Started by upstream project "deca" build number 121 originally caused by: Started by an SCM change [EnvInject] - Loading node environment variables. Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos > git rev-parse --is-inside-work-tree # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/deca.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/deca.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/deca.git +refs/heads/*:refs/remotes/origin/* Checking out Revision f65d894a969e99f10a8c823b2cd2204e0043d0dd (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f f65d894a969e99f10a8c823b2cd2204e0043d0dd > git rev-list 45be0249b893e18bff15869d0d78f3c7367c6c7d # timeout=10 [centos] $ /bin/bash /tmp/hudson5912160081146034058.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/deca/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 DECA_MVN_TMP_DIR=$(mktemp -d -t decaTestMvnXXXXXXX) ++ mktemp -d -t decaTestMvnXXXXXXX + DECA_MVN_TMP_DIR=/tmp/decaTestMvnv9g61Zh # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/decaTestMvnv9g61Zh: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 ${BASH_SOURCE[0]} ) && pwd ) +++ dirname /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/jenkins-test ++ cd /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts ++ pwd + DIR=/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/deca/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/deca/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=0.1.1-SNAPSHOT # is the hadoop version set? if ! [[ ${HADOOP_VERSION} ]]; then echo "HADOOP_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.3.0 ]] # is the spark version set? if ! [[ ${SPARK_VERSION} ]]; then echo "SPARK_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.0.0 ]] # print versions echo "Testing DECA version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing DECA version 0.1.1-SNAPSHOT on Spark 2.0.0 and Hadoop 2.3.0' Testing DECA version 0.1.1-SNAPSHOT on Spark 2.0.0 and Hadoop 2.3.0 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${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.deca:deca-core_2.11:jar:0.1.1-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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 357, 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 361, 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 365, 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 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-parent_2.11 --- [INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-core_2.11 --- [INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-cli_2.11 --- [INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [0.165s] [INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.051s] [INFO] deca-cli: Command line interface for a distributed variant caller SUCCESS [0.048s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.445s [INFO] Finished at: Mon Jan 08 09:57:18 PST 2018 [INFO] Final Memory: 19M/1472M [INFO] ------------------------------------------------------------------------ # make sure we can build the native code mvn -U \ -P native-lgpl \ package \ -DskipTests \ -Dhadoop.version=${HADOOP_VERSION} \ -Dspark.version=${SPARK_VERSION} \ -DargLine=${DECA_MVN_TMP_DIR} + mvn -U -P native-lgpl package -DskipTests -Dhadoop.version=2.3.0 -Dspark.version=2.0.0 -DargLine=/tmp/decaTestMvnv9g61Zh 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_2.11:jar:0.1.1-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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 357, 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 361, 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 365, 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 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/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) @ deca-parent_2.11 --- [INFO] Modified 0 of 30 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/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) @ deca-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 --- [INFO] Modified 0 of 20 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala:-1: info: compiling [INFO] Compiling 15 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/classes at 1515434245253 [WARNING] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure [WARNING] case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector) [WARNING] ^ [WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details [WARNING] two warnings found [INFO] prepare-compile in 0 s [INFO] compile in 11 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 17 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala:-1: info: compiling [INFO] Compiling 5 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/test-classes at 1515434257170 [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-core_2.11 --- [INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT.jar [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ deca-core_2.11 --- [INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 --- [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/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 --- [INFO] Modified 0 of 10 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] Compiling 10 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes at 1515434267721 [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/test-classes at 1515434274155 [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-cli_2.11 --- [INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar [INFO] [INFO] --- maven-shade-plugin:2.4.3:shade (default) @ deca-cli_2.11 --- [INFO] Including net.fnothaft:jsr203-s3a:jar:0.0.1 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 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-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.11.8 in the shaded jar. [INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-serialization-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-SNAPSHOT in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar. [INFO] Including commons-io:commons-io:jar:2.4 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.23.