SuccessConsole Output

Started by upstream project "gnocchi-prb" build number 8
originally caused by:
 GitHub pull request #12 of commit 2451ba26b67b77aa4a4b3a4d02e576ee2483daec automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-08 (centos spark-test) in workspace /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/gnocchi.git
 > git init /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/gnocchi.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url https://github.com/bigdatagenomics/gnocchi.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/gnocchi.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/gnocchi.git
 > git fetch --tags --progress https://github.com/bigdatagenomics/gnocchi.git +refs/pull/*:refs/remotes/origin/pr/*
Checking out Revision 529ea812d26e613b4292e3186abf8a2b8157bf8d (origin/pr/12/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 529ea812d26e613b4292e3186abf8a2b8157bf8d
 > git rev-list f6408f09807326466868dc15ec0c0ad0561bf7d7 # timeout=10
First time build. Skipping changelog.
[centos] $ /bin/bash /tmp/hudson5934016685386894188.sh
+ set -e
+ export JAVA_HOME=/usr/java/jdk1.8.0_60
+ JAVA_HOME=/usr/java/jdk1.8.0_60
+ export PATH=/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.model.JDK/JDK_7u60/bin:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
+ PATH=/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.model.JDK/JDK_7u60/bin:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
+ set +x
+ /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/scripts/jenkins-test

# make a tempdir for writing maven cruft to
GNOCCHI_MVN_TMP_DIR=$(mktemp -d -t gnocchiTestMvnXXXXXXX)
++ mktemp -d -t gnocchiTestMvnXXXXXXX
+ GNOCCHI_MVN_TMP_DIR=/tmp/gnocchiTestMvn3vJwsGP

# add this tempdir to the poms...
find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${GNOCCHI_MVN_TMP_DIR}:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/gnocchiTestMvn3vJwsGP:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/java/jdk1.8.0_60/bin/:/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.model.JDK/JDK_7u60/bin:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
+ PATH=/usr/java/jdk1.8.0_60/bin/:/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.model.JDK/JDK_7u60/bin:/home/jenkins/.cargo/bin:/home/anaconda/bin:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/android-sdk/:/usr/local/bin:/bin:/usr/bin
export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8"
+ export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
+ MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )
+++ dirname /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/scripts/jenkins-test
++ cd /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/scripts
++ pwd
+ DIR=/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/scripts/..
VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
++ grep '<version>' /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.0.1-SNAPSHOT

# is the hadoop version set?
if ! [[ ${HADOOP_VERSION} ]];
then
    echo "HADOOP_VERSION environment variable is not set."
    echo "Please set this variable before running."
    
    exit 1
fi
+ [[ -n 2.3.0 ]]

# is the spark version set?
if ! [[ ${SPARK_VERSION} ]];
then
    echo "SPARK_VERSION environment variable is not set."
    echo "Please set this variable before running."
    
    exit 1
fi
+ [[ -n 1.6.1 ]]

# this next line is supposed to fail
set +e
+ set +e

echo "Rewriting POM.xml files to Scala 2.10 and Spark 1 should error..."
+ echo 'Rewriting POM.xml files to Scala 2.10 and Spark 1 should error...'
Rewriting POM.xml files to Scala 2.10 and Spark 1 should error...
./scripts/move_to_spark_1.sh
+ ./scripts/move_to_spark_1.sh
POM is already set up for Spark 1 (Spark 1/2 artifacts are missing -spark2 suffix in artifact names).
Cowardly refusing to move to Spark 1 a second time...
if [[ $? == 0 ]];
then
    echo "Running move_to_spark_1.sh when POMs are set up for Spark 1 should fail, but error code was 0 (success)."
    exit 1
fi
+ [[ 1 == 0 ]]

./scripts/move_to_scala_2.10.sh
+ ./scripts/move_to_scala_2.10.sh
Scala version is already set to 2.10 (Scala artifacts have _2.10 version suffix in artifact name).
Cowardly refusing to move to Scala 2.10 a second time...
if [[ $? == 0 ]];
then
    echo "Running move_to_scala_2.10.sh when POMs are set up for Scala 2.10 should fail, but error code was 0 (success)."
    exit 1
fi
+ [[ 1 == 0 ]]

set -e
+ set -e

# are we testing for spark 2.0.0? if so, we need to rewrite our poms first
if [ ${SPARK_VERSION} == 2.0.0 ];
then
    
    echo "Rewriting POM.xml files for Spark 2."
    ./scripts/move_to_spark_2.sh

    # shouldn't be able to move to spark 2 twice
    set +e
    ./scripts/move_to_spark_2.sh
    if [[ $? == 0 ]];
    then
        echo "We have already moved to Spark 2, so running move_to_spark_2.sh a second time should fail, but error code was 0 (success)."
        exit 1
    fi
    set -e
fi
+ '[' 1.6.1 == 2.0.0 ']'

# are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first
if [ ${SCALAVER} == 2.11 ];
then
    echo "Rewriting POM.xml files for Scala 2.11."
    ./scripts/move_to_scala_2.11.sh

    # shouldn't be able to move to scala 2.11 twice
    set +e
    ./scripts/move_to_scala_2.11.sh
    if [[ $? == 0 ]];
    then
        echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)."
        exit 1
    fi
    set -e
fi
+ '[' 2.10 == 2.11 ']'

