Started by upstream project "gnocchi-prb" build number 11 originally caused by: GitHub pull request #12 of commit eed5afc4d87729ab23d512bc18aa2116c7ebf697 automatically merged. [EnvInject] - Loading node environment variables. Building remotely on amp-jenkins-worker-02 (centos spark-test spark-compile) in workspace /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/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 770a253263125291be0b333bac7c10eb8a6b9709 (origin/pr/12/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 770a253263125291be0b333bac7c10eb8a6b9709 > git rev-list 1aff34746d1424d089087d03539fbfe41ab53e0a # timeout=10 First time build. Skipping changelog. [centos] $ /bin/bash /tmp/hudson4837092619163318675.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/2.11/SPARK_VERSION/1.6.1/label/centos/scripts/jenkins-test # make a tempdir for writing maven cruft to GNOCCHI_MVN_TMP_DIR=$(mktemp -d -t gnocchiTestMvnXXXXXXX) ++ mktemp -d -t gnocchiTestMvnXXXXXXX + GNOCCHI_MVN_TMP_DIR=/tmp/gnocchiTestMvnBCqyn4P # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/gnocchiTestMvnBCqyn4P: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 ${BASH_SOURCE[0]} ) && pwd ) +++ dirname /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/scripts/jenkins-test ++ cd /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/scripts ++ pwd + DIR=/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/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 + '[' 2.11 == 2.11 ']' + echo 'Rewriting POM.xml files for Scala 2.11.' Rewriting POM.xml files for Scala 2.11. + ./scripts/move_to_scala_2.11.sh + set +e + ./scripts/move_to_scala_2.11.sh Scala version is already set to 2.11 (Scala artifacts have _2.11 version suffix in artifact name). Cowardly refusing to move to Scala 2.11 a second time... + [[ 1 == 0 ]] + set -e # 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_2.11: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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11: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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11: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_2.11 --- [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_2.11 --- [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_2.11 --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] gnocchi: Genotype store and query engine .......... SUCCESS [0.142s] [INFO] gnocchi-core: Core APIs and queries ............... SUCCESS [0.011s] [INFO] gnocchi-cli: Command line interface for managing and querying variant store SUCCESS [0.009s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.301s [INFO] Finished at: Tue Feb 28 23:00:25 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_2.11: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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11: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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11:0.0.1-SNAPSHOT, /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11: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_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-parent_2.11 --- [INFO] Modified 0 of 74 .scala files [INFO] [INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ gnocchi-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-parent_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-parent_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-parent_2.11 --- [INFO] Modified 0 of 74 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ gnocchi-parent_2.11 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.1.5:compile (scala-compile-first) @ gnocchi-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ gnocchi-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-parent_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-parent_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-parent_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building gnocchi-core: Core APIs and queries 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core_2.11/0.19.0/adam-core_2.11-0.19.0.pom 4/8 KB 7/8 KB 8/8 KB Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core_2.11/0.19.0/adam-core_2.11-0.19.0.pom (8 KB at 30.4 KB/sec) Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-parent_2.11/0.19.0/adam-parent_2.11-0.19.0.pom 4/24 KB 6/24 KB 8/24 KB 10/24 KB 11/24 KB 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KB 1536/1542 KB 1540/1542 KB 1541/1542 KB 1542/1542 KB Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core_2.11/0.19.0/adam-core_2.11-0.19.0-tests.jar (1542 KB at 3788.5 KB/sec) [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-core_2.11 --- [INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 55 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gnocchi-core_2.11 --- [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/2.11/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_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.scalatest:scalatest_2.11:2.2.2 requires scala version: 2.11.2 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala:-1: info: compiling [INFO] Compiling 44 source files to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/classes at 1488351634754 [WARNING] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala/net/fnothaft/gnocchi/sql/GnocchiContext.scala:32: warning: no valid targets for annotation on value sqlContext - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class GnocchiContext private[sql] (@transient sqlContext: SQLContext) extends Serializable { [WARNING] ^ [WARNING] warning: there was one feature warning; re-run with -feature for details [WARNING] warning: there was one inliner warning; re-run with -Yinline-warnings for details [WARNING] three warnings found [INFO] prepare-compile in 0 s [INFO] compile in 19 s [INFO] [INFO] --- maven-compiler-plugin:2.5.1:compile (default-compile) @ gnocchi-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-core_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.scalatest:scalatest_2.11:2.2.2 requires scala version: 2.11.2 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/test/scala:-1: info: compiling [INFO] Compiling 11 source files to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes at 1488351654648 [WARNING] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/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 15 s [INFO] [INFO] --- maven-compiler-plugin:2.5.1:testCompile (default-testCompile) @ gnocchi-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ gnocchi-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ gnocchi-core_2.11 --- Discovery starting. Discovery completed in 277 milliseconds. Run starting. Expected test count is: 32 LoadPhenotypesWithoutCovariatesSuite: 2017-02-28 23:01:11 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/2.11/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/2.11/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/2.11/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/2.11/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 