Started by upstream project "cannoli" build number 2127 originally caused by: Started by timer [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-09 (ubuntu ubuntu-gpu research-09 ubuntu-avx2) in workspace /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu Cloning the remote Git repository Cloning repository https://github.com/bigdatagenomics/cannoli.git > git init /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/heads/*:refs/remotes/origin/* > git config remote.origin.url https://github.com/bigdatagenomics/cannoli.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/cannoli.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git > git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/heads/*:refs/remotes/origin/* Checking out Revision 111c645ff0fb9b021a0efec16078d46596481be0 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 111c645ff0fb9b021a0efec16078d46596481be0 > git rev-list 111c645ff0fb9b021a0efec16078d46596481be0 # timeout=10 Cleaning workspace > git rev-parse --verify HEAD # timeout=10 Resetting working tree > git reset --hard # timeout=10 > git clean -fdx # timeout=10 [ubuntu] $ /bin/bash /tmp/hudson2922308073046650625.sh + set -e + export JAVA_HOME=/usr/lib/jvm/java-8-oracle + JAVA_HOME=/usr/lib/jvm/java-8-oracle + export CONDA_BIN=/home/anaconda/bin/ + CONDA_BIN=/home/anaconda/bin/ + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + set +x + /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to CANNOLI_MVN_TMP_DIR=$(mktemp -d -t cannoliTestMvnXXXXXXX) mktemp -d -t cannoliTestMvnXXXXXXX ++ mktemp -d -t cannoliTestMvnXXXXXXX + CANNOLI_MVN_TMP_DIR=/tmp/cannoliTestMvnfOUIKd5 # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${CANNOLI_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/cannoliTestMvnfOUIKd5:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' # variable declarations export PATH=${JAVA_HOME}/bin/:${PATH} + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games 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 ) cd $( dirname ${BASH_SOURCE[0]} ) && pwd dirname ${BASH_SOURCE[0]} +++ dirname /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts/.. VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g') grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g' ++ grep '<version>' /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.11.0-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 2.7.5 ]] # is the scala version set? if ! [[ ${SCALA_VERSION} ]]; then echo "SCALA_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.12 ]] # 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 2.4.7 ]] # print versions echo "Testing Cannoli version ${VERSION} on Spark ${SPARK_VERSION} Scala ${SCALA_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing Cannoli version 0.11.0-SNAPSHOT on Spark 2.4.7 Scala 2.12 and Hadoop 2.7.5' Testing Cannoli version 0.11.0-SNAPSHOT on Spark 2.4.7 Scala 2.12 and Hadoop 2.7.5 # move to Scala 2.11 if requested if [ ${SCALA_VERSION} == 2.11 ]; then set +e ./scripts/move_to_scala_2.11.sh set -e fi + '[' 2.12 == 2.11 ']' # move to Scala 2.12 if requested if [ ${SCALA_VERSION} == 2.12 ]; then set +e ./scripts/move_to_scala_2.12.sh set -e fi + '[' 2.12 == 2.12 ']' + set +e + ./scripts/move_to_scala_2.12.sh Scala version is already set to 2.12 (Scala artifacts have _2.12 version suffix in artifact name). Cowardly refusing to move to Scala 2.12 a second time... + set -e # move to Spark 2.x if requested if [ ${SPARK_VERSION} == 2.4.7 ]; then set +e ./scripts/move_to_spark_2.sh set -e fi + '[' 2.4.7 == 2.4.7 ']' + set +e + ./scripts/move_to_spark_2.sh + set -e # move to Spark 3.x if requested if [ ${SPARK_VERSION} == 3.0.1 ]; then set +e ./scripts/move_to_spark_3.sh set -e fi + '[' 2.4.7 == 3.0.1 ']' # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${HADOOP_VERSION} + mvn clean -Dhadoop.version=2.7.5 OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Cannoli_2.12 [pom] [INFO] Cannoli_2.12: Builder [jar] [INFO] Cannoli_2.12: Core [jar] [INFO] Cannoli_2.12: CLI [jar] [INFO] Cannoli_2.12: Assembly [jar] [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark2_2.12 >---------- [INFO] Building Cannoli_2.12 0.11.0-SNAPSHOT [1/5] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark2_2.12 >--------- [INFO] Building Cannoli_2.12: Builder 0.11.0-SNAPSHOT [2/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark2_2.12 >----------- [INFO] Building Cannoli_2.12: Core 0.11.0-SNAPSHOT [3/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark2_2.12 >----------- [INFO] Building Cannoli_2.12: CLI 0.11.0-SNAPSHOT [4/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark2_2.12 >--------- [INFO] Building Cannoli_2.12: Assembly 0.11.0-SNAPSHOT [5/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-assembly-spark2_2.12 --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Cannoli_2.12 0.11.0-SNAPSHOT: [INFO] [INFO] Cannoli_2.12 ....................................... SUCCESS [ 0.263 s] [INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 0.003 s] [INFO] Cannoli_2.12: Core ................................. SUCCESS [ 0.008 s] [INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 0.026 s] [INFO] Cannoli_2.12: Assembly ............................. SUCCESS [ 0.003 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.490 s [INFO] Finished at: 2020-10-30T03:37:36-07:00 [INFO] ------------------------------------------------------------------------ # if this is a pull request, we need to set the coveralls pr id if [[ ! -z $ghprbPullId ]]; then COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}" fi + [[ ! -z '' ]] # coveralls token should not be visible set +x +v + set +x +v OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Cannoli_2.12 [pom] [INFO] Cannoli_2.12: Builder [jar] [INFO] Cannoli_2.12: Core [jar] [INFO] Cannoli_2.12: CLI [jar] [INFO] Cannoli_2.12: Assembly [jar] [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark2_2.12 >---------- [INFO] Building Cannoli_2.12 0.11.0-SNAPSHOT [1/5] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark2_2.12 --- [INFO] Modified 0 of 55 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-parent-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark2_2.12 --- [INFO] Modified 0 of 55 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-parent-spark2_2.12 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-parent-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark2_2.12 >--------- [INFO] Building Cannoli_2.12: Builder 0.11.0-SNAPSHOT [2/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-builder-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-builder-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-builder-spark2_2.12 --- [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/java:-1: info: compiling [INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/scala-2.12.8/classes at 1604054262625 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-builder-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/scala-2.12.8/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-builder-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-builder-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-builder-spark2_2.12 --- [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/test/java:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/scala-2.12.8/test-classes