# print versions
echo "Testing GNOCCHI version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing GNOCCHI version 0.0.1-SNAPSHOT on Spark 1.6.1 and Hadoop 2.3.0'
Testing GNOCCHI version 0.0.1-SNAPSHOT on Spark 1.6.1 and Hadoop 2.3.0

# first, build the sources, run the unit tests, and generate a coverage report
mvn clean \
    -Dhadoop.version=${HADOOP_VERSION} \
    -Dspark.version=${SPARK_VERSION} 
+ mvn clean -Dhadoop.version=2.3.0 -Dspark.version=1.6.1
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for net.fnothaft:gnocchi-core_2.10:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.commons:commons-math3:jar -> version (?) vs 3.6.1 @ line 96, column 17
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for net.fnothaft:gnocchi-cli_2.10: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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for net.fnothaft:gnocchi-parent_2.10: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 336, 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 348, 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 352, 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] gnocchi: Genotype store and query engine
[INFO] gnocchi-core: Core APIs and queries
[INFO] gnocchi-cli: Command line interface for managing and querying variant store
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi: Genotype store and query engine 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ gnocchi-parent_2.10 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi-core: Core APIs and queries 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ gnocchi-core_2.10 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi-cli: Command line interface for managing and querying variant store 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ gnocchi-cli_2.10 ---
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] gnocchi: Genotype store and query engine .......... SUCCESS [0.298s]
[INFO] gnocchi-core: Core APIs and queries ............... SUCCESS [0.259s]
[INFO] gnocchi-cli: Command line interface for managing and querying variant store  SUCCESS [0.011s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.700s
[INFO] Finished at: Tue Feb 28 17:35:24 PST 2017
[INFO] Final Memory: 19M/1472M
[INFO] ------------------------------------------------------------------------
    
# if this is a pull request, we need to set the coveralls pr id
if [[ ! -z $ghprbPullId ]];
then
    COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}"
fi
+ [[ ! -z 12 ]]
+ COVERALLS_PRB_OPTION=-DpullRequest=12