23:01:17 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2017-02-28 23:01:17 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS 2017-02-28 23:01:17 WARN LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK 2017-02-28 23:01:17 WARN LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 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Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental 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Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental 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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 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 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 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 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 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;@71039ce1)) - Load a simple phenotypes example manually List((Sample1,[Ljava.lang.String;@527d48db), (Sample2,[Ljava.lang.String;@194037f9)) 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@4fea5ee0), MultipleRegressionDoublePhenotype(pheno3,pheno1,pheno2,pheno5,Sample1,[D@65f5cae3)) - Test -oneTwo flag Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt. List((Sample1,[Ljava.lang.String;@f2becb2)) - Read in a 2-line file Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/MissingPhenotypes.txt. List((Sample1,[Ljava.lang.String;@3831f4c2), (Sample2,[Ljava.lang.String;@75f2ff80), (Sample3,[Ljava.lang.String;@253b1cbd), (Sample4,[Ljava.lang.String;@a859c5), (Sample5,[Ljava.lang.String;@37083af6)) - 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 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 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 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 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 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 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 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 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 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 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 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 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 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 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 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 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 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 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 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 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 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 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nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 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 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 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: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 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: Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: 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(,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) 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, 747 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_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-core_2.11 --- [INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 55 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ gnocchi-core_2.11 --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gnocchi-core_2.11 --- [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/2.11/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_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.scalatest:scalatest_2.11:2.2.2 requires scala version: 2.11.2 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala:-1: info: compiling [INFO] Compiling 44 source files to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/scoverage-classes at 1488351683351 [WARNING] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/src/main/scala/net/fnothaft/gnocchi/sql/GnocchiContext.scala:32: warning: no valid targets for annotation on value sqlContext - it is discarded unused. You may specify targets with meta-annotations, e.g. @(transient @param) [WARNING] class GnocchiContext private[sql] (@transient sqlContext: SQLContext) extends Serializable { [WARNING] ^ [INFO] [info] Cleaning datadir [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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 [1491 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/scoverage-data] [WARNING] warning: there was one feature warning; re-run with -feature for details [WARNING] warning: there was one inliner warning; 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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ gnocchi-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-core_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.scalatest:scalatest_2.11:2.2.2 requires scala version: 2.11.2 [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_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ gnocchi-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ gnocchi-core_2.11 --- Discovery starting. Discovery completed in 284 milliseconds. Run starting. Expected test count is: 32 LoadPhenotypesWithoutCovariatesSuite: 2017-02-28 23:01:42 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/2.11/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/2.11/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/2.11/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/2.11/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 23:01:48 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2017-02-28 23:01:48 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS 2017-02-28 23:01:48 WARN LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK 2017-02-28 23:01:48 WARN LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 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1.0 0.0 Incremental actual, pred: 1.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 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 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental 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 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 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 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 0.