Started by upstream project "deca-prb" build number 7 originally caused by: GitHub pull request #2 of commit 77981d8e6e849f6419e082ce8150e50e04677844 automatically merged. [EnvInject] - Loading node environment variables. Building remotely on amp-jenkins-worker-02 (centos spark-test spark-compile) in workspace /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos Cloning the remote Git repository Cloning repository https://github.com/fnothaft/deca.git > git init /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos # timeout=10 Fetching upstream changes from https://github.com/fnothaft/deca.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/fnothaft/deca.git +refs/heads/*:refs/remotes/origin/* > git config remote.origin.url https://github.com/fnothaft/deca.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/fnothaft/deca.git # timeout=10 Fetching upstream changes from https://github.com/fnothaft/deca.git > git fetch --tags --progress https://github.com/fnothaft/deca.git +refs/pull/*:refs/remotes/origin/pr/* Checking out Revision 91903450d9b8fa3c69248715df697b77a7f00391 (origin/pr/2/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 91903450d9b8fa3c69248715df697b77a7f00391 First time build. Skipping changelog. [centos] $ /bin/bash /tmp/hudson1971561202414143926.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 + java -version java version "1.8.0_60" Java(TM) SE Runtime Environment (build 1.8.0_60-b27) Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode) + javac -version javac 1.8.0_60 + /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/scripts/jenkins-test # make a tempdir for writing maven cruft to DECA_MVN_TMP_DIR=$(mktemp -d -t decaTestMvnXXXXXXX) ++ mktemp -d -t decaTestMvnXXXXXXX + DECA_MVN_TMP_DIR=/tmp/decaTestMvniQoAX0K # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${DECA_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/decaTestMvniQoAX0K: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 ${BASH_SOURCE[0]} ) && pwd ) +++ dirname /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/scripts/jenkins-test ++ cd /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/scripts ++ pwd + DIR=/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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 2.6.0 ]] # 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 1.4.1 ]] # 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 + '[' 1.4.1 == 2.0.0 ']' # are we testing for scala 2.11? if so, we need to rewrite our poms to 2.11 first if [ ${SCALAVER} == 2.11 ]; then echo "Rewriting POM.xml files for Scala 2.11." ./scripts/move_to_scala_2.11.sh # shouldn't be able to move to scala 2.11 twice set +e ./scripts/move_to_scala_2.11.sh if [[ $? == 0 ]]; then echo "We have already moved to Scala 2.11, so running move_to_scala_2.11.sh a second time should fail, but error code was 0 (success)." exit 1 fi set -e fi + '[' 2.10 == 2.11 ']' # print versions echo "Testing DECA version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing DECA version 0.0.1-SNAPSHOT on Spark 1.4.1 and Hadoop 2.6.0' Testing DECA version 0.0.1-SNAPSHOT on Spark 1.4.1 and Hadoop 2.6.0 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${HADOOP_VERSION} \ -Dspark.version=${SPARK_VERSION} + mvn clean -Dhadoop.version=2.6.0 -Dspark.version=1.4.1 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 org.bdgenomics.deca:deca-core_2.10:jar:0.0.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 67, 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 135, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-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. @ 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-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 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. @ line 356, 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 360, 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] deca: Distributed Exome CNV Analyzer [INFO] deca-core: Core variant calling algorithms [INFO] deca-cli: Command line interface for a distributed variant caller [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca: Distributed Exome CNV Analyzer 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-parent_2.10 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-core: Core variant calling algorithms 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-core_2.10 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-cli: Command line interface for a distributed variant caller 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-cli_2.10 --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [0.124s] [INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.017s] [INFO] deca-cli: Command line interface for a distributed variant caller SUCCESS [0.015s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.293s [INFO] Finished at: Mon Jan 30 13:56:05 PST 2017 [INFO] Final Memory: 19M/1472M [INFO] ------------------------------------------------------------------------ # if those pass, build the distribution package and the integration tests mvn -U \ test \ -P coverage scoverage:report + mvn -U test -P coverage scoverage:report 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.deca:deca-core_2.10:jar:0.0.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 67, 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 135, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-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. @ 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-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 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. @ line 356, 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 360, 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] deca: Distributed Exome CNV Analyzer [INFO] deca-core: Core variant calling algorithms [INFO] deca-cli: Command line interface for a distributed variant caller [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca: Distributed Exome CNV Analyzer 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.10 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.10 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.10 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.10 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.10 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-parent_2.10 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.10 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-parent_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.10 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.10 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.10 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-core: Core variant calling algorithms 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.10 --- [INFO] Modified 0 of 2 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile [INFO] Using incremental compilation [INFO] Compiling 1 Scala source to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scala-2.10.4/classes... [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile [INFO] Using