# coveralls token should not be visible
set +x +v
+ set +x +v
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for net.fnothaft:gnocchi-core_2.10:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.commons:commons-math3:jar -> version (?) vs 3.6.1 @ line 96, column 17
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for net.fnothaft:gnocchi-cli_2.10: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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for net.fnothaft:gnocchi-parent_2.10: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 336, 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 348, 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 352, 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] gnocchi: Genotype store and query engine
[INFO] gnocchi-core: Core APIs and queries
[INFO] gnocchi-cli: Command line interface for managing and querying variant store
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi: Genotype store and query engine 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-parent_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-parent_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-parent_2.10 ---
[INFO] Modified 0 of 84 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ gnocchi-parent_2.10 ---
[INFO] No sources to compile
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[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-parent_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ gnocchi-parent_2.10 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-parent_2.10 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-parent_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-parent_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/src/main/scala added.
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[INFO] Modified 0 of 84 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ gnocchi-parent_2.10 ---
[INFO] Skipping SCoverage execution for project with packaging type 'pom'
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ gnocchi-parent_2.10 ---
[INFO] No sources to compile
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[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-parent_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ gnocchi-parent_2.10 ---
[INFO] No sources to compile
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-parent_2.10 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-parent_2.10 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi-core: Core APIs and queries 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-core_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-core_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-core_2.10 ---
[INFO] Modified 0 of 65 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gnocchi-core_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ gnocchi-core_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.scalatest:scalatest_2.10:2.2.2 requires scala version: 2.10.4
[WARNING]  org.scala-lang:scala-reflect:2.10.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.2 requires scala version: 2.10.5
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala:-1: info: compiling
[INFO] Compiling 52 source files to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/classes at 1488332133487
[WARNING] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala/net/fnothaft/gnocchi/models/AdditiveLogisticGnocchiModel.scala:25: warning: case classes without a parameter list have been deprecated;
[WARNING] use either case objects or case classes with `()' as parameter list.
[WARNING] case class AdditiveLogisticGnocchiModel extends Serializable with GnocchiModel with Additive {
[WARNING]                                        ^
[WARNING] warning: there were 1 feature warning(s); re-run with -feature for details
[WARNING] warning: there were 6 inliner warning(s); re-run with -Yinline-warnings for details
[WARNING] three warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 18 s
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:compile (default-compile) @ gnocchi-core_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-core_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ gnocchi-core_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 7 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ gnocchi-core_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.scalatest:scalatest_2.10:2.2.2 requires scala version: 2.10.4
[WARNING]  org.scala-lang:scala-reflect:2.10.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.2 requires scala version: 2.10.5
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/test/scala:-1: info: compiling
[INFO] Compiling 13 source files to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes at 1488332152888
[WARNING] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/test/scala/net/fnothaft/gnocchi/gnocchiModel/BuildGnocchiModelSuite.scala:22: warning: imported `BuildAdditiveLogisticVariantModel' is permanently hidden by definition of object BuildAdditiveLogisticVariantModel in package gnocchiModel
[WARNING] import net.fnothaft.gnocchi.gnocchiModel.BuildAdditiveLogisticVariantModel
[WARNING]                                          ^
[WARNING] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/test/scala/net/fnothaft/gnocchi/gnocchiModel/LogisticGnocchiModelSuite.scala:22: warning: imported `BuildAdditiveLogisticVariantModel' is permanently hidden by definition of object BuildAdditiveLogisticVariantModel in package gnocchiModel
[WARNING] import net.fnothaft.gnocchi.gnocchiModel.BuildAdditiveLogisticVariantModel
[WARNING]                                          ^
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 12 s
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:testCompile (default-testCompile) @ gnocchi-core_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ gnocchi-core_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ gnocchi-core_2.10 ---
Discovery starting.
Discovery completed in 320 milliseconds.
Run starting. Expected test count is: 32
LoadPhenotypesWithoutCovariatesSuite:
2017-02-28 17:36:07 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- Load a simple phenotypes file, including no covariates.
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/BadFormatting.txt.
- Test file format
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
- Read in a 2-line file
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
- Read in a 2-line file; call with phenoName typo
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/MissingPhenotypes.txt.
- Read in a 5-line file but with one sample missing the phenotype.
GenotypeStateMatrixSuite:
- should filter out reference calls
- correctly process nonref calls
LogisticGnocchiModelSuite:
2017-02-28 17:36:15 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2017-02-28 17:36:15 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2017-02-28 17:36:15 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
2017-02-28 17:36:15 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
Incremental actual, pred: 0.0 0.0
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nonIncremental actual, pred: 0.0 0.0
nonIncremental actual, pred: 0.0 0.0
nonIncremental actual, pred: 0.0 0.0
nonIncremental actual, pred: 0.0 0.0
non incremental: 0.705
 Weights: List(-3.4495483976684627, 0.0022939595044433277, 0.7770135737198527, -0.5600313868499897)
incremental: 0.7025
 Weights: List(-4.757349875457931, 0.0028276500119430886, 1.0971441479547293, -0.6967919285389909)
- Build AdditiveLogisticGnocchiModel from data and update