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 nonIncremental actual, pred: 1.0 0.0 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 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;@6ac756b)) - Load a simple phenotypes example manually List((Sample1,[Ljava.lang.String;@59f7c106), (Sample2,[Ljava.lang.String;@136fece2)) 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@27e21083), MultipleRegressionDoublePhenotype(pheno3,pheno1,pheno2,pheno5,Sample1,[D@67a6a2d0)) - Test -oneTwo flag Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/2Liner.txt. List((Sample1,[Ljava.lang.String;@2a531637)) - Read in a 2-line file Loading phenotypes from /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-core/target/test-classes/MissingPhenotypes.txt. List((Sample1,[Ljava.lang.String;@4e9bd2c8), (Sample2,[Ljava.lang.String;@18f13756), (Sample3,[Ljava.lang.String;@665b441e), (Sample4,[Ljava.lang.String;@2ac3d530), (Sample5,[Ljava.lang.String;@3a5e4f32)) - 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 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 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 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 0.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 1.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 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 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 0.0 1.0 Incremental actual, pred: 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nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 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 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 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 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 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: 1.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 nonIncremental actual, pred: 0.0 1.0 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: Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: 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Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,1.0)) | Theirs: (,(0.0,1.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,1.0)) | Theirs: (,(1.0,1.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(1.0,0.0)) | Theirs: (,(1.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) Ours: (,(0.0,0.0)) | Theirs: (,(0.0,0.0)) 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, 279 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_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-core_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building gnocchi-cli: Command line interface for managing and querying variant store 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-cli_2.11/0.19.0/adam-cli_2.11-0.19.0.pom 4/9 KB 6/9 KB 9/9 KB Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-cli_2.11/0.19.0/adam-cli_2.11-0.19.0.pom (9 KB at 157.7 KB/sec) [WARNING] The POM for org.bdgenomics.adam:adam-cli_2.11:jar:0.19.0 is invalid, transitive dependencies (if any) will not be available, enable debug logging for more details Downloading: http://repo.maven.apache.org/maven2/org/apache/directory/studio/org.apache.commons.io/2.4/org.apache.commons.io-2.4.pom 4/5 KB 5/5 KB Downloaded: http://repo.maven.apache.org/maven2/org/apache/directory/studio/org.apache.commons.io/2.4/org.apache.commons.io-2.4.pom 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[INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-cli_2.11 --- [INFO] Modified 0 of 17 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gnocchi-cli_2.11 --- [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/2.11/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_2.11 --- [WARNING] Invalid POM for org.bdgenomics.adam:adam-cli_2.11: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: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io_2.11:0.2.4 requires scala version: 2.11.4 [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:1.1.1 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/classes at 1488351717661 [INFO] prepare-compile in 0 s [INFO] compile in 10 s [INFO] [INFO] --- maven-compiler-plugin:2.5.1:compile (default-compile) @ gnocchi-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-cli_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io_2.11:0.2.4 requires scala version: 2.11.4 [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:1.1.1 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes at 1488351727947 [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:2.5.1:testCompile (default-testCompile) @ gnocchi-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.17:test (default-test) @ gnocchi-cli_2.11 --- [INFO] [INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ gnocchi-cli_2.11 --- Discovery starting. Discovery completed in 152 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_2.11/0.19.0/adam-cli_2.11-0.19.0.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 23:02:14 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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/10samples5Phenotypes2covars.txt. List((sample1,[Ljava.lang.String;@7685912e), (sample2,[Ljava.lang.String;@3ea3b20d), (sample3,[Ljava.lang.String;@17856f0), (sample4,[Ljava.lang.String;@3ffa424d), (sample5,[Ljava.lang.String;@652cb87d)) 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 17 seconds, 427 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_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ gnocchi-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ gnocchi-cli_2.11 --- [INFO] Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11 --- [INFO] Modified 0 of 17 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ gnocchi-cli_2.11 --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ gnocchi-cli_2.11 --- [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/2.11/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_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io_2.11:0.2.4 requires scala version: 2.11.4 [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:1.1.1 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/scoverage-classes at 1488351752479 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [813 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 12 s [INFO] [INFO] --- maven-compiler-plugin:2.5.1:compile (default-compile) @ gnocchi-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ gnocchi-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ gnocchi-cli_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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_2.11 --- [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_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-misc_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-cli_2.11:0.2.8 requires scala version: 2.11.4 [WARNING] org.bdgenomics.utils:utils-io_2.11:0.2.4 requires scala version: 2.11.4 [WARNING] org.scoverage:scalac-scoverage-plugin_2.11:1.1.1 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:2.5.1:testCompile (default-testCompile) @ gnocchi-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.17:test (default-test) @ gnocchi-cli_2.11 --- [INFO] [INFO] --- scalatest-maven-plugin:1.0-RC2:test (test) @ gnocchi-cli_2.11 --- Discovery starting. Discovery completed in 159 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_2.11/0.19.0/adam-cli_2.11-0.19.0.