at 1604054266345 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-builder-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/scala-2.12.8/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.bdgenomics.cannoli.builder.LocalBuilderTest [INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.121 s - in org.bdgenomics.cannoli.builder.LocalBuilderTest [INFO] Running org.bdgenomics.cannoli.builder.DockerBuilderTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.bdgenomics.cannoli.builder.DockerBuilderTest [INFO] Running org.bdgenomics.cannoli.builder.CommandBuildersTest [INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.bdgenomics.cannoli.builder.CommandBuildersTest [INFO] Running org.bdgenomics.cannoli.builder.SingularityBuilderTest [INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.bdgenomics.cannoli.builder.SingularityBuilderTest [INFO] [INFO] Results: [INFO] [INFO] Tests run: 40, Failures: 0, Errors: 0, Skipped: 0 [INFO] [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-builder-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-builder-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-builder-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-builder-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-builder-spark2_2.12 --- [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/scala-2.12.8/classes at 1604054270075 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-builder-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/scala-2.12.8/classes [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-builder-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-builder-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-builder-spark2_2.12 --- [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/test/java:-1: info: compiling [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/generated-test-sources/test-annotations:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/scala-2.12.8/test-classes at 1604054272780 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-builder-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-builder-spark2_2.12 --- [INFO] Skipping execution of surefire because it has already been run for this configuration [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-builder-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-builder-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark2_2.12 >----------- [INFO] Building Cannoli_2.12: Core 0.11.0-SNAPSHOT [3/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-core-spark2_2.12 --- [INFO] Modified 0 of 28 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-core-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala:-1: info: compiling [INFO] Compiling 27 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/scala-2.12.8/classes at 1604054276645 [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala:93: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala:94: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala:106: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala:107: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala:101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala:102: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala:91: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val file = List(optA, optB).flatten.get(0) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala:118: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala:119: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala:134: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] builder.addFiles(files(args.db + "*")) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala:151: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Blastn.scala:152: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala:81: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] builder.addFiles(files(args.indexPath + "*.ebwt")) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala:98: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala:99: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala:97: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] builder.addFiles(files(args.indexPath + "*.bt2")) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala:114: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala:115: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BwaMem.scala:140: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BwaMem.scala:141: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BwaMem2.scala:140: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/BwaMem2.scala:141: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala:115: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala:116: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Gem.scala:94: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Gem.scala:95: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/MagicBlast.scala:135: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] builder.addFiles(files(args.db + "*")) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/MagicBlast.scala:152: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/MagicBlast.scala:153: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala:109: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala:110: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala:101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala:102: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala:101: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] builder.addFiles(files(args.indexPath + "*.bt2")) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala:118: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala:119: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndStar.scala:102: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] builder.addFiles(files(args.genomePath + "**")) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndStar.scala:120: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SingleEndStar.scala:121: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Snap.scala:124: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Snap.scala:125: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala:91: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala:92: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Star.scala:103: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] builder.addFiles(files(args.genomePath + "**")) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Star.scala:122: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Star.scala:123: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala:118: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala:119: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/VtNormalize.scala:104: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/VtNormalize.scala:105: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] files = builder.getFiles() [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/util/QuerynameGroupingIterator.scala:58: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] .setAlignments(readsInFragment) [WARNING] ^ [WARNING] 51 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 9 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-core-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-core-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/test/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/scala-2.12.8/test-classes