- [NOT IMPLEMENTED YET] Build logistic gnocchi model, update, and check results.
- [NOT IMPLEMENTED YET] Load logistic gnocchi model, update, and check results.
LoadPhenotypesWithCovariatesSuite:
List((Sample1,[Ljava.lang.String;@da34eb0))
- Load a simple phenotypes example manually
List((Sample1,[Ljava.lang.String;@5cbe95b1), (Sample2,[Ljava.lang.String;@28fa541))
MapPartitionsRDD[23] at map at LoadPhenotypesWithCovariates.scala:216
oneTwo flagged
toRet: List(Sample2, 1.0, 2.0, 1.0, 4.0, 5.0, Sample2, 1.0, 2.0, 3.0, 4.0, 5.0)
oneTwo flagged
toRet: List(Sample1, 1.0, 2.0, 0.0, 4.0, 5.0, Sample1, 1.0, 2.0, 3.0, 4.0, 5.0)
List(MultipleRegressionDoublePhenotype(pheno3,pheno1,pheno2,pheno5,Sample2,[D@191e654), MultipleRegressionDoublePhenotype(pheno3,pheno1,pheno2,pheno5,Sample1,[D@3a6556b6))
- Test -oneTwo flag
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/BadFormatting.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/BadFormatting.txt.
- Test file format
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
List((Sample1,[Ljava.lang.String;@53fbb2b4))
- Read in a 2-line file
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
- Read in a 2-line file; call with phenoName typo
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
- Read in a 2-line file; call with covarNames typo
2017-02-28 17:36:18 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 56470. Attempting port 56471.
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/MissingPhenotypes.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/MissingPhenotypes.txt.
List((Sample1,[Ljava.lang.String;@60861e5d), (Sample2,[Ljava.lang.String;@37d81587), (Sample3,[Ljava.lang.String;@7f3e9acc), (Sample4,[Ljava.lang.String;@47d4e28a), (Sample5,[Ljava.lang.String;@177068db))
- Read in a 5-line file but with one sample missing the phenotype and two others two different covariates.
LinearGnocchiModelSuite:
Incremental actual, pred: 0.0 1.0
Incremental actual, pred: 1.0 1.0
Incremental actual, pred: 1.0 1.0
Incremental actual, pred: 1.0 1.0
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nonIncremental actual, pred: 1.0 1.0
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nonIncremental actual, pred: 1.0 1.0
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nonIncremental actual, pred: 0.0 1.0
non incremental: 0.3275
 Weights: List(-0.18241267522530813, 4.4242584928089917E-4, 0.15104023279371884, -0.10950192416277833)
incremental: 0.3275
 Weights: List(-0.25114270484529644, 4.193279012494379E-4, 0.16822939360505731, -0.10450054548581064)
- Build AdditiveLinearGnocchiModel from data and update
- [NOT IMPLEMENTED YET] Build logistic gnocchi model, update, and check results.
- [NOT IMPLEMENTED YET] Load logistic gnocchi model, update, and check results.
LinearSiteRegressionSuite:
- rsquared should be 1 if all the points lie on a line
- The rsquared for Ascombe I should be within .001 of expected results 0.6665
- The rsquared for Ascombe II should be within .001 of expected results 0.6662
- The rsquared for Ascombe III should be within .001 of expected results 0.6663
- The rsquared for Ascombe IV should be within .001 of expected results 0.6667
- Test multiple regression on PIQ data
LogisticValidationRegressionSuite:
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Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0))
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400
- Test logistic regression prediction on binary data
BuildGnocchiModelSuite:
- Build AdditiveLogisticGnocchiModel from data
LogisticSiteRegressionSuite:
- Test logisticRegression on binary data
FillGenotypesSuite:
- fill in a single variant context
- fill in with diploid no call
- fill in with haploid ref call
Run completed in 14 seconds, 256 milliseconds.
Total number of tests run: 32
Suites: completed 11, aborted 0
Tests: succeeded 32, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-core_2.10 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-core_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-core_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-core_2.10 ---
[INFO] Modified 0 of 65 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ gnocchi-core_2.10 ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gnocchi-core_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ gnocchi-core_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.scalatest:scalatest_2.10:2.2.2 requires scala version: 2.10.4
[WARNING]  org.scala-lang:scala-reflect:2.10.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.2 requires scala version: 2.10.5
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala:-1: info: compiling
[INFO] Compiling 52 source files to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/scoverage-classes at 1488332181842
[WARNING] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala/net/fnothaft/gnocchi/models/AdditiveLogisticGnocchiModel.scala:25: warning: case classes without a parameter list have been deprecated;
[WARNING] use either case objects or case classes with `()' as parameter list.
[WARNING] case class AdditiveLogisticGnocchiModel extends Serializable with GnocchiModel with Additive {
[WARNING]                                        ^
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [1495 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/scoverage-data]
[WARNING] warning: there were 1 feature warning(s); re-run with -feature for details
[WARNING] warning: there were 6 inliner warning(s); re-run with -Yinline-warnings for details
[WARNING] three warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 18 s
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:compile (default-compile) @ gnocchi-core_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ gnocchi-core_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-core_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ gnocchi-core_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 7 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ gnocchi-core_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.scalatest:scalatest_2.10:2.2.2 requires scala version: 2.10.4
[WARNING]  org.scala-lang:scala-reflect:2.10.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.2 requires scala version: 2.10.5
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:testCompile (default-testCompile) @ gnocchi-core_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ gnocchi-core_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ gnocchi-core_2.10 ---
Discovery starting.
Discovery completed in 269 milliseconds.
Run starting. Expected test count is: 32
LoadPhenotypesWithoutCovariatesSuite:
2017-02-28 17:36:41 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
- Load a simple phenotypes file, including no covariates.
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/BadFormatting.txt.
- Test file format
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
- Read in a 2-line file
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
- Read in a 2-line file; call with phenoName typo
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/MissingPhenotypes.txt.
- Read in a 5-line file but with one sample missing the phenotype.
GenotypeStateMatrixSuite:
- should filter out reference calls
- correctly process nonref calls
LogisticGnocchiModelSuite:
2017-02-28 17:36:47 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2017-02-28 17:36:47 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2017-02-28 17:36:47 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
2017-02-28 17:36:47 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
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non incremental: 0.705
