FailedConsole Output

Started by upstream project "avocado-prb" build number 211
originally caused by:
 GitHub pull request #266 of commit 71f0e3e20a56ebb549470159cb4a98047089f566 automatically merged.
[EnvInject] - Loading node environment variables.
Building remotely on amp-jenkins-worker-04 (centos spark-test) in workspace /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos
Cloning the remote Git repository
Cloning repository https://github.com/bigdatagenomics/avocado.git
 > git init /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git
 > git --version # timeout=10
 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/heads/*:refs/remotes/origin/*
 > git config remote.origin.url https://github.com/bigdatagenomics/avocado.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/avocado.git # timeout=10
Fetching upstream changes from https://github.com/bigdatagenomics/avocado.git
 > git fetch --tags --progress https://github.com/bigdatagenomics/avocado.git +refs/pull/*:refs/remotes/origin/pr/*
Checking out Revision 1e39b43d08478a1cd9446a41270d58820e652a38 (origin/pr/266/merge)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f 1e39b43d08478a1cd9446a41270d58820e652a38
First time build. Skipping changelog.
[centos] $ /bin/bash /tmp/hudson5089784857729438129.sh
+ set -e
+ export JAVA_HOME=/usr/java/jdk1.8.0_60
+ JAVA_HOME=/usr/java/jdk1.8.0_60
+ export CONDA_BIN=/home/anaconda/bin/
+ CONDA_BIN=/home/anaconda/bin/
+ export MVN_BIN=/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/
+ MVN_BIN=/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/
+ export PATH=/usr/java/jdk1.8.0_60/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/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.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/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/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/jenkins-test

# make a tempdir for writing maven cruft to
AVOCADO_MVN_TMP_DIR=$(mktemp -d -t avocadoTestMvnXXXXXXX)
++ mktemp -d -t avocadoTestMvnXXXXXXX
+ AVOCADO_MVN_TMP_DIR=/tmp/avocadoTestMvn1rGkfR4

# 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=${AVOCADO_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/avocadoTestMvn1rGkfR4: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.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/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.tasks.Maven_MavenInstallation/Maven_3.1.1/bin/:/home/anaconda/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 ${BASH_SOURCE[0]} ) && pwd )
+++ dirname /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/jenkins-test
++ cd /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts
++ pwd
+ DIR=/home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.0.3-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 2.0.0 ]]

# 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
+ '[' 2.0.0 == 2.0.0 ']'
+ echo 'Rewriting POM.xml files for Spark 2.'
Rewriting POM.xml files for Spark 2.
+ ./scripts/move_to_spark_2.sh
+ set +e
+ ./scripts/move_to_spark_2.sh
POM is already set up for Spark 2 (Spark 1/2 artifacts have -spark2 suffix in artifact names).
Cowardly refusing to move to Spark 2 a second time...
+ [[ 1 == 0 ]]
+ set -e

# 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 AVOCADO version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing AVOCADO version 0.0.3-SNAPSHOT on Spark 2.0.0 and Hadoop 2.3.0'
Testing AVOCADO version 0.0.3-SNAPSHOT on Spark 2.0.0 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=2.0.0
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 org.bdgenomics.avocado:avocado-core-spark2_2.11:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-cli-spark2_2.11:jar:0.0.3-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-parent-spark2_2.11:pom:0.0.3-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 340, 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 344, 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] avocado: A Variant Caller, Distributed
[INFO] avocado-core: Core variant calling algorithms
[INFO] avocado-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado: A Variant Caller, Distributed 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ avocado-parent-spark2_2.11 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-core: Core variant calling algorithms 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ avocado-core-spark2_2.11 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ avocado-cli-spark2_2.11 ---
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed ............ SUCCESS [0.114s]
[INFO] avocado-core: Core variant calling algorithms ..... SUCCESS [0.016s]
[INFO] avocado-cli: Command line interface for a distributed variant caller  SUCCESS [0.013s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 0.262s
[INFO] Finished at: Thu Oct 12 00:30:55 PDT 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 266 ]]
+ COVERALLS_PRB_OPTION=-DpullRequest=266