at 1604054286498 [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/test/scala/org/bdgenomics/cannoli/util/QuerynameGroupingIteratorSuite.scala:41: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val readNames = fragments.flatMap(_.getAlignments.map(r => r.getReadName)) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/test/scala/org/bdgenomics/cannoli/util/QuerynameGroupingIteratorSuite.scala:71: warning: object JavaConversions in package collection is deprecated (since 2.12.0): use JavaConverters [WARNING] val readNames = fragments.flatMap(_.getAlignments.map(r => r.getReadName)) [WARNING] ^ [WARNING] two warnings found [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-core-spark2_2.12 --- Discovery starting. Discovery completed in 156 milliseconds. Run starting. Expected test count is: 3 QuerynameGroupingIteratorSuite: - can't call next when empty - if no paired reads, return fragments of single reads - return fragments on iterator with paired reads Run completed in 677 milliseconds. Total number of tests run: 3 Suites: completed 2, aborted 0 Tests: succeeded 3, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-core-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-core-spark2_2.12 --- [INFO] Modified 0 of 28 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-core-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-core-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-core-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-core-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-core-spark2_2.12 --- [INFO] Skipping execution of surefire because it has already been run for this configuration [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-core-spark2_2.12 --- Discovery starting. Discovery completed in 179 milliseconds. Run starting. Expected test count is: 3 QuerynameGroupingIteratorSuite: - can't call next when empty - if no paired reads, return fragments of single reads - return fragments on iterator with paired reads Run completed in 692 milliseconds. Total number of tests run: 3 Suites: completed 2, aborted 0 Tests: succeeded 3, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-core-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-core-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark2_2.12 >----------- [INFO] Building Cannoli_2.12: CLI 0.11.0-SNAPSHOT [4/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark2_2.12 --- [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/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark2_2.12 --- [INFO] Modified 0 of 26 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-cli-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala:-1: info: compiling [INFO] Compiling 25 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/scala-2.12.8/classes at 1604054297993 [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala/org/bdgenomics/cannoli/cli/InterleaveFastq.scala:108: warning: constructor AsciiLineReader in class AsciiLineReader is deprecated: see corresponding Javadoc for more information. [WARNING] val pair1Reader = new AsciiLineReaderIterator(new AsciiLineReader(cIs1)) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala/org/bdgenomics/cannoli/cli/InterleaveFastq.scala:109: warning: constructor AsciiLineReader in class AsciiLineReader is deprecated: see corresponding Javadoc for more information. [WARNING] val pair2Reader = new AsciiLineReaderIterator(new AsciiLineReader(cIs2)) [WARNING] ^ [WARNING] two warnings found [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-cli-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/scala-2.12.8/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-cli-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/test/scala:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/scala-2.12.8/test-classes at 1604054307053 [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/test/scala/org/bdgenomics/cannoli/cli/InterleaveFastqSuite.scala:69: warning: constructor AsciiLineReader in class AsciiLineReader is deprecated: see corresponding Javadoc for more information. [WARNING] val iter = new AsciiLineReaderIterator(new AsciiLineReader(cIs)) [WARNING] ^ [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 5 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark2_2.12 --- Discovery starting. Discovery completed in 181 milliseconds. Run starting. Expected test count is: 12 CannoliSuite: - default command groups is non empty - module provides default command groups - inject default command groups when called via main - command groups is empty when called via apply - single command group - add new command group to default command groups - module restores default command groups when called via apply - custom module with single command group - custom module with new command group added to default command groups InterleaveFastqSuite: 2020-10-30 03:38:35 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-10-30 03:38:35 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address 2020-10-30 03:38:36 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - interleave two paired FASTQ files - interleave two paired FASTQ files and save as BAM - interleave gzipped and bzipped files Run completed in 6 seconds, 412 milliseconds. Total number of tests run: 12 Suites: completed 3, aborted 0 Tests: succeeded 12, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-cli-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark2_2.12 --- [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/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark2_2.12 --- [INFO] Modified 0 of 26 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-cli-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-cli-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala:-1: info: compiling [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 25 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/scala-2.12.8/classes at 1604054320895 [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala/org/bdgenomics/cannoli/cli/InterleaveFastq.scala:108: warning: constructor AsciiLineReader in class AsciiLineReader is deprecated: see corresponding Javadoc for more information. [WARNING] val pair1Reader = new AsciiLineReaderIterator(new AsciiLineReader(cIs1)) [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala/org/bdgenomics/cannoli/cli/InterleaveFastq.scala:109: warning: constructor AsciiLineReader in class AsciiLineReader is deprecated: see corresponding Javadoc for more information. [WARNING] val pair2Reader = new AsciiLineReaderIterator(new AsciiLineReader(cIs2)) [WARNING] ^ [WARNING] two warnings found [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-cli-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-cli-spark2_2.12 --- [INFO] Skipping execution of surefire because it has already been run for this configuration [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark2_2.12 --- Discovery starting. Discovery completed in 205 milliseconds. Run starting. Expected test count is: 12 CannoliSuite: - default command groups is non empty - module provides default command groups - inject default command groups when called via main - command groups is empty when called via apply - single command group - add