 Weights: List(-3.4495483976684627, 0.0022939595044433277, 0.7770135737198527, -0.5600313868499897)
incremental: 0.7025
 Weights: List(-4.757349875457931, 0.0028276500119430886, 1.0971441479547293, -0.6967919285389909)
- Build AdditiveLogisticGnocchiModel from data and update
- [NOT IMPLEMENTED YET] Build logistic gnocchi model, update, and check results.
- [NOT IMPLEMENTED YET] Load logistic gnocchi model, update, and check results.
LoadPhenotypesWithCovariatesSuite:
List((Sample1,[Ljava.lang.String;@15186ce0))
- Load a simple phenotypes example manually
List((Sample1,[Ljava.lang.String;@16ccd2bc), (Sample2,[Ljava.lang.String;@12f8682a))
MapPartitionsRDD[23] at map at LoadPhenotypesWithCovariates.scala:216
oneTwo flagged
toRet: List(Sample2, 1.0, 2.0, 1.0, 4.0, 5.0, Sample2, 1.0, 2.0, 3.0, 4.0, 5.0)
oneTwo flagged
toRet: List(Sample1, 1.0, 2.0, 0.0, 4.0, 5.0, Sample1, 1.0, 2.0, 3.0, 4.0, 5.0)
List(MultipleRegressionDoublePhenotype(pheno3,pheno1,pheno2,pheno5,Sample2,[D@18483b8b), MultipleRegressionDoublePhenotype(pheno3,pheno1,pheno2,pheno5,Sample1,[D@24fc2c80))
- Test -oneTwo flag
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/BadFormatting.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/BadFormatting.txt.
- Test file format
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
List((Sample1,[Ljava.lang.String;@6c1b82cd))
- Read in a 2-line file
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
- Read in a 2-line file; call with phenoName typo
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt.
- Read in a 2-line file; call with covarNames typo
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/MissingPhenotypes.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/MissingPhenotypes.txt.
List((Sample1,[Ljava.lang.String;@3c5e4aac), (Sample2,[Ljava.lang.String;@20afd96f), (Sample3,[Ljava.lang.String;@565a6af), (Sample4,[Ljava.lang.String;@21bf308), (Sample5,[Ljava.lang.String;@4cded2cd))
- Read in a 5-line file but with one sample missing the phenotype and two others two different covariates.
LinearGnocchiModelSuite:
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nonIncremental actual, pred: 1.0 1.0
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nonIncremental actual, pred: 0.0 1.0
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nonIncremental actual, pred: 1.0 1.0
nonIncremental actual, pred: 1.0 1.0
nonIncremental actual, pred: 1.0 1.0
nonIncremental actual, pred: 1.0 1.0
nonIncremental actual, pred: 1.0 1.0
nonIncremental actual, pred: 0.0 1.0
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nonIncremental actual, pred: 0.0 1.0
nonIncremental actual, pred: 0.0 1.0
non incremental: 0.3275
 Weights: List(-0.18241267522530813, 4.4242584928089917E-4, 0.15104023279371884, -0.10950192416277833)
incremental: 0.3275
 Weights: List(-0.25114270484529644, 4.193279012494379E-4, 0.16822939360505731, -0.10450054548581064)
- Build AdditiveLinearGnocchiModel from data and update
- [NOT IMPLEMENTED YET] Build logistic gnocchi model, update, and check results.
- [NOT IMPLEMENTED YET] Load logistic gnocchi model, update, and check results.
LinearSiteRegressionSuite:
- rsquared should be 1 if all the points lie on a line
- The rsquared for Ascombe I should be within .001 of expected results 0.6665
- The rsquared for Ascombe II should be within .001 of expected results 0.6662
- The rsquared for Ascombe III should be within .001 of expected results 0.6663
- The rsquared for Ascombe IV should be within .001 of expected results 0.6667
- Test multiple regression on PIQ data
LogisticValidationRegressionSuite:
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Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0))
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400
- Test logistic regression prediction on binary data
BuildGnocchiModelSuite:
- Build AdditiveLogisticGnocchiModel from data
LogisticSiteRegressionSuite:
- Test logisticRegression on binary data
FillGenotypesSuite:
- fill in a single variant context
- fill in with diploid no call
- fill in with haploid ref call
Run completed in 11 seconds, 870 milliseconds.
Total number of tests run: 32
Suites: completed 11, aborted 0
Tests: succeeded 32, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-core_2.10 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-core_2.10 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi-cli: Command line interface for managing and querying variant store 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[WARNING] The POM for org.bdgenomics.adam:adam-cli_2.10:jar:0.19.0 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-cli_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-cli_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-cli_2.10 ---
[INFO] Modified 0 of 17 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gnocchi-cli_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ gnocchi-cli_2.10 ---
[WARNING] Invalid POM for org.bdgenomics.adam:adam-cli_2.10:jar:0.19.0, transitive dependencies (if any) will not be available, enable debug logging for more details
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.2 requires scala version: 2.10.5
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 14 source files to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/classes at 1488332215779
[INFO] prepare-compile in 0 s
[INFO] compile in 9 s
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:compile (default-compile) @ gnocchi-cli_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-cli_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ gnocchi-cli_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 189 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ gnocchi-cli_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.2 requires scala version: 2.10.5
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 3 source files to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes at 1488332225778
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:testCompile (default-testCompile) @ gnocchi-cli_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ gnocchi-cli_2.10 ---
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ gnocchi-cli_2.10 ---
Discovery starting.
Discovery completed in 211 milliseconds.
Run starting. Expected test count is: 10
RegressPhenotypesSuite:
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli_2.10/0.19.0/adam-cli_2.10-0.19.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/jenkins/.m2/repository/org/slf4j/slf4j-log4j12/1.7.12/slf4j-log4j12-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
2017-02-28 17:37:13 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/2Liner.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/2Liner.txt.
- Test LoadPhenotypes: Read in a 2-line phenotype file; call with one of the covariate names same as pheno name
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
List([1_14522_A,14521,14522,G,A,sample1,1,0], [1_752721_G,752720,752721,A,G,sample1,0,0])
- Test LoadPhenotypes: Read in a 2-line phenotype file; call with ADDDITIVE_LINEAR but with no phenoName
List([1_14522_A,14521,14522,G,A,sample1,1,0], [1_752721_G,752720,752721,A,G,sample1,0,0])
- Test LoadPhenotypes: Read in a 2-line phenotype file; call with -covar but not -covarNames