# 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 org.bdgenomics.avocado:avocado-core-spark2_2.11:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-cli-spark2_2.11:jar:0.0.3-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.11:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-parent-spark2_2.11:pom:0.0.3-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 340, 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 344, 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] avocado: A Variant Caller, Distributed
[INFO] avocado-core: Core variant calling algorithms
[INFO] avocado-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado: A Variant Caller, Distributed 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent-spark2_2.11 ---
[INFO] Modified 0 of 54 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-parent-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-parent-spark2_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent-spark2_2.11 ---
[INFO] Modified 0 of 54 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ avocado-parent-spark2_2.11 ---
[INFO] Skipping SCoverage execution for project with packaging type 'pom'
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ avocado-parent-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-parent-spark2_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-parent-spark2_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-parent-spark2_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-parent-spark2_2.11 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-core: Core variant calling algorithms 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml
Downloading: http://people.apache.org/repo/m2-snapshot-repository/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml
Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml

2/2 KB   
2/2 KB   2/2 KB   
                  
Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (2 KB at 1.7 KB/sec)
                  
Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (2 KB at 1.6 KB/sec)
Downloading: http://people.apache.org/repo/m2-snapshot-repository/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml
Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml
625/625 B         
625/625 B   625/625 B   
                        
Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (625 B at 2.8 KB/sec)
                        
                        
Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (625 B at 1.6 KB/sec)
Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/adam-parent-spark2_2.11-0.23.0-20171011.201218-464.pom
                        
Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-parent-spark2_2.11/0.23.0-SNAPSHOT/adam-parent-spark2_2.11-0.23.0-20171011.201218-464.pom (0 B at 0.0 KB/sec)
Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml
Downloading: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml
Downloading: http://people.apache.org/repo/m2-snapshot-repository/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml
2/2 KB                  
2/2 KB   2/2 KB   
                  
Downloaded: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (2 KB at 6.3 KB/sec)
                  
                  
Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/maven-metadata.xml (2 KB at 3.3 KB/sec)
Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/adam-core-spark2_2.11-0.23.0-20171011.201339-464.jar
Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/adam-codegen-spark2_2.11-0.23.0-20171011.201225-224.jar
                  
Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/adam-codegen-spark2_2.11-0.23.0-20171011.201225-224.jar (0 B at 0.0 KB/sec)
                  
Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/adam-core-spark2_2.11-0.23.0-20171011.201339-464.jar (0 B at 0.0 KB/sec)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-core-spark2_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-core-spark2_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-core-spark2_2.11 ---
[INFO] Modified 0 of 45 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-core-spark2_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-core-spark2_2.11 ---
Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/adam-codegen-spark2_2.11-0.23.0-20171011.201225-224.pom
                  
Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-codegen-spark2_2.11/0.23.0-SNAPSHOT/adam-codegen-spark2_2.11-0.23.0-20171011.201225-224.pom (0 B at 0.0 KB/sec)
[WARNING]  Expected all dependencies to require Scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.11 requires scala version: 2.11.4
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/scala:-1: info: compiling
[INFO] Compiling 24 source files to /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/target/scala-2.11.4/classes at 1507793465079
[ERROR] /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/JointAnnotatorCaller.scala:20: error: not found: object breeze
[ERROR] import breeze.stats.distributions.Binomial
[ERROR]        ^
[ERROR] /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/JointAnnotatorCaller.scala:95: error: value setQuality is not a member of org.bdgenomics.formats.avro.Variant.Builder
[ERROR] possible cause: maybe a semicolon is missing before `value setQuality'?
[ERROR]         }).setQuality(variantQuality)
[ERROR]            ^
[ERROR] /home/jenkins/workspace/avocado-prb/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/scala/org/bdgenomics/avocado/genotyping/JointAnnotatorCaller.scala:161: error: not found: value Binomial
[ERROR]           val dist = Binomial(cn, minorAlleleFrequency)
[ERROR]                      ^
[ERROR] three errors found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Skipping avocado: A Variant Caller, Distributed
[INFO] This project has been banned from the build due to previous failures.
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed ............ SUCCESS [3.553s]
[INFO] avocado-core: Core variant calling algorithms ..... FAILURE [9.590s]
[INFO] avocado-cli: Command line interface for a distributed variant caller  SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 13.367s
[INFO] Finished at: Thu Oct 12 00:31:10 PDT 2017
[INFO] Final Memory: 31M/1119M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal net.alchim31.maven:scala-maven-plugin:3.2.2:compile (scala-compile-first) on project avocado-core-spark2_2.11: wrap: org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :avocado-core-spark2_2.11
Build step 'Execute shell' marked build as failure
Recording test results
ERROR: Step ?Publish JUnit test result report? failed: No test report files were found. Configuration error?
Publishing Scoverage XML and HTML report...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/avocado/commit/1e39b43d08478a1cd9446a41270d58820e652a38
Finished: FAILURE