new command group to default command groups - module restores default command groups when called via apply - custom module with single command group - custom module with new command group added to default command groups 2020-10-30 03:38:52 WARN Utils:66 - Your hostname, research-jenkins-worker-09 resolves to a loopback address: 127.0.1.1; using 192.168.10.31 instead (on interface enp4s0f0) 2020-10-30 03:38:52 WARN Utils:66 - Set SPARK_LOCAL_IP if you need to bind to another address InterleaveFastqSuite: 2020-10-30 03:38:52 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable - interleave two paired FASTQ files - interleave two paired FASTQ files and save as BAM - interleave gzipped and bzipped files Run completed in 6 seconds, 823 milliseconds. Total number of tests run: 12 Suites: completed 3, aborted 0 Tests: succeeded 12, failed 0, canceled 0, ignored 0, pending 0 All tests passed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-cli-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-cli-spark2_2.12 --- [INFO] Skipping SCoverage report generation [INFO] [INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark2_2.12 >--------- [INFO] Building Cannoli_2.12: Assembly 0.11.0-SNAPSHOT [5/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-assembly-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-assembly-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/main/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/scala-2.12.8/classes at 1604054337714 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-assembly-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-assembly-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-assembly-spark2_2.12 --- [INFO] No tests to run. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-assembly-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-assembly-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-assembly-spark2_2.12 --- [WARNING] Skipping SCoverage execution - unsupported Scala version "2.12.8" [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-assembly-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-assembly-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-assembly-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-assembly-spark2_2.12 --- [INFO] No tests to run. [INFO] Skipping execution of surefire because it has already been run for this configuration [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-assembly-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-assembly-spark2_2.12 --- [INFO] [scoverage] Generating aggregated cobertura XML report... [INFO] [scoverage] Generating aggregated scoverage XML report... [INFO] [scoverage] Generating aggregated scoverage HTML report... [INFO] Skipping SCoverage report generation [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark2_2.12 >---------- [INFO] Building Cannoli_2.12 0.11.0-SNAPSHOT [6/5] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- coveralls-maven-plugin:4.3.0:report (default-cli) @ cannoli-parent-spark2_2.12 --- [INFO] Starting Coveralls job for jenkins (2127 / https://amplab.cs.berkeley.edu/jenkins/job/cannoli/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=2.4.7,label=ubuntu/2127/) [INFO] Using repository token <secret> [INFO] Git commit 111c645 in master [INFO] Writing Coveralls data to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/target/coveralls.json... [INFO] Processing coverage report from /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/target/cobertura.xml [INFO] Successfully wrote Coveralls data in 83ms [INFO] Gathered code coverage metrics for 0 source files with 0 lines of code: [INFO] - 0 relevant lines [INFO] - 0 covered lines [INFO] - 0 missed lines [INFO] Submitting Coveralls data to API [INFO] Successfully submitted Coveralls data in 922ms for Job #2127.2 [INFO] https://coveralls.io/jobs/69958756 [INFO] *** It might take hours for Coveralls to update the actual coverage numbers for a job [INFO] If you see question marks in the report, please be patient [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Cannoli_2.12 0.11.0-SNAPSHOT: [INFO] [INFO] Cannoli_2.12 ....................................... SUCCESS [ 1.596 s] [INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 13.575 s] [INFO] Cannoli_2.12: Core ................................. SUCCESS [ 21.273 s] [INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 40.827 s] [INFO] Cannoli_2.12: Assembly ............................. SUCCESS [ 3.427 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:24 min [INFO] Finished at: 2020-10-30T03:39:02-07:00 [INFO] ------------------------------------------------------------------------ # we are done with maven, so clean up the maven temp dir find ${CANNOLI_MVN_TMP_DIR} + find /tmp/cannoliTestMvnfOUIKd5 /tmp/cannoliTestMvnfOUIKd5 /tmp/cannoliTestMvnfOUIKd5/2059021092938277225 /tmp/cannoliTestMvnfOUIKd5/2059021092938277225/test.bam /tmp/cannoliTestMvnfOUIKd5/2059021092938277225/.test.bam.crc /tmp/cannoliTestMvnfOUIKd5/8346268437306967513 /tmp/cannoliTestMvnfOUIKd5/8346268437306967513/test.bam /tmp/cannoliTestMvnfOUIKd5/8346268437306967513/.test.bam.crc /tmp/cannoliTestMvnfOUIKd5/8539724013064105851 /tmp/cannoliTestMvnfOUIKd5/8539724013064105851/test.ifq /tmp/cannoliTestMvnfOUIKd5/8539724013064105851/.test.ifq.crc /tmp/cannoliTestMvnfOUIKd5/3030472410070714958 /tmp/cannoliTestMvnfOUIKd5/3030472410070714958/test.ifq.bz2 /tmp/cannoliTestMvnfOUIKd5/3030472410070714958/.test.ifq.bz2.crc /tmp/cannoliTestMvnfOUIKd5/4114484194327981187 /tmp/cannoliTestMvnfOUIKd5/4114484194327981187/test.ifq /tmp/cannoliTestMvnfOUIKd5/4114484194327981187/.test.ifq.crc /tmp/cannoliTestMvnfOUIKd5/6644029770894374661 /tmp/cannoliTestMvnfOUIKd5/6644029770894374661/double.ifq /tmp/cannoliTestMvnfOUIKd5/6644029770894374661/.double.ifq.crc /tmp/cannoliTestMvnfOUIKd5/1238534676426848982 /tmp/cannoliTestMvnfOUIKd5/1238534676426848982/.test.ifq.gz.crc /tmp/cannoliTestMvnfOUIKd5/1238534676426848982/test.ifq.gz /tmp/cannoliTestMvnfOUIKd5/4918849391743780709 /tmp/cannoliTestMvnfOUIKd5/4918849391743780709/test.ifq.bz2 /tmp/cannoliTestMvnfOUIKd5/4918849391743780709/.test.ifq.bz2.crc /tmp/cannoliTestMvnfOUIKd5/976533117992381120 /tmp/cannoliTestMvnfOUIKd5/976533117992381120/double.ifq /tmp/cannoliTestMvnfOUIKd5/976533117992381120/.double.ifq.crc /tmp/cannoliTestMvnfOUIKd5/5061435996584568858 /tmp/cannoliTestMvnfOUIKd5/5061435996584568858/.test.ifq.gz.crc /tmp/cannoliTestMvnfOUIKd5/5061435996584568858/test.ifq.gz rm -rf ${CANNOLI_MVN_TMP_DIR} + rm -rf /tmp/cannoliTestMvnfOUIKd5 # and move our poms back to their original values # this will allow us to pass our porcelain test at the end if [ ${SCALA_VERSION} == 2.11 ]; then echo "Rewriting POM.xml files back to Scala 2.12." ./scripts/move_to_scala_2.12.sh fi + '[' 2.12 == 2.11 ']' if [ ${SPARK_VERSION} == 2.4.7 ]; then echo "Rewriting POM.xml files back to Spark 3." ./scripts/move_to_spark_3.sh fi + '[' 2.4.7 == 2.4.7 ']' + echo 'Rewriting POM.xml files back to Spark 3.' Rewriting POM.xml files back to Spark 3. + ./scripts/move_to_spark_3.sh find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${CANNOLI_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/cannoliTestMvnfOUIKd5:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' if test -n "$(git status --porcelain)" then echo "Applying move_to_xyz script marred