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51282. Attempting port 51283.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51283. Attempting port 51284.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51284. Attempting port 51285.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51285. Attempting port 51286.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51286. Attempting port 51287.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51287. Attempting port 51288.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51288. Attempting port 51289.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51289. Attempting port 51290.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51290. Attempting port 51291.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51291. Attempting port 51292.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51292. Attempting port 51293.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51293. Attempting port 51294.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51294. Attempting port 51295.
2017-02-28 17:37:24 WARN  Utils:70 - Service 'sparkDriver' could not bind on port 51295. Attempting port 51296.
List([1_14522_A,14521,14522,G,A,sample1,1,0], [1_752721_G,752720,752721,A,G,sample1,0,0])
- Test loadGenotypes: output from vcf input
List([1_752721_G,752720,752721,A,G,sample1,2,0], [1_752721_G,752720,752721,A,G,sample2,2,0], [1_752721_G,752720,752721,A,G,sample3,2,0], [1_752721_G,752720,752721,A,G,sample4,2,0], [1_752721_G,752720,752721,A,G,sample5,1,0], [1_752721_G,752720,752721,A,G,sample6,1,0], [1_752721_G,752720,752721,A,G,sample7,1,0], [1_752721_G,752720,752721,A,G,sample8,0,0], [1_752721_G,752720,752721,A,G,sample9,0,0], [1_752721_G,752720,752721,A,G,sample10,0,0])
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/10samples1Phenotype.txt.
- Test full pipeline: 1 snp, 10 samples, 1 phenotype, no covars
List([1_752721_G,752720,752721,A,G,sample1,2,0], [1_752721_G,752720,752721,A,G,sample2,2,0], [1_752721_G,752720,752721,A,G,sample3,2,0], [1_752721_G,752720,752721,A,G,sample4,2,0], [1_752721_G,752720,752721,A,G,sample5,1,0], [1_752721_G,752720,752721,A,G,sample6,1,0], [1_752721_G,752720,752721,A,G,sample7,1,0], [1_752721_G,752720,752721,A,G,sample8,0,0], [1_752721_G,752720,752721,A,G,sample9,0,0], [1_752721_G,752720,752721,A,G,sample10,0,0])
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/12samples1Phenotype.txt.
- Test full pipeline: 1 snp, 10 samples, 12 samples in phenotype file (10 matches) 1 phenotype, no covar
/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/5snps10samples.vcf
List([1_752721_G,752720,752721,A,G,sample1,2,0], [1_752721_G,752720,752721,A,G,sample2,2,0], [1_752721_G,752720,752721,A,G,sample3,2,0], [1_752721_G,752720,752721,A,G,sample4,1,0], [1_752721_G,752720,752721,A,G,sample5,1,0], [1_752721_G,752720,752721,A,G,sample6,1,0], [1_752721_G,752720,752721,A,G,sample7,0,0], [1_752721_G,752720,752721,A,G,sample8,0,0], [1_752721_G,752720,752721,A,G,sample9,0,0], [1_752721_G,752720,752721,A,G,sample10,0,0])
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/10samples5Phenotypes2covars.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/10samples5Phenotypes2covars.txt.
List((sample1,[Ljava.lang.String;@7220ff10), (sample2,[Ljava.lang.String;@776eb512), (sample3,[Ljava.lang.String;@4ba29b51), (sample4,[Ljava.lang.String;@35e7cdb2), (sample5,[Ljava.lang.String;@404a7c61))
SNP Name: 1_752721_G
SNP Locus: 752720-752721
Phenotypes: pheno1,pheno4,pheno5
logPValue: -0.03119679506700715
SNP Name: 1_752722_T
SNP Locus: 752721-752722
Phenotypes: pheno1,pheno4,pheno5
logPValue: -Infinity
SNP Name: 1_752724_T
SNP Locus: 752723-752724
Phenotypes: pheno1,pheno4,pheno5
logPValue: -0.024531307840048987
SNP Name: 1_752723_G
SNP Locus: 752722-752723
Phenotypes: pheno1,pheno4,pheno5
logPValue: -0.5640859336668335
SNP Name: 1_752725_A
SNP Locus: 752724-752725
Phenotypes: pheno1,pheno4,pheno5
logPValue: -0.16728616498042978
- Test full pipeline: 5 snps, 10 samples, 1 phenotype, 2 random noise covars
EvaluateModelSuite:
- Test Average Ensembler: Pass in potential SNP and values 
- Test MaxProb Ensembler: Pass in potential SNP and values 
- Test WeightedAverage Ensembler: Pass in potential SNP and values 
Run completed in 18 seconds, 360 milliseconds.
Total number of tests run: 10
Suites: completed 3, aborted 0
Tests: succeeded 10, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-cli_2.10 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-cli_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-cli_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-cli_2.10 ---
[INFO] Modified 0 of 17 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ gnocchi-cli_2.10 ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gnocchi-cli_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ gnocchi-cli_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.2 requires scala version: 2.10.5
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/src/main/scala:-1: info: compiling
[INFO] Compiling 14 source files to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/scoverage-classes at 1488332251745
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [814 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 11 s
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:compile (default-compile) @ gnocchi-cli_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ gnocchi-cli_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-cli_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ gnocchi-cli_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 189 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.1.5:testCompile (scala-test-compile-first) @ gnocchi-cli_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli_2.10:0.2.8 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io_2.10:0.2.4 requires scala version: 2.10.4
[WARNING]  org.scoverage:scalac-scoverage-plugin_2.10:1.1.1 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.adam:adam-core_2.10:0.19.0 requires scala version: 2.10.4
[WARNING]  com.twitter:chill_2.10:0.5.0 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-remote_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-actor_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  com.typesafe.akka:akka-slf4j_2.10:2.3.11 requires scala version: 2.10.4
[WARNING]  org.apache.spark:spark-core_2.10:1.6.2 requires scala version: 2.10.5
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:2.5.1:testCompile (default-testCompile) @ gnocchi-cli_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.17:test (default-test) @ gnocchi-cli_2.10 ---
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ gnocchi-cli_2.10 ---
Discovery starting.
Discovery completed in 172 milliseconds.
Run starting. Expected test count is: 10
RegressPhenotypesSuite:
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/jenkins/.m2/repository/org/bdgenomics/adam/adam-cli_2.10/0.19.0/adam-cli_2.10-0.19.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/jenkins/.m2/repository/org/slf4j/slf4j-log4j12/1.7.12/slf4j-log4j12-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory]
2017-02-28 17:37:44 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/2Liner.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/2Liner.txt.
- Test LoadPhenotypes: Read in a 2-line phenotype file; call with one of the covariate names same as pheno name
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
List([1_14522_A,14521,14522,G,A,sample1,1,0], [1_752721_G,752720,752721,A,G,sample1,0,0])
- Test LoadPhenotypes: Read in a 2-line phenotype file; call with ADDDITIVE_LINEAR but with no phenoName
List([1_14522_A,14521,14522,G,A,sample1,1,0], [1_752721_G,752720,752721,A,G,sample1,0,0])
- Test LoadPhenotypes: Read in a 2-line phenotype file; call with -covar but not -covarNames
List([1_14522_A,14521,14522,G,A,sample1,1,0], [1_752721_G,752720,752721,A,G,sample1,0,0])
- Test loadGenotypes: output from vcf input
