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos
 > git rev-parse --is-inside-work-tree
Fetching changes from the remote Git repository
 > git config remote.origin.url https://github.com/bigdatagenomics/bdg-services.git
Fetching upstream changes from https://github.com/bigdatagenomics/bdg-services.git
 > git --version
 > git fetch --tags --progress https://github.com/bigdatagenomics/bdg-services.git +refs/pull/*:refs/remotes/origin/pr/*
Checking out Revision 8f5e31e5e167b3f8362504d4dea4ed32ab487c55 (detached)
 > git config core.sparsecheckout
 > git checkout -f 8f5e31e5e167b3f8362504d4dea4ed32ab487c55
 > git rev-list 11420d8dda66a0e57b4b96df77d3f4bc711d5ed9
[centos] $ /home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/mvn -DghprbTargetBranch=master -DghprbSourceBranch=bdg-formats-0.2.0 -Dhadoop.version=1.0.4 -DghprbPullId=6 -Dlabel=centos -Dsha1=origin/pr/6/merge -DghprbPullLink=https://github.com/bigdatagenomics/bdg-services/pull/6 -DghprbActualCommit=7b1605afc70e5636f97df9512de88e488d575fd4 "-DghprbPullTitle=Update to use against bdg-formats 0.2.0" -DghprbPullAuthorEmail=carl@yeksigian.com "-DghprbPullDescription=GitHub pull request #6 of commit 7b1605afc70e5636f97df9512de88e488d575fd4 automatically merged." clean package
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-core:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-reads:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:build-helper-maven-plugin is missing. @ line 115, column 21
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 169, column 21
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-cli:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:build-helper-maven-plugin is missing. @ line 115, column 21
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 166, column 21
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-service-manager:jar:0.0.1-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.codehaus.mojo:build-helper-maven-plugin is missing. @ line 128, column 21
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 181, column 21
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 220, column 37
[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.services:bdgs-parent:0.0.1-SNAPSHOT, /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/pom.xml, line 224, column 37
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.services:bdgs-parent:pom:0.0.1-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 220, column 37
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 224, column 37
[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] BDG Services: Service setup and management for BDG Projects
[INFO] BDGS: Core
[INFO] BDGS: Read API Module
[INFO] BDGS: CLI Module
[INFO] BDGS: Service Manager
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building BDG Services: Service setup and management for BDG Projects 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ bdgs-parent ---
[INFO] Deleting /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/target
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ bdgs-parent ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ bdgs-parent ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ bdgs-parent ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ bdgs-parent ---
[INFO] No sources to compile
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building BDGS: Core 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
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Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent/0.12.2-SNAPSHOT/maven-metadata.xml
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Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core/0.12.2-SNAPSHOT/adam-core-0.12.2-20140805.144651-103.jar (2032 KB at 1588.6 KB/sec)
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ bdgs-core ---
[INFO] Deleting /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/target
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ bdgs-core ---
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default) @ bdgs-core ---
[INFO] Modified 0 of 7 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ bdgs-core ---
[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) @ bdgs-core ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.3
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:0.99.2 requires scala version: 2.10.4
[WARNING] Multiple versions of scala libraries detected!
[WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile
[INFO] Using incremental compilation
[INFO] Compiling 5 Scala sources to /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/target/scala-2.10.3/classes...
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/ServiceContext.scala:57: type BDG is not a member of package org.bdgenomics.formats.avro
[ERROR]         classOf[org.bdgenomics.formats.avro.BDG].asInstanceOf[Class[Any]],
[ERROR]                                             ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:28: object AlignmentRecord is not a member of package org.bdgenomics.formats.avro
[ERROR] import org.bdgenomics.formats.avro.{ AlignmentRecord, FlatGenotype }
[ERROR]        ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:81: not found: type AlignmentRecord
[ERROR]                          select: Option[CombinedFilter[AlignmentRecord, IDRangeIndexEntry]] = None): RDD[AlignmentRecord] = {
[ERROR]                                                                                                          ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:81: not found: type AlignmentRecord
[ERROR]                          select: Option[CombinedFilter[AlignmentRecord, IDRangeIndexEntry]] = None): RDD[AlignmentRecord] = {
[ERROR]                                                        ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:47: not found: type AlignmentRecord
[ERROR]       case "reads"             => loadADAMRecordsRDD(sc, proj, select.asInstanceOf[Option[CombinedFilter[AlignmentRecord, IDRangeIndexEntry]]]).asInstanceOf[RDD[T]]
[ERROR]                                                                                                          ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:72: not found: type FlatGenotype
[ERROR]                            select: Option[CombinedFilter[FlatGenotype, IDRangeIndexEntry]] = None): RDD[FlatGenotype] = {
[ERROR]                                                                                                         ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:72: not found: type FlatGenotype
[ERROR]                            select: Option[CombinedFilter[FlatGenotype, IDRangeIndexEntry]] = None): RDD[FlatGenotype] = {
[ERROR]                                                          ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:48: not found: type FlatGenotype
[ERROR]       case "genotypes"         => loadADAMGenotypesRDD(sc, proj, select.asInstanceOf[Option[CombinedFilter[FlatGenotype, IDRangeIndexEntry]]]).asInstanceOf[RDD[T]]
[ERROR]                                                                                                            ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:63: not found: type FlatGenotype
[ERROR]                                   select: Option[CombinedFilter[FlatGenotype, IDRangeIndexEntry]] = None): RDD[FlatGenotype] = {
[ERROR]                                                                                                                ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:63: not found: type FlatGenotype
[ERROR]                                   select: Option[CombinedFilter[FlatGenotype, IDRangeIndexEntry]] = None): RDD[FlatGenotype] = {
[ERROR]                                                                 ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:49: not found: type FlatGenotype
[ERROR]       case "indexed_genotypes" => loadIndexedADAMGenotypesRDD(sc, proj, select.asInstanceOf[Option[CombinedFilter[FlatGenotype, IDRangeIndexEntry]]]).asInstanceOf[RDD[T]]
[ERROR]                                                                                                                   ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:67: not found: type FlatGenotype
[ERROR]     new AvroIndexedParquetRDD[FlatGenotype](sc.sparkContext, select.get, index, dataRoot, proj)
[ERROR]                               ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:76: not found: type FlatGenotype
[ERROR]     new AvroParquetRDD[FlatGenotype](sc.sparkContext, filter, loc, proj)
[ERROR]                        ^
[ERROR] /home/jenkins/workspace/bdg-services-prb/hadoop.version/1.0.4/label/centos/bdgs-core/src/main/scala/org/bdgenomics/services/TypedLocation.scala:85: not found: type AlignmentRecord
[ERROR]     new AvroParquetRDD[AlignmentRecord](sc.sparkContext, filter, loc, proj)
[ERROR]                        ^
[ERROR] 14 errors found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] BDG Services: Service setup and management for BDG Projects  SUCCESS [2.060s]
[INFO] BDGS: Core ........................................ FAILURE [8.985s]
[INFO] BDGS: Read API Module ............................. SKIPPED
[INFO] BDGS: CLI Module .................................. SKIPPED
[INFO] BDGS: Service Manager ............................. SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 11.228s
[INFO] Finished at: Tue Aug 05 15:06:10 PDT 2014
[INFO] Final Memory: 48M/1963M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal net.alchim31.maven:scala-maven-plugin:3.1.5:compile (scala-compile-first) on project bdgs-core: Execution scala-compile-first of goal net.alchim31.maven:scala-maven-plugin:3.1.5:compile failed. CompileFailed -> [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/PluginExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :bdgs-core
Build step 'Invoke top-level Maven targets' marked build as failure
Finished: FAILURE