a pom.xml file." echo "Exiting..." exit 1 fi git status --porcelain ++ git status --porcelain + test -n '' ./scripts/format-source + ./scripts/format-source +++ dirname ./scripts/format-source ++ cd ./scripts ++ pwd + DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts + pushd /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts/.. ~/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu ~/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu + mvn org.scalariform:scalariform-maven-plugin:format license:format OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Cannoli_2.12 [pom] [INFO] Cannoli_2.12: Builder [jar] [INFO] Cannoli_2.12: Core [jar] [INFO] Cannoli_2.12: CLI [jar] [INFO] Cannoli_2.12: Assembly [jar] [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark3_2.12 >---------- [INFO] Building Cannoli_2.12 0.11.0-SNAPSHOT [1/5] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark3_2.12 --- [INFO] Modified 0 of 55 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ cannoli-parent-spark3_2.12 --- [INFO] Updating license headers... [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark3_2.12 >--------- [INFO] Building Cannoli_2.12: Builder 0.11.0-SNAPSHOT [2/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-builder-spark3_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ cannoli-builder-spark3_2.12 --- [INFO] Updating license headers... [INFO] [INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark3_2.12 >----------- [INFO] Building Cannoli_2.12: Core 0.11.0-SNAPSHOT [3/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-core-spark3_2.12 --- [INFO] Modified 0 of 28 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ cannoli-core-spark3_2.12 --- [INFO] Updating license headers... [INFO] [INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark3_2.12 >----------- [INFO] Building Cannoli_2.12: CLI 0.11.0-SNAPSHOT [4/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark3_2.12 --- [INFO] Modified 0 of 26 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ cannoli-cli-spark3_2.12 --- [INFO] Updating license headers... [INFO] [INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark3_2.12 >--------- [INFO] Building Cannoli_2.12: Assembly 0.11.0-SNAPSHOT [5/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-assembly-spark3_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ cannoli-assembly-spark3_2.12 --- [INFO] Updating license headers... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Cannoli_2.12 0.11.0-SNAPSHOT: [INFO] [INFO] Cannoli_2.12 ....................................... SUCCESS [ 2.228 s] [INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 0.009 s] [INFO] Cannoli_2.12: Core ................................. SUCCESS [ 0.403 s] [INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 0.217 s] [INFO] Cannoli_2.12: Assembly ............................. SUCCESS [ 0.015 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 3.084 s [INFO] Finished at: 2020-10-30T03:39:06-07:00 [INFO] ------------------------------------------------------------------------ + popd ~/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu if test -n "$(git status --porcelain)" then echo "Please run './scripts/format-source'" exit 1 fi git status --porcelain ++ git status --porcelain + test -n '' echo + echo echo "All the tests passed" + echo 'All the tests passed' All the tests passed echo + echo + '[' 2.12 == 2.11 ']' + '[' 2.12 == 2.12 ']' + echo 'Moving build to Scala 2.12...' Moving build to Scala 2.12... + set +e + /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts/move_to_scala_2.12.sh Scala version is already set to 2.12 (Scala artifacts have _2.12 version suffix in artifact name). Cowardly refusing to move to Scala 2.12 a second time... + set -e + '[' 2.4.7 == 2.4.7 ']' + echo 'Moving build to Spark 2.x...' Moving build to Spark 2.x... + set +e + /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/scripts/move_to_spark_2.sh + set -e + '[' 2.4.7 == 3.0.1 ']' + mvn --settings=/home/jenkins/workspace/settings.xml deploy -DskipTests -Pdistribution [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] Cannoli_2.12 [pom] [INFO] Cannoli_2.12: Builder [jar] [INFO] Cannoli_2.12: Core [jar] [INFO] Cannoli_2.12: CLI [jar] [INFO] Cannoli_2.12: Assembly [jar] [INFO] Cannoli_2.12: Distribution [pom] [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark2_2.12 >---------- [INFO] Building Cannoli_2.12 0.11.0-SNAPSHOT [1/6] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark2_2.12 --- [INFO] Modified 0 of 55 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-parent-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-parent-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-parent-spark2_2.12 --- [INFO] No source files found [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-parent-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-parent-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-parent-spark2_2.12 --- [INFO] No source files found [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-parent-spark2_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-parent-spark2_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/0.11.0-SNAPSHOT/cannoli-parent-spark2_2.12-0.11.0-SNAPSHOT.pom [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-parent-spark2_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml Progress (1): 629 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml (629 B at 816 B/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/0.11.0-SNAPSHOT/cannoli-parent-spark2_2.12-0.11.0-20201030.103913-76.pom Progress (1): 4.1/21 kB Progress (1): 8.2/21 kB Progress (1): 12/21 kB Progress (1): 16/21 kB Progress (1): 20/21 kB Progress (1): 21 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/0.11.0-SNAPSHOT/cannoli-parent-spark2_2.12-0.11.0-20201030.103913-76.pom (21 kB at 36 kB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/maven-metadata.xml Progress (1): 370 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/maven-metadata.xml (370 B at 2.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml Progress (1): 629 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml (629 B at 1.3 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/maven-metadata.xml Progress (1): 370 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark2_2.12/maven-metadata.xml (370 B at 753 B/s) [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark2_2.12 >--------- [INFO] Building Cannoli_2.12: Builder 0.11.0-SNAPSHOT [2/6] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-builder-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-builder-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-builder-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-builder-spark2_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/scala-2.12.8/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-builder-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-builder-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-builder-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-builder-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-builder-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-builder-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-builder-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-builder-spark2_2.12 --- [INFO] Loading source files for package org.bdgenomics.cannoli.builder... Constructing Javadoc information... Standard Doclet version 1.8.0_222 Building tree for all the packages and classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/CommandBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/CommandBuilders.