List([1_752721_G,752720,752721,A,G,sample1,2,0], [1_752721_G,752720,752721,A,G,sample2,2,0], [1_752721_G,752720,752721,A,G,sample3,2,0], [1_752721_G,752720,752721,A,G,sample4,2,0], [1_752721_G,752720,752721,A,G,sample5,1,0], [1_752721_G,752720,752721,A,G,sample6,1,0], [1_752721_G,752720,752721,A,G,sample7,1,0], [1_752721_G,752720,752721,A,G,sample8,0,0], [1_752721_G,752720,752721,A,G,sample9,0,0], [1_752721_G,752720,752721,A,G,sample10,0,0])
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/10samples1Phenotype.txt.
- Test full pipeline: 1 snp, 10 samples, 1 phenotype, no covars
List([1_752721_G,752720,752721,A,G,sample1,2,0], [1_752721_G,752720,752721,A,G,sample2,2,0], [1_752721_G,752720,752721,A,G,sample3,2,0], [1_752721_G,752720,752721,A,G,sample4,2,0], [1_752721_G,752720,752721,A,G,sample5,1,0], [1_752721_G,752720,752721,A,G,sample6,1,0], [1_752721_G,752720,752721,A,G,sample7,1,0], [1_752721_G,752720,752721,A,G,sample8,0,0], [1_752721_G,752720,752721,A,G,sample9,0,0], [1_752721_G,752720,752721,A,G,sample10,0,0])
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/12samples1Phenotype.txt.
- Test full pipeline: 1 snp, 10 samples, 12 samples in phenotype file (10 matches) 1 phenotype, no covar
/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/5snps10samples.vcf
List([1_752721_G,752720,752721,A,G,sample1,2,0], [1_752721_G,752720,752721,A,G,sample2,2,0], [1_752721_G,752720,752721,A,G,sample3,2,0], [1_752721_G,752720,752721,A,G,sample4,1,0], [1_752721_G,752720,752721,A,G,sample5,1,0], [1_752721_G,752720,752721,A,G,sample6,1,0], [1_752721_G,752720,752721,A,G,sample7,0,0], [1_752721_G,752720,752721,A,G,sample8,0,0], [1_752721_G,752720,752721,A,G,sample9,0,0], [1_752721_G,752720,752721,A,G,sample10,0,0])
Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/10samples5Phenotypes2covars.txt.
Loading covars form /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/10samples5Phenotypes2covars.txt.
List((sample1,[Ljava.lang.String;@4b6abf4e), (sample2,[Ljava.lang.String;@27959922), (sample3,[Ljava.lang.String;@794daa09), (sample4,[Ljava.lang.String;@796267e8), (sample5,[Ljava.lang.String;@676c3745))
SNP Name: 1_752721_G
SNP Locus: 752720-752721
Phenotypes: pheno1,pheno4,pheno5
logPValue: -0.03119679506700715
SNP Name: 1_752722_T
SNP Locus: 752721-752722
Phenotypes: pheno1,pheno4,pheno5
logPValue: -Infinity
SNP Name: 1_752724_T
SNP Locus: 752723-752724
Phenotypes: pheno1,pheno4,pheno5
logPValue: -0.024531307840048987
SNP Name: 1_752723_G
SNP Locus: 752722-752723
Phenotypes: pheno1,pheno4,pheno5
logPValue: -0.5640859336668335
SNP Name: 1_752725_A
SNP Locus: 752724-752725
Phenotypes: pheno1,pheno4,pheno5
logPValue: -0.16728616498042978
- Test full pipeline: 5 snps, 10 samples, 1 phenotype, 2 random noise covars
EvaluateModelSuite:
- Test Average Ensembler: Pass in potential SNP and values 
- Test MaxProb Ensembler: Pass in potential SNP and values 
- Test WeightedAverage Ensembler: Pass in potential SNP and values 
Run completed in 18 seconds, 758 milliseconds.
Total number of tests run: 10
Suites: completed 3, aborted 0
Tests: succeeded 10, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-cli_2.10 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-cli_2.10 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi: Genotype store and query engine 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:3.0.1:report (default-cli) @ gnocchi-parent_2.10 ---
[INFO] Starting Coveralls job for jenkins (8 / https://amplab.cs.berkeley.edu/jenkins/job/gnocchi-prb/HADOOP_VERSION=2.3.0,SCALAVER=2.10,SPARK_VERSION=1.6.1,label=centos/8/)
[INFO] Using repository token <secret>
[INFO] Git commit 529ea81 in issues/10-add-ci
[INFO] Writing Coveralls data to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/target/coveralls.json...
[INFO] Processing coverage report from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 169ms
[INFO] Gathered code coverage metrics for 67 source files with 7542 lines of code:
[INFO] - 1165 relevant lines
[INFO] - 430 covered lines
[INFO] - 735 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 1254ms for Job #8.2
[INFO] https://coveralls.io/jobs/23395679
[INFO] *** It might take hours for Coveralls to update the actual coverage numbers for a job
[INFO]     If you see question marks in the report, please be patient
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] gnocchi: Genotype store and query engine .......... SUCCESS [1.857s]
[INFO] gnocchi-core: Core APIs and queries ............... SUCCESS [1:23.792s]
[INFO] gnocchi-cli: Command line interface for managing and querying variant store  SUCCESS [1:09.939s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2:40.416s
[INFO] Finished at: Tue Feb 28 17:38:06 PST 2017
[INFO] Final Memory: 41M/1507M
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${GNOCCHI_MVN_TMP_DIR}
+ find /tmp/gnocchiTestMvn3vJwsGP
/tmp/gnocchiTestMvn3vJwsGP
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/parquetInputFiles
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/parquetInputFiles/part-r-00000.gz.parquet
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/parquetInputFiles/._common_metadata.crc
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/parquetInputFiles/_metadata
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/parquetInputFiles/._metadata.crc
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/parquetInputFiles/.part-r-00000.gz.parquet.crc
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/parquetInputFiles/._SUCCESS.crc
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/parquetInputFiles/_SUCCESS
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/parquetInputFiles/_common_metadata
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/Association
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/Association/part-00000
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/Association/.part-00001.crc
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/Association/._SUCCESS.crc
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/Association/part-00001
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/Association/.part-00000.crc
/tmp/gnocchiTestMvn3vJwsGP/5493962740588722774/src/test/resources/testData/Association/_SUCCESS
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/parquetInputFiles
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/parquetInputFiles/part-r-00000.gz.parquet
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/parquetInputFiles/._common_metadata.crc
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/parquetInputFiles/_metadata
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/parquetInputFiles/._metadata.crc
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/parquetInputFiles/.part-r-00000.gz.parquet.crc
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/parquetInputFiles/._SUCCESS.crc
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/parquetInputFiles/_SUCCESS
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/parquetInputFiles/_common_metadata
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/Association
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/Association/part-00000
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/Association/.part-00001.crc
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/Association/._SUCCESS.crc
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/Association/part-00001
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/Association/.part-00000.crc
/tmp/gnocchiTestMvn3vJwsGP/7768488786516312868/src/test/resources/testData/Association/_SUCCESS
rm -rf ${GNOCCHI_MVN_TMP_DIR}
+ rm -rf /tmp/gnocchiTestMvn3vJwsGP