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.hammerlab:genomic-loci_2.11:jar:1.4.4 in the shaded jar. [INFO] Including org.hammerlab:args4s_2.11:jar:1.0.0 in the shaded jar. [INFO] Including org.hammerlab:iterator_2.11:jar:1.0.0 in the shaded jar. [INFO] Including org.hammerlab:string-utils_2.11:jar:1.0.0 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 org.bdgenomics.bdg-formats:bdg-formats:jar:0.11.3 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.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.2 in the shaded jar. [INFO] Including org.seqdoop:hadoop-bam:jar:7.9.1 in the shaded jar. [INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar. [INFO] Including com.github.samtools:htsjdk:jar:2.11.0 in the shaded jar. [INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar. [INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:1.2.4 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.google.guava:guava:jar:16.0.1 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.23.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.23.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.23.0 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.11:jar:4.1.0 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.1.0 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:4.1.0 in the shaded jar. [INFO] Including org.apache.commons:commons-math3:jar:3.4.1 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:1.7.16 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.1.2.4 in the shaded jar. [INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar. [INFO] Including org.scalanlp:breeze_2.11:jar:0.12 in the shaded jar. [INFO] Including org.scalanlp:breeze-macros_2.11:jar:0.12 in the shaded jar. [INFO] Including com.github.fommil.netlib:core:jar:1.1.2 in the shaded jar. [INFO] Including net.sourceforge.f2j:arpack_combined_all:jar:0.1 in the shaded jar. [INFO] Including net.sf.opencsv:opencsv:jar:2.3 in the shaded jar. [INFO] Including com.github.rwl:jtransforms:jar:2.4.0 in the shaded jar. [INFO] Including junit:junit:jar:4.8.2 in the shaded jar. [INFO] Including org.spire-math:spire_2.11:jar:0.7.4 in the shaded jar. [INFO] Including org.spire-math:spire-macros_2.11:jar:0.7.4 in the shaded jar. [INFO] Including com.chuusai:shapeless_2.11:jar:2.0.0 in the shaded jar. [INFO] Including org.scalanlp:breeze-natives_2.11:jar:0.12 in the shaded jar. [INFO] Skipping pom dependency com.github.fommil.netlib:all:pom:1.1.2 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_ref-osx-x86_64:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:native_ref-java:jar:1.1 in the shaded jar. [INFO] Including com.github.fommil:jniloader:jar:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-x86_64:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-i686:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_ref-win-x86_64:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_ref-win-i686:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-armhf:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_system-osx-x86_64:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:native_system-java:jar:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_system-linux-x86_64:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_system-linux-i686:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_system-linux-armhf:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_system-win-x86_64:jar:natives:1.1 in the shaded jar. [INFO] Including com.github.fommil.netlib:netlib-native_system-win-i686:jar:natives:1.1 in the shaded jar. [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar with /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-shaded.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.404s] [INFO] deca-core: Core variant calling algorithms ........ SUCCESS [23.533s] [INFO] deca-cli: Command line interface for a distributed variant caller SUCCESS [25.256s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 51.377s [INFO] Finished at: Mon Jan 08 09:58:11 PST 2018 [INFO] Final Memory: 97M/1366M [INFO] ------------------------------------------------------------------------ # if those pass, build the distribution package and the integration tests mvn -U \ clean \ test \ -P coverage scoverage:report + mvn -U clean 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_2.11:jar:0.1.1-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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 357, 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 361, 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 365, 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 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-parent_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/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) @ deca-parent_2.11 --- [INFO] Modified 0 of 30 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/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) @ deca-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/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) @ deca-parent_2.11 --- [INFO] Modified 0 of 30 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-parent_2.11 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/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) @ deca-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 --- [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-core_2.11 --- [INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 --- [INFO] Modified 0 of 20 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala:-1: info: compiling [INFO] Compiling 15 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/classes at 1515434298896 [WARNING] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure [WARNING] case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector) [WARNING] ^ [WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details [WARNING] two warnings found [INFO] prepare-compile in 0 s [INFO] compile in 12 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 17 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala:-1: info: compiling [INFO] Compiling 5 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/test-classes at 1515434311728 [INFO] prepare-compile in 0 s [INFO] compile in 9 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 --- Discovery starting. Discovery completed in 570 milliseconds. Run starting. Expected test count is: 16 NormalizationSuite: 2018-01-08 09:58:42 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2018-01-08 09:58:45 WARN Executor:66 - 1 block locks were not released by TID = 7: [rdd_0_3] 2018-01-08 09:58:45 WARN Executor:66 - 1 block locks were not released by TID = 5: [rdd_0_1] - mean centers data by columns - zScores data by rows 2018-01-08 09:58:46 WARN Executor:66 - 1 block locks were not released by TID = 11: [rdd_3_3] 2018-01-08 09:58:46 WARN Executor:66 - 1 block locks were not released by TID = 9: [rdd_3_1] 2018-01-08 09:58:46 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2018-01-08 09:58:46 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS 2018-01-08 09:58:46 WARN LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK 2018-01-08 09:58:46 WARN LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK 2018-01-08 09:58:47 WARN Executor:66 - 1 block locks were not released by TID = 21: [rdd_3_1] 2018-01-08 09:58:47 WARN Executor:66 - 1 block locks were not released by TID = 23: [rdd_3_3] - removes top k components of data 2018-01-08 09:58:47 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:58:47 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] 2018-01-08 09:58:47 WARN RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:58:47 WARN ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK 2018-01-08 09:58:48 WARN ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK 2018-01-08 09:58:48 WARN RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:58:48 WARN Executor:66 - 1 block locks were not released by TID = 35: [rdd_23_0] 2018-01-08 09:58:48 WARN Executor:66 - 1 block locks were not released by TID = 41: [rdd_23_0] 2018-01-08 09:58:48 WARN Executor:66 - 1 block locks were not released by TID = 44: [rdd_4_0] - produces same results with fixed k 2018-01-08 09:58:49 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:58:49 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] 2018-01-08 09:58:49 WARN Executor:66 - 1 block locks were not released by TID = 7: [rdd_7_0] 2018-01-08 09:58:49 WARN Executor:66 - 1 block locks were not released by TID = 13: [rdd_7_0] 2018-01-08 09:58:49 WARN Executor:66 - 1 block locks were not released by TID = 18: [rdd_4_0] - filters and centers SVD results 2018-01-08 09:58:49 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:58:50 WARN Executor:66 - 1 block locks were not released by TID = 8: [rdd_1_0] 2018-01-08 09:58:50 WARN Executor:66 - 1 block locks were not released by TID = 9: [rdd_10_0] 2018-01-08 09:58:50 WARN Executor:66 - 1 block locks were not released by TID = 15: [rdd_10_0] 2018-01-08 09:58:50 WARN Executor:66 - 1 block locks were not released by TID = 24: [rdd_21_0] 2018-01-08 09:58:50 WARN RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:58:50 WARN RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:58:50 WARN RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:58:51 WARN RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:58:51 WARN Executor:66 - 1 block locks were not released by TID = 99: [rdd_64_0] - filters and normalizes read depth data HMMSuite: 2018-01-08 09:58:51 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:58:52 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] - Generates transition matrix for array of distances - Handles contig boundaries in computing transition matrix 2018-01-08 09:58:52 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:58:52 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] - Discovers CNVs DecaSuite: 2018-01-08 09:58:54 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:58:54 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] - read XHMM matrix 2018-01-08 09:58:54 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:58:54 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] 2018-01-08 09:58:54 WARN Executor:66 - 1 block locks were not released by TID = 9: [rdd_9_0] 2018-01-08 09:58:54 WARN Executor:66 - 1 block locks were not released by TID = 15: [rdd_9_0] - write XHMM matrix CoverageSuite: - Finds correct first target - computes coverage for targets - counts fragments not just reads - counts imperfectly paired fragments - incorporates CIGAR into fragment analysis Run completed in 16 seconds, 489 milliseconds. Total number of tests run: 16 Suites: completed 5, aborted 0 Tests: succeeded 16, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 --- [INFO] Modified 0 of 20 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-core_2.11 --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala:-1: info: compiling [INFO] Compiling 15 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/scoverage-classes at 1515434338893 [WARNING] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure [WARNING] case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector) [WARNING] ^ [INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos. [INFO] [info] Instrumentation completed [1316 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scoverage-data] [WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details [WARNING] two warnings found [INFO] prepare-compile in 0 s [INFO] compile in 12 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 17 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 --- Discovery starting. Discovery completed in 635 milliseconds. Run starting. Expected test count is: 16 NormalizationSuite: 2018-01-08 09:59:13 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable 2018-01-08 09:59:17 WARN Executor:66 - 1 block locks were not released by TID = 5: [rdd_0_1] 2018-01-08 09:59:17 WARN Executor:66 - 1 block locks were not released by TID = 7: [rdd_0_3] - mean centers data by columns - zScores data by rows 2018-01-08 09:59:18 WARN Executor:66 - 1 block locks were not released by TID = 9: [rdd_3_1] 2018-01-08 09:59:18 WARN Executor:66 - 1 block locks were not released by TID = 11: [rdd_3_3] 2018-01-08 09:59:18 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS 2018-01-08 09:59:18 WARN BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS 2018-01-08 09:59:18 WARN LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK 2018-01-08 09:59:18 WARN LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK 2018-01-08 09:59:18 WARN Executor:66 - 1 block locks were not released by TID = 23: [rdd_3_3] 2018-01-08 09:59:18 WARN Executor:66 - 1 block locks were not released by TID = 21: [rdd_3_1] - removes top k components of data 2018-01-08 09:59:19 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:59:19 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] 2018-01-08 09:59:19 WARN RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:59:19 WARN ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK 2018-01-08 09:59:19 WARN ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK 2018-01-08 09:59:20 WARN RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:59:20 WARN Executor:66 - 1 block locks were not released by TID = 35: [rdd_23_0] 2018-01-08 09:59:20 WARN Executor:66 - 1 block locks were not released by TID = 41: [rdd_23_0] 2018-01-08 09:59:20 WARN Executor:66 - 1 block locks were not released by TID = 44: [rdd_4_0] - produces same results with fixed k 2018-01-08 09:59:20 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:59:21 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] 2018-01-08 09:59:21 WARN Executor:66 - 1 block locks were not released by TID = 7: [rdd_7_0] 2018-01-08 09:59:21 WARN Executor:66 - 1 block locks were not released by TID = 13: [rdd_7_0] 2018-01-08 09:59:21 WARN Executor:66 - 1 block locks were not released by TID = 18: [rdd_4_0] - filters and centers SVD results 2018-01-08 09:59:21 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:59:21 WARN Executor:66 - 1 block locks were not released by TID = 8: [rdd_1_0] 2018-01-08 09:59:21 WARN Executor:66 - 1 block locks were not released by TID = 9: [rdd_10_0] 2018-01-08 09:59:22 WARN Executor:66 - 1 block locks were not released by TID = 15: [rdd_10_0] 2018-01-08 09:59:22 WARN Executor:66 - 1 block locks were not released by TID = 24: [rdd_21_0] 2018-01-08 09:59:22 WARN RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:59:22 WARN RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:59:22 WARN RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:59:23 WARN RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached. 2018-01-08 09:59:23 WARN Executor:66 - 1 block locks were not released by TID = 99: [rdd_64_0] - filters and normalizes read depth data HMMSuite: 2018-01-08 09:59:24 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:59:24 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] - Generates transition matrix for array of distances - Handles contig boundaries in computing transition matrix 2018-01-08 09:59:24 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:59:24 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] - Discovers CNVs DecaSuite: 2018-01-08 09:59:26 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:59:26 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] - read XHMM matrix 2018-01-08 09:59:27 WARN Executor:66 - 1 block locks were not released by TID = 0: [rdd_1_0] 2018-01-08 09:59:27 WARN Executor:66 - 1 block locks were not released by TID = 6: [rdd_1_0] 2018-01-08 09:59:27 WARN Executor:66 - 1 block locks were not released by TID = 9: [rdd_9_0] 2018-01-08 09:59:27 WARN Executor:66 - 1 block locks were not released by TID = 15: [rdd_9_0] - write XHMM matrix CoverageSuite: - Finds correct first target - computes coverage for targets - counts fragments not just reads - counts imperfectly paired fragments - incorporates CIGAR into fragment analysis Run completed in 17 seconds, 961 milliseconds. Total number of tests run: 16 Suites: completed 5, aborted 0 Tests: succeeded 16, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ deca-cli_2.11 --- [INFO] Deleting /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 --- [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/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 --- [INFO] Modified 0 of 10 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] Compiling 10 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes at 1515434373906 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/test-classes at 1515434380845 [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 --- Discovery starting. Discovery completed in 140 milliseconds. Run starting. Expected test count is: 0 DecaMainSuite: - no op to test setup !!! IGNORED !!! Run completed in 215 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_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 --- [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/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 --- [INFO] Modified 0 of 10 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-cli_2.11 --- [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 10 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/scoverage-classes at 1515434386799 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [316 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/scoverage-classes [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 --- Discovery starting. Discovery completed in 173 milliseconds. Run starting. Expected test count is: 0 DecaMainSuite: - no op to test setup !!! IGNORED !!! Run completed in 268 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_2.11 <<< [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.953s] [INFO] deca-core: Core variant calling algorithms ........ SUCCESS [1:16.319s] [INFO] deca-cli: Command line interface for a distributed variant caller SUCCESS [23.611s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1:43.110s [INFO] Finished at: Mon Jan 08 09:59:56 PST 2018 [INFO] Final Memory: 67M/1328M [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=2.3.0 -Dspark.version=2.0.0 -DargLine=/tmp/decaTestMvnv9g61Zh 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_2.11:jar:0.1.1-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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-distribution_2.11:pom:0.1.1-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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 357, 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 361, 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 365, 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 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/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) @ deca-parent_2.11 --- [INFO] Modified 0 of 30 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-parent_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/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) @ deca-parent_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-parent_2.11 --- [INFO] [INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ deca-parent_2.11 --- [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_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-parent_2.11 --- [INFO] No source files found [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 --- [INFO] Modified 0 of 20 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 17 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-core_2.11 --- [INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-core_2.11 --- [INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ deca-core_2.11 --- [INFO] [INFO] --- maven-jar-plugin:2.4:test-jar (default) @ deca-core_2.11 --- [INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT-tests.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added. [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 --- [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/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 --- [INFO] Modified 0 of 10 .scala files [INFO] [INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling [INFO] Compiling 10 source files to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes at 1515434406061 [INFO] prepare-compile in 0 s [INFO] compile in 6 s [INFO] [INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 --- [WARNING] Expected all dependencies to require Scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8 [WARNING] org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8 [WARNING] org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8 [WARNING] net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8 [WARNING] com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-cli_2.11 --- [INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-cli_2.11 --- [INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ deca-cli_2.11 --- [INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:2.10.4:javadoc' has not been previously called for the module: 'org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-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/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/apidocs [ERROR] Error fetching link: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/About.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-frame.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-summary.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-tree.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/class-use/About.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/index-all.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/index.html... Generating /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-shade-plugin:2.4.3:shade (default) @ deca-cli_2.11 --- [INFO] Including net.fnothaft:jsr203-s3a:jar:0.0.1 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 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-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.11.8 in the shaded jar. [INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-serialization-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-SNAPSHOT in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar. [INFO] Including commons-io:commons-io:jar:2.4 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.23.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar. [INFO] Including org.hammerlab:genomic-loci_2.11:jar:1.4.4 in the shaded jar. [INFO] Including org.hammerlab:args4s_2.11:jar:1.0.0 in the shaded jar. [INFO] Including org.hammerlab:iterator_2.11:jar:1.0.0 in the shaded jar. [INFO] Including org.hammerlab:string-utils_2.11:jar:1.0.0 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 org.bdgenomics.bdg-formats:bdg-formats:jar:0.11.3 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.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.2 in the shaded jar. [INFO] Including org.seqdoop:hadoop-bam:jar:7.9.1 in the shaded jar. [INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar. [INFO] Including com.github.samtools:htsjdk:jar:2.11.0 in the shaded jar. [INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar. [INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:1.2.4 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.google.guava:guava:jar:16.0.1 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.11:jar:0.23.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.23.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.23.0 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.11:jar:4.1.0 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.1.0 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:4.1.0 in the shaded jar. [INFO] Including org.apache.commons:commons-math3:jar:3.4.1 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:1.7.16 in the shaded jar. [INFO] Including org.xerial.snappy:snappy-java:jar:1.1.2.4 in the shaded jar. [INFO] Including org.