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/DockerBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/LocalBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/SingularityBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/package-frame.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/package-summary.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/package-tree.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/serialized-form.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/SingularityBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/CommandBuilders.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/DockerBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/CommandBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/LocalBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/index-all.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/index.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-builder-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-builder-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-builder-spark2_2.12 --- model contains 10 documentable templates /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/java/org/bdgenomics/cannoli/builder/CommandBuilder.java:449: warning: Could not find any member to link for "IllegalStateException". /** ^ one warning found [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-builder-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-builder-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-builder-spark2_2.12 --- model contains 10 documentable templates /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/src/main/java/org/bdgenomics/cannoli/builder/CommandBuilder.java:449: warning: Could not find any member to link for "IllegalStateException". /** ^ one warning found [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-builder-spark2_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-builder-spark2_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-sources.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/builder/target/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/cannoli-builder-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-builder-spark2_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 7.9 kB/s) Uploading to sonatype-nexus-snapshots: 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Progress (1): 1.0/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.1/1.2 MB Progress (1): 1.2/1.2 MB Progress (1): 1.2/1.2 MB Progress (1): 1.2 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/cannoli-builder-spark2_2.12-0.11.0-20201030.103928-76-javadoc.jar (1.2 MB at 2.1 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/maven-metadata.xml Progress (1): 371 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/maven-metadata.xml (371 B at 2.3 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 2.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/maven-metadata.xml Progress (1): 371 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark2_2.12/maven-metadata.xml (371 B at 752 B/s) [INFO] [INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark2_2.12 >----------- [INFO] Building Cannoli_2.12: Core 0.11.0-SNAPSHOT [3/6] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-core-spark2_2.12 --- [INFO] Modified 0 of 28 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-core-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-core-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-core-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-core-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-core-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-core-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-core-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-core-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-core-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-core-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-core-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! model contains 54 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-core-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-core-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-core-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! model contains 54 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-core-spark2_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-core-spark2_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/0.11.0-SNAPSHOT/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/0.11.0-SNAPSHOT/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/0.11.0-SNAPSHOT/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT-sources.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/0.11.0-SNAPSHOT/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/0.11.0-SNAPSHOT/cannoli-core-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-core-spark2_2.12 --- Downloading from sonatype-nexus-snapshots: 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https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/0.11.0-SNAPSHOT/cannoli-core-spark2_2.12-0.11.0-20201030.103956-76-javadoc.jar (1.4 MB at 2.5 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/maven-metadata.xml Progress (1): 368 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/maven-metadata.xml (368 B at 1.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 2.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/maven-metadata.xml Progress (1): 368 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark2_2.12/maven-metadata.xml (368 B at 743 B/s) [INFO] [INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark2_2.12 >----------- [INFO] Building Cannoli_2.12: CLI 0.11.0-SNAPSHOT [4/6] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark2_2.12 --- [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/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark2_2.12 --- [INFO] Modified 0 of 26 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-cli-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala:-1: info: compiling [INFO] Compiling 25 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/scala-2.12.8/classes at 1604054404728 [WARNING] warning: there were two deprecation warnings; re-run with -deprecation for details [WARNING] one warning found [INFO] prepare-compile in 0 s [INFO] compile in 8 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-cli-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-cli-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-cli-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-cli-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-cli-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-cli-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-cli-spark2_2.12 --- [INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:3.1.0:javadoc' has not been previously called for the module: 'org.bdgenomics.cannoli:cannoli-core-spark2_2.12:jar:0.11.0-SNAPSHOT'. Trying to invoke it... [WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/apidocs [ERROR] Error fetching link: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/core/target/apidocs. Ignored it. [INFO] Loading source files for package org.bdgenomics.cannoli.cli... Constructing Javadoc information... Standard Doclet version 1.8.0_222 Building tree for all the packages and classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/About.