# and move our poms back to their original values
# this will allow us to pass our porcelain test at the end
if [ ${SPARK_VERSION} == 2.0.0 ];
then
    
    echo "Rewriting POM.xml files back to Spark 1."
    ./scripts/move_to_spark_1.sh
fi
+ '[' 1.6.1 == 2.0.0 ']'
if [ ${SCALAVER} == 2.11 ];
then
    echo "Rewriting POM.xml files back to Scala 2.10."
    ./scripts/move_to_scala_2.10.sh
fi
+ '[' 2.10 == 2.11 ']'

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${GNOCCHI_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/gnocchiTestMvn3vJwsGP:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

if test -n "$(git status --porcelain)"
then
    echo "Applying move_to_xyz script marred a pom.xml file."
    echo "Exiting..."
    exit 1
fi
++ git status --porcelain
+ test -n ''

pushd ${PROJECT_ROOT}
+ pushd /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/scripts/..
~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos ~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos
./scripts/format-source
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/scripts
+ pushd /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/scripts/..
~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos ~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos
+ mvn org.scalariform:scalariform-maven-plugin:format license:format
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for net.fnothaft:gnocchi-core_2.10:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.apache.commons:commons-math3:jar -> version (?) vs 3.6.1 @ line 96, column 17
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for net.fnothaft:gnocchi-cli_2.10: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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, column 25
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 336, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 348, 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. @ net.fnothaft:gnocchi-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/pom.xml, line 352, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for net.fnothaft:gnocchi-parent_2.10: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 336, 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 348, 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 352, 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] gnocchi: Genotype store and query engine
[INFO] gnocchi-core: Core APIs and queries
[INFO] gnocchi-cli: Command line interface for managing and querying variant store
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Downloading: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-gpg-plugin/1.5/maven-gpg-plugin-1.5.jar
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Downloaded: http://repo.maven.apache.org/maven2/org/apache/maven/plugins/maven-gpg-plugin/1.5/maven-gpg-plugin-1.5.jar (44 KB at 483.6 KB/sec)
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi: Genotype store and query engine 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-parent_2.10 ---
[INFO] Modified 0 of 84 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ gnocchi-parent_2.10 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi-core: Core APIs and queries 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-core_2.10 ---
[INFO] Modified 0 of 65 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ gnocchi-core_2.10 ---
[INFO] Updating license headers...
[WARNING] Unknown file extension: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala/net/fnothaft/gnocchi/README.md
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building gnocchi-cli: Command line interface for managing and querying variant store 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-cli_2.10 ---
[INFO] Modified 0 of 17 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ gnocchi-cli_2.10 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] gnocchi: Genotype store and query engine .......... SUCCESS [2.542s]
[INFO] gnocchi-core: Core APIs and queries ............... SUCCESS [0.699s]
[INFO] gnocchi-cli: Command line interface for managing and querying variant store  SUCCESS [0.242s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 4.448s
[INFO] Finished at: Tue Feb 28 17:38:12 PST 2017
[INFO] Final Memory: 17M/1086M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/1.6.1/label/centos
if test -n "$(git status --porcelain)"
then
    echo "Please run './scripts/format-source'"
    exit 1
fi
++ git status --porcelain
+ test -n ''

echo
+ echo

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

Recording test results
Finished: SUCCESS