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 23:02:45 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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/gnocchi-cli/target/test-classes/10samples5Phenotypes2covars.txt. List((sample1,[Ljava.lang.String;@7d25d10e), (sample2,[Ljava.lang.String;@3979ff82), (sample3,[Ljava.lang.String;@77524169), (sample4,[Ljava.lang.String;@74161ed7), (sample5,[Ljava.lang.String;@27e80cfa)) 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, 591 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_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ gnocchi-cli_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [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_2.11 --- [INFO] Starting Coveralls job for jenkins (11 / https://amplab.cs.berkeley.edu/jenkins/job/gnocchi-prb/HADOOP_VERSION=2.3.0,SCALAVER=2.11,SPARK_VERSION=1.6.1,label=centos/11/) [INFO] Using repository token <secret> [INFO] Git commit 770a253 in issues/10-add-ci [INFO] Writing Coveralls data to /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/target/cobertura.xml [INFO] Successfully wrote Coveralls data in 145ms [INFO] Gathered code coverage metrics for 67 source files with 7527 lines of code: [INFO] - 1165 relevant lines [INFO] - 431 covered lines [INFO] - 734 missed lines [INFO] Submitting Coveralls data to API [INFO] Successfully submitted Coveralls data in 897ms for Job #11.4 [INFO] https://coveralls.io/jobs/23398894 [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 [1.397s] [INFO] gnocchi-core: Core APIs and queries ............... SUCCESS [1:24.465s] [INFO] gnocchi-cli: Command line interface for managing and querying variant store SUCCESS [1:10.730s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 2:40.826s [INFO] Finished at: Tue Feb 28 23:03:07 PST 2017 [INFO] Final Memory: 45M/1510M [INFO] ------------------------------------------------------------------------ # we are done with maven, so clean up the maven temp dir find ${GNOCCHI_MVN_TMP_DIR} + find /tmp/gnocchiTestMvnBCqyn4P /tmp/gnocchiTestMvnBCqyn4P /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802 /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/Association /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/Association/_SUCCESS /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/Association/.part-00001.crc /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/Association/part-00001 /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/Association/._SUCCESS.crc /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/Association/part-00000 /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/Association/.part-00000.crc /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/parquetInputFiles /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/parquetInputFiles/._metadata.crc /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/parquetInputFiles/_SUCCESS /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/parquetInputFiles/.part-r-00000.gz.parquet.crc /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/parquetInputFiles/_metadata /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/parquetInputFiles/part-r-00000.gz.parquet /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/parquetInputFiles/._SUCCESS.crc /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/parquetInputFiles/_common_metadata /tmp/gnocchiTestMvnBCqyn4P/4153546614713743802/src/test/resources/testData/parquetInputFiles/._common_metadata.crc /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043 /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/Association /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/Association/_SUCCESS /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/Association/.part-00001.crc /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/Association/part-00001 /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/Association/._SUCCESS.crc /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/Association/part-00000 /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/Association/.part-00000.crc /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/parquetInputFiles /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/parquetInputFiles/._metadata.crc /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/parquetInputFiles/_SUCCESS /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/parquetInputFiles/.part-r-00000.gz.parquet.crc /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/parquetInputFiles/_metadata /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/parquetInputFiles/part-r-00000.gz.parquet /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/parquetInputFiles/._SUCCESS.crc /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/parquetInputFiles/_common_metadata /tmp/gnocchiTestMvnBCqyn4P/6808561850381917043/src/test/resources/testData/parquetInputFiles/._common_metadata.crc rm -rf ${GNOCCHI_MVN_TMP_DIR} + rm -rf /tmp/gnocchiTestMvnBCqyn4P # 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 [ ${SCALAVER} == 2.11 ]; then echo "Rewriting POM.xml files back to Scala 2.10." ./scripts/move_to_scala_2.10.sh fi + '[' 2.11 == 2.11 ']' + echo 'Rewriting POM.xml files back to Scala 2.10.' Rewriting POM.xml files back to Scala 2.10. + ./scripts/move_to_scala_2.10.sh find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/gnocchiTestMvnBCqyn4P: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/2.11/SPARK_VERSION/1.6.1/label/centos/scripts/.. ~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos ~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/SPARK_VERSION/1.6.1/label/centos/scripts + pushd /home/jenkins/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos/scripts/.. ~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/1.6.1/label/centos ~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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/2.11/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] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ gnocchi-parent_2.10 --- [INFO] Modified 0 of 74 .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 55 .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/2.11/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 [2.426s] [INFO] gnocchi-core: Core APIs and queries ............... SUCCESS [0.594s] [INFO] gnocchi-cli: Command line interface for managing and querying variant store SUCCESS [0.216s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 3.598s [INFO] Finished at: Tue Feb 28 23:03:12 PST 2017 [INFO] Final Memory: 17M/1080M [INFO] ------------------------------------------------------------------------ + popd ~/workspace/gnocchi-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/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