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-frame.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-summary.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-tree.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/class-use/About.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-use.html... Building index for all the packages and classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/index-all.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/index.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-cli-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark2_2.12 --- [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/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-cli-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-cli-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! model contains 78 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-cli-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark2_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark2_2.12 --- [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/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-cli-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-cli-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] com.twitter:chill_2.12:0.9.3 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! model contains 78 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-cli-spark2_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-cli-spark2_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-sources.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/cli/target/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/cannoli-cli-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-cli-spark2_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 8.2 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/cannoli-cli-spark2_2.12-0.11.0-20201030.104039-76.jar Progress (1): 4.1/212 kB Progress (1): 8.2/212 kB Progress (1): 12/212 kB Progress (1): 16/212 kB Progress (1): 20/212 kB Progress (1): 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Progress (1): 1.4/1.6 MB Progress (1): 1.4/1.6 MB Progress (1): 1.4/1.6 MB Progress (1): 1.4/1.6 MB Progress (1): 1.4/1.6 MB Progress (1): 1.4/1.6 MB Progress (1): 1.5/1.6 MB Progress (1): 1.5/1.6 MB Progress (1): 1.5/1.6 MB Progress (1): 1.5/1.6 MB Progress (1): 1.5/1.6 MB Progress (1): 1.5/1.6 MB Progress (1): 1.5/1.6 MB Progress (1): 1.5/1.6 MB Progress (1): 1.6/1.6 MB Progress (1): 1.6 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/cannoli-cli-spark2_2.12-0.11.0-20201030.104039-76-javadoc.jar (1.6 MB at 2.8 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/maven-metadata.xml Progress (1): 367 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/maven-metadata.xml (367 B at 2.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 2.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/maven-metadata.xml Progress (1): 367 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark2_2.12/maven-metadata.xml (367 B at 703 B/s) [INFO] [INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark2_2.12 >--------- [INFO] Building Cannoli_2.12: Assembly 0.11.0-SNAPSHOT [5/6] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-assembly-spark2_2.12 --- [INFO] Modified 0 of 1 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-assembly-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-assembly-spark2_2.12 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-assembly-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-assembly-spark2_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-assembly-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-assembly-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-assembly-spark2_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-assembly-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-assembly-spark2_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-assembly-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-assembly-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-assembly-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-assembly-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-assembly-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-assembly-spark2_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-misc-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-io-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] org.clapper:grizzled-slf4j_2.12:1.3.4 requires scala version: 2.12.8 [WARNING] org.bdgenomics.utils:utils-cli-spark2_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] net.codingwell:scala-guice_2.12:4.2.1 requires scala version: 2.12.6 [WARNING] Multiple versions of scala libraries detected! model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-shade-plugin:3.2.0:shade (default) @ cannoli-assembly-spark2_2.12 --- [INFO] Including org.bdgenomics.cannoli:cannoli-cli-spark2_2.12:jar:0.11.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.12:jar:0.32.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.12:jar:0.3.0 in the shaded jar. [INFO] Including org.scala-lang:scala-library:jar:2.12.8 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-io-spark2_2.12:jar:0.3.0 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.7 in the shaded jar. [INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.11 in the shaded jar. [INFO] Including commons-logging:commons-logging:jar:1.2 in the shaded jar. [INFO] Including commons-codec:commons-codec:jar:1.11 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.12:jar:0.3.0 in the shaded jar. [INFO] Including org.clapper:grizzled-slf4j_2.12:jar:1.3.4 in the shaded jar. [INFO] Including org.slf4j:slf4j-api:jar:1.7.9 in the shaded jar. [INFO] Including org.apache.parquet:parquet-avro:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-column:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-common:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-encoding:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-hadoop:jar:1.10.1 in the shaded jar. [INFO] Including org.apache.parquet:parquet-jackson:jar:1.10.1 in the shaded jar. [INFO] Including commons-pool:commons-pool:jar:1.6 in the shaded jar. [INFO] Including org.apache.parquet:parquet-format:jar:2.4.0 in the shaded jar. [INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.15.0 in the shaded jar. [INFO] Including org.apache.avro:avro:jar:1.8.2 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.xerial.snappy:snappy-java:jar:1.1.1.3 in the shaded jar. [INFO] Including org.apache.commons:commons-compress:jar:1.8.1 in the shaded jar. [INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-core-spark2_2.12:jar:0.32.