incremental compilation [INFO] Compiling 1 Scala source to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scala-2.10.4/test-classes... [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.10 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.10 --- Discovery starting. Discovery completed in 68 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 134 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.10 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.10 --- [INFO] Modified 0 of 2 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-core_2.10 --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile [INFO] Using incremental compilation [INFO] Compiling 1 Scala source to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scala-2.10.4/scoverage-classes... [INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [1 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/scoverage-data] [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-core_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile [INFO] Using incremental compilation [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.10 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.10 --- Discovery starting. Discovery completed in 60 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 117 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.10 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.10 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-cli: Command line interface for a distributed variant caller 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.10 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.10 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] Copied 1 files to output directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.10 --- [INFO] Modified 0 of 2 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.10.4/classes at 1485813383590 [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.10 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.10.4/classes [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/test/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.10.4/test-classes at 1485813387753 [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.10 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.10 --- Discovery starting. Discovery completed in 108 milliseconds. Run starting. Expected test count is: 0 DecaMainSuite: - no op to test setup !!! IGNORED !!! Run completed in 181 milliseconds. Total number of tests run: 0 Suites: completed 2, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 1, pending 0 No tests were executed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.10 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.10 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.10 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.10 --- [INFO] Modified 0 of 2 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-cli_2.10 --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.10.4/scoverage-classes at 1485813392477 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [49 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.10 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.10.4/scoverage-classes [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-cli_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.10 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.10 --- Discovery starting. Discovery completed in 105 milliseconds. Run starting. Expected test count is: 0 DecaMainSuite: - no op to test setup !!! IGNORED !!! Run completed in 176 milliseconds. Total number of tests run: 0 Suites: completed 2, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 1, pending 0 No tests were executed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.10 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.10 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [1.481s] [INFO] deca-core: Core variant calling algorithms ........ SUCCESS [14.661s] [INFO] deca-cli: Command line interface for a distributed variant caller SUCCESS [15.101s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 31.471s [INFO] Finished at: Mon Jan 30 13:56:37 PST 2017 [INFO] Final Memory: 58M/1315M [INFO] ------------------------------------------------------------------------ # if those pass, build the distribution package mvn -U \ -P distribution \ package \ -DskipTests \ -Dhadoop.version=${HADOOP_VERSION} \ -Dspark.version=${SPARK_VERSION} \ -DargLine=${DECA_MVN_TMP_DIR} + mvn -U -P distribution package -DskipTests -Dhadoop.version=2.6.0 -Dspark.version=1.4.1 -DargLine=/tmp/decaTestMvniQoAX0K 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.deca:deca-core_2.10:jar:0.0.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 67, 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 135, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-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. @ 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-distribution_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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-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 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. @ line 356, 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 360, 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] deca: Distributed Exome CNV Analyzer [INFO] deca-core: Core variant calling algorithms [INFO] deca-cli: Command line interface for a distributed variant caller [INFO] deca: distribution [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca: Distributed Exome CNV Analyzer 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.10 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.10 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-parent_2.10 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ deca-parent_2.10 --- [INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ deca-parent_2.10 --- [INFO] Not executing Javadoc as the project is not a Java classpath-capable package [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.10 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.10 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.10 --- [INFO] No source files found [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-core: Core variant calling algorithms 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.10 --- [INFO] Modified 0 of 2 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile [INFO] Using incremental compilation [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Zinc server is not available at port 3030 - reverting to normal incremental compile [INFO] Using incremental compilation [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.10 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.10 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-core_2.10 --- [INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/deca-core_2.10-0.0.1-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ deca-core_2.10 --- [INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/deca-core_2.10-0.0.1-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ deca-core_2.10 --- [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ deca-core_2.10 --- [INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/deca-core_2.10-0.0.1-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-cli: Command line interface for a distributed variant caller 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.10 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.10 --- [INFO] Coping files with filtering to temporary directory. [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 1 resource [INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.10 --- [INFO] Modified 0 of 2 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/scala-2.10.4/classes at 1485813405692 [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.10 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.10 --- [WARNING] Expected all dependencies to require Scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-metrics_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-cli_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-misc_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-serialization_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.utils:utils-io_2.10:0.2.11 requires scala version: 2.10.4 [WARNING] org.bdgenomics.adam:adam-core_2.10:0.21.0 requires scala version: 2.10.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.10 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.10 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.10 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-cli_2.10 --- [INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.10-0.0.1-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ deca-cli_2.10 --- [INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.10-0.0.1-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ deca-cli_2.10 --- [INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:2.9.1:javadoc' has not been previously called for the module: 'org.bdgenomics.deca:deca-core_2.10:jar:0.0.1-SNAPSHOT'. Trying to invoke it... Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/apidocs [ERROR] Error fetching link: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-core/target/apidocs/package-list. Ignored it. [INFO] Loading source files for package org.bdgenomics.deca.cli... Constructing Javadoc information... Standard Doclet version 1.8.0_60 Building tree for all the packages and classes... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/About.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-frame.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-summary.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-tree.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/class-use/About.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/index-all.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/index.html... Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.10-0.0.1-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-shade-plugin:2.4.3:shade (default) @ deca-cli_2.10 --- [INFO] Including org.bdgenomics.utils:utils-cli_2.10:jar:0.2.11 in the shaded jar. [INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-column:jar:1.8.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-common:jar:1.8.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-hadoop:jar:1.8.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-jackson:jar:1.8.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-format:jar:2.3.0-incubating in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc_2.10:jar:0.2.11 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics_2.10:jar:0.2.11 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.10.4 in the shaded jar. [INFO] Including args4j:args4j:jar:2.0.23 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-serialization_2.10:jar:0.2.11 in the shaded jar. [INFO] Including org.seqdoop:hadoop-bam:jar:7.0.0 in the shaded jar. [INFO] Including commons-cli:commons-cli:jar:1.2 in the shaded jar. [INFO] Including commons-httpclient:commons-httpclient:jar:3.1 in the shaded jar. [INFO] Including com.github.samtools:htsjdk:jar:2.5.0 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.1.1 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar. [INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:1.2.4 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.10.1 in the shaded jar. [INFO] Including org.bdgenomics.deca:deca-core_2.10:jar:0.0.1-SNAPSHOT in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar. [INFO] Including commons-io:commons-io:jar:1.3.2 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core_2.10:jar:0.21.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io_2.10:jar:0.2.11 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd_2.10:jar:0.2.11 in the shaded jar. [INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar. [INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar. [INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar. [INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar. [INFO] Including org.apache.avro:avro:jar:1.8.0 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar. [INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar. [INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 in the shaded jar. [INFO] Including org.slf4j:slf4j-log4j12:jar:1.7.21 in the shaded jar. [INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.1 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.10.0 in the shaded jar. [INFO] Including com.google.code.findbugs:annotations:jar:2.0.0 in the shaded jar. [INFO] Including com.netflix.servo:servo-internal:jar:0.10.0 in the shaded jar. [INFO] Including com.google.guava:guava:jar:16.0.1 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli_2.10:jar:0.21.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis_2.10:jar:0.21.0 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.10:jar:4.0.1 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.0 in the shaded jar. [INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar. [INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar. [INFO] Including com.google.inject.extensions:guice-multibindings:jar:4.0 in the shaded jar. [INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.10 in the shaded jar. [INFO] Including log4j:log4j:jar:1.2.17 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.1.1.7 in the shaded jar. [WARNING] annotations-2.0.0.jar, jsr305-1.3.9.jar define 34 overlapping classes: [WARNING] - javax.annotation.RegEx [WARNING] - javax.annotation.concurrent.Immutable [WARNING] - javax.annotation.meta.TypeQualifierDefault [WARNING] - javax.annotation.meta.TypeQualifier [WARNING] - javax.annotation.Syntax [WARNING] - javax.annotation.CheckForNull [WARNING] - javax.annotation.Nonnull [WARNING] - javax.annotation.CheckReturnValue [WARNING] - javax.annotation.meta.TypeQualifierNickname [WARNING] - javax.annotation.MatchesPattern [WARNING] - 24 more... [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.10-0.0.1-SNAPSHOT.jar with /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-cli/target/deca-cli_2.10-0.0.1-SNAPSHOT-shaded.