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar. [INFO] Including org.scalanlp:breeze_2.11:jar:0.12 in the shaded jar. [INFO] Including org.scalanlp:breeze-macros_2.11:jar:0.12 in the shaded jar. [INFO] Including com.github.fommil.netlib:core:jar:1.1.2 in the shaded jar. [INFO] Including net.sourceforge.f2j:arpack_combined_all:jar:0.1 in the shaded jar. [INFO] Including net.sf.opencsv:opencsv:jar:2.3 in the shaded jar. [INFO] Including com.github.rwl:jtransforms:jar:2.4.0 in the shaded jar. [INFO] Including junit:junit:jar:4.8.2 in the shaded jar. [INFO] Including org.spire-math:spire_2.11:jar:0.7.4 in the shaded jar. [INFO] Including org.spire-math:spire-macros_2.11:jar:0.7.4 in the shaded jar. [INFO] Including com.chuusai:shapeless_2.11:jar:2.0.0 in the shaded jar. [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar with /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-shaded.jar [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca: distribution 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-distribution_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-distribution_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-distribution_2.11 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-distribution_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-distribution_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-distribution_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-distribution_2.11 --- [INFO] [INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ deca-distribution_2.11 --- [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_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-distribution_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-distribution_2.11 --- [INFO] Source directory: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.11 <<< [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.11 --- [INFO] No source files found [INFO] [INFO] --- maven-assembly-plugin:2.4.1:single (default) @ deca-distribution_2.11 --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [INFO] Building tar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/target/deca-distribution_2.11-0.1.1-SNAPSHOT-bin.tar.gz [INFO] Building tar: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/target/deca-distribution_2.11-0.1.1-SNAPSHOT-bin.tar.bz2 [INFO] Building zip: /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/target/deca-distribution_2.11-0.1.1-SNAPSHOT-bin.zip [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [3.368s] [INFO] deca-core: Core variant calling algorithms ........ SUCCESS [3.329s] [INFO] deca-cli: Command line interface for a distributed variant caller SUCCESS [22.972s] [INFO] deca: distribution ................................ SUCCESS [0.899s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 30.751s [INFO] Finished at: Mon Jan 08 10:00:28 PST 2018 [INFO] Final Memory: 91M/1277M [INFO] ------------------------------------------------------------------------ # we are done with maven, so clean up the maven temp dir find ${DECA_MVN_TMP_DIR} + find /tmp/decaTestMvnv9g61Zh /tmp/decaTestMvnv9g61Zh /tmp/decaTestMvnv9g61Zh/1515434353296-0 /tmp/decaTestMvnv9g61Zh/1515434353296-0/test.txt /tmp/decaTestMvnv9g61Zh/1515434353296-0/.test.txt.crc /tmp/decaTestMvnv9g61Zh/1515434321858-0 /tmp/decaTestMvnv9g61Zh/1515434321858-0/test.txt /tmp/decaTestMvnv9g61Zh/1515434321858-0/.test.txt.crc rm -rf ${DECA_MVN_TMP_DIR} + rm -rf /tmp/decaTestMvnv9g61Zh find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/decaTestMvnv9g61Zh:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' ./scripts/format-source + ./scripts/format-source +++ dirname ./scripts/format-source ++ cd ./scripts ++ pwd + DIR=/home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts + pushd /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/.. ~/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos ~/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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_2.11:jar:0.1.1-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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT [WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25 [WARNING] [WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 357, 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 361, 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 365, 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 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 --- [INFO] Modified 0 of 30 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-parent_2.11 --- [INFO] Updating license headers... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 --- [INFO] Modified 0 of 20 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-core_2.11 --- [INFO] Updating license headers... [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT [INFO] ------------------------------------------------------------------------ [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 --- [INFO] Modified 0 of 10 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-cli_2.11 --- [INFO] Updating license headers... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] [INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.000s] [INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.416s] [INFO] deca-cli: Command line interface for a distributed variant caller SUCCESS [0.101s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 2.934s [INFO] Finished at: Mon Jan 08 10:00:32 PST 2018 [INFO] Final Memory: 17M/1116M [INFO] ------------------------------------------------------------------------ + popd ~/workspace/deca/HADOOP_VERSION/2.3.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/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 + '[' 2.0.0 == 1.5.2 ']' + '[' 2.0.0 == 2.0.0 ']' + '[' 2.3.0 == 2.6.0 ']' Recording test results Sending e-mails to: fnothaft@berkeley.edu Finished: SUCCESS