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.12:jar:0.3.0 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 commons-io:commons-io:jar:2.6 in the shaded jar. [INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar. [INFO] Including org.seqdoop:hadoop-bam:jar:7.9.2 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:2.19.0 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:2.9.0 in the shaded jar. [INFO] Including com.google.guava:guava:jar:27.0.1-jre in the shaded jar. [INFO] Including com.google.guava:failureaccess:jar:1.0.1 in the shaded jar. [INFO] Including com.google.guava:listenablefuture:jar:9999.0-empty-to-avoid-conflict-with-guava in the shaded jar. [INFO] Including org.checkerframework:checker-qual:jar:2.5.2 in the shaded jar. [INFO] Including com.google.errorprone:error_prone_annotations:jar:2.2.0 in the shaded jar. [INFO] Including com.google.j2objc:j2objc-annotations:jar:1.1 in the shaded jar. [INFO] Including org.codehaus.mojo:animal-sniffer-annotations:jar:1.17 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.12:jar:0.32.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.12:jar:0.32.0 in the shaded jar. [INFO] Including args4j:args4j:jar:2.33 in the shaded jar. [INFO] Including net.codingwell:scala-guice_2.12:jar:4.2.1 in the shaded jar. [INFO] Including com.google.inject:guice:jar:4.2.0 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 org.scala-lang:scala-reflect:jar:2.12.6 in the shaded jar. [INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar. [INFO] Including org.bdgenomics.cannoli:cannoli-core-spark2_2.12:jar:0.11.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.cannoli:cannoli-builder-spark2_2.12:jar:0.11.0-SNAPSHOT in the shaded jar. [WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$2.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar [WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar [WARNING] WORKAROUND: refusing to add class org/apache/parquet/avro/AvroSchemaConverter$1.class from jar /home/jenkins/.m2/repository/org/apache/parquet/parquet-avro/1.10.1/parquet-avro-1.10.1.jar [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT.jar with /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-shaded.jar [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-assembly-spark2_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-assembly-spark2_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/0.11.0-SNAPSHOT/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/0.11.0-SNAPSHOT/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/0.11.0-SNAPSHOT/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-sources.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/0.11.0-SNAPSHOT/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/assembly/target/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/0.11.0-SNAPSHOT/cannoli-assembly-spark2_2.12-0.11.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-assembly-spark2_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.2 kB Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/0.11.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 7.7 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/0.11.0-SNAPSHOT/cannoli-assembly-spark2_2.12-0.11.0-20201030.104057-76.jar Progress (1): 0.5/46 MB Progress (1): 0.9/46 MB Progress (1): 1.4/46 MB Progress (1): 1.8/46 MB Progress (1): 2.3/46 MB Progress (1): 2.7/46 MB Progress (1): 3.2/46 MB Progress (1): 3.6/46 MB Progress (1): 4.1/46 MB Progress (1): 4.5/46 MB Progress (1): 5.0/46 MB Progress (1): 5.5/46 MB Progress (1): 5.9/46 MB Progress (1): 6.4/46 MB Progress (1): 6.8/46 MB Progress (1): 7.3/46 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Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/maven-metadata.xml Progress (1): 372 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark2_2.12/maven-metadata.xml (372 B at 639 B/s) [INFO] [INFO] ------< org.bdgenomics.cannoli:cannoli-distribution-spark2_2.12 >------- [INFO] Building Cannoli_2.12: Distribution 0.11.0-SNAPSHOT [6/6] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-distribution-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-distribution-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/distribution/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-distribution-spark2_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-distribution-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-distribution-spark2_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/distribution/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-distribution-spark2_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-distribution-spark2_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-distribution-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-distribution-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-distribution-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/distribution/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-distribution-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-distribution-spark2_2.12 --- [INFO] No source files found [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-distribution-spark2_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-distribution-spark2_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-distribution-spark2_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-distribution-spark2_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/distribution/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-distribution-spark2_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-distribution-spark2_2.12 --- [INFO] No source files found [INFO] [INFO] --- maven-assembly-plugin:3.1.0:single (default) @ cannoli-distribution-spark2_2.12 --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [INFO] Building tar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/distribution/target/cannoli-distribution-spark2_2.12-0.11.0-SNAPSHOT-bin.tar.gz [WARNING] Entry: cannoli-distribution-spark2_2.12-0.11.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliAlignmentDataset.html longer than 100 characters. 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[INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-distribution-spark2_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/distribution/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-distribution-spark2_2.12/0.11.0-SNAPSHOT/cannoli-distribution-spark2_2.12-0.11.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/distribution/target/cannoli-distribution-spark2_2.12-0.11.0-SNAPSHOT-bin.tar.gz to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-distribution-spark2_2.12/0.11.0-SNAPSHOT/cannoli-distribution-spark2_2.12-0.11.0-SNAPSHOT-bin.tar.gz [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/2.4.7/label/ubuntu/distribution/target/cannoli-distribution-spark2_2.12-0.11.0-SNAPSHOT-bin.tar.bz2 to 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SUCCESS [ 6.754 s] [INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 17.929 s] [INFO] Cannoli_2.12: Core ................................. SUCCESS [ 29.875 s] [INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 40.966 s] [INFO] Cannoli_2.12: Assembly ............................. SUCCESS [ 20.392 s] [INFO] Cannoli_2.12: Distribution ......................... SUCCESS [ 44.196 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:40 min [INFO] Finished at: 2020-10-30T03:41:48-07:00 [INFO] ------------------------------------------------------------------------ Recording test results Publishing Scoverage XML and HTML report... Finished: SUCCESS