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca: distribution 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-distribution_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-distribution_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-distribution/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.3.2:exec (Generate Documentation) @ deca-distribution_2.10 --- ! LaTeX Error: File `ifxetex.sty' not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.10 \usepackage pandoc: Error producing PDF [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-distribution_2.10 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-distribution_2.10 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-distribution_2.10 --- [INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-distribution/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-distribution_2.10 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ deca-distribution_2.10 --- [INFO] [INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ deca-distribution_2.10 --- [INFO] Not executing Javadoc as the project is not a Java classpath-capable package [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.10 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-distribution_2.10 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-distribution_2.10 --- [INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-distribution/src/main/scala added. [INFO] [INFO] --- exec-maven-plugin:1.3.2:exec (Generate Documentation) @ deca-distribution_2.10 --- ! LaTeX Error: File `ifxetex.sty' not found. Type X to quit or <RETURN> to proceed, or enter new name. (Default extension: sty) Enter file name: ! Emergency stop. <read *> l.10 \usepackage pandoc: Error producing PDF [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.10 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.10 --- [INFO] No source files found [INFO] [INFO] --- maven-assembly-plugin:2.4.1:single (default) @ deca-distribution_2.10 --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [INFO] Building tar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-distribution/target/deca-distribution_2.10-0.0.1-SNAPSHOT-bin.tar.gz [INFO] Building tar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-distribution/target/deca-distribution_2.10-0.0.1-SNAPSHOT-bin.tar.bz2 [INFO] Building zip: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/deca-distribution/target/deca-distribution_2.10-0.0.1-SNAPSHOT-bin.zip [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.003s] [INFO] deca-core: Core variant calling algorithms ........ SUCCESS [3.375s] [INFO] deca-cli: Command line interface for a distributed variant caller SUCCESS [13.646s] [INFO] deca: distribution ................................ SUCCESS [1.642s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 20.796s [INFO] Finished at: Mon Jan 30 13:56:59 PST 2017 [INFO] Final Memory: 80M/1435M [INFO] ------------------------------------------------------------------------ # we are done with maven, so clean up the maven temp dir find ${DECA_MVN_TMP_DIR} + find /tmp/decaTestMvniQoAX0K /tmp/decaTestMvniQoAX0K rm -rf ${DECA_MVN_TMP_DIR} + rm -rf /tmp/decaTestMvniQoAX0K # 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 + '[' 1.4.1 == 2.0.0 ']' if [ ${SCALAVER} == 2.11 ]; then echo "Rewriting POM.xml files back to Scala 2.10." ./scripts/move_to_scala_2.10.sh fi + '[' 2.10 == 2.11 ']' find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${DECA_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/decaTestMvniQoAX0K:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' if test -n "$(git status --porcelain | grep -v -e html -e pdf)" then echo "Applying move_to_xyz script marred a pom.xml file." echo "Exiting..." exit 1 fi ++ git status --porcelain ++ grep -v -e html -e pdf + test -n '' ./scripts/format-source + ./scripts/format-source +++ dirname ./scripts/format-source ++ cd ./scripts ++ pwd + DIR=/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/scripts + pushd /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/scripts/.. ~/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos ~/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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 org.bdgenomics.deca:deca-core_2.10:jar:0.0.1-SNAPSHOT [WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 67, 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 135, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-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. @ 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/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. @ org.bdgenomics.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 356, 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.deca:deca-parent_2.10:0.0.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos/pom.xml, line 360, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-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 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. @ line 356, 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 360, 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] deca: Distributed Exome CNV Analyzer [INFO] deca-core: Core variant calling algorithms [INFO] deca-cli: Command line interface for a distributed variant caller [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca: Distributed Exome CNV Analyzer 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.10 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-parent_2.10 --- [INFO] Updating license headers... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-core: Core variant calling algorithms 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.10 --- [INFO] Modified 0 of 2 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-core_2.10 --- [INFO] Updating license headers... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-cli: Command line interface for a distributed variant caller 0.0.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.10 --- [INFO] Modified 0 of 2 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-cli_2.10 --- [INFO] Updating license headers... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [0.977s] [INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.075s] [INFO] deca-cli: Command line interface for a distributed variant caller SUCCESS [0.049s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1.497s [INFO] Finished at: Mon Jan 30 13:57:02 PST 2017 [INFO] Final Memory: 16M/1107M [INFO] ------------------------------------------------------------------------ + popd ~/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.10/SPARK_VERSION/1.4.1/label/centos if test -n "$(git status --porcelain | grep -v -e html -e pdf)" then echo "Please run './scripts/format-source'" exit 1 fi ++ git status --porcelain ++ grep -v -e html -e pdf + test -n '' echo + echo echo "All the tests passed" + echo 'All the tests passed' All the tests passed echo + echo Recording test results Publishing Scoverage XML and HTML report... Finished: SUCCESS