Started by upstream project "cannoli" build number 2222 originally caused by: Started by timer Running as SYSTEM [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-01 (ubuntu20 worker-01 ubuntu) in workspace /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu The recommended git tool is: NONE No credentials specified > git rev-parse --is-inside-work-tree # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/bigdatagenomics/cannoli.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/cannoli.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/bigdatagenomics/cannoli.git +refs/heads/*:refs/remotes/origin/* # timeout=10 Checking out Revision 211e500289ff9ec1f6fe07f7f56c4857406df505 (refs/remotes/origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 211e500289ff9ec1f6fe07f7f56c4857406df505 # timeout=10 Commit message: "Update default container images for bcftools and samtools to 1.12." > git rev-list --no-walk 211e500289ff9ec1f6fe07f7f56c4857406df505 # 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/jenkins6611670098859334026.sh + set -e + unset SPARK_TESTING + export JAVA_HOME=/usr/java/latest + JAVA_HOME=/usr/java/latest + export CONDA_BIN=/home/anaconda/bin/ + CONDA_BIN=/home/anaconda/bin/ + export PATH=/usr/java/latest/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:/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:/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:/snap/bin + PATH=/usr/java/latest/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:/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:/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:/snap/bin + /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to CANNOLI_MVN_TMP_DIR=$(mktemp -d -t cannoliTestMvnXXXXXXX) ++ mktemp -d -t cannoliTestMvnXXXXXXX + CANNOLI_MVN_TMP_DIR=/tmp/cannoliTestMvnFkY0bVI # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/cannoliTestMvnFkY0bVI:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' # variable declarations export PATH=${JAVA_HOME}/bin/:${PATH} + export PATH=/usr/java/latest/bin/:/usr/java/latest/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:/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:/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:/snap/bin + PATH=/usr/java/latest/bin/:/usr/java/latest/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:/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:/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:/snap/bin export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8" + export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' + MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd ) +++ dirname /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/.. VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g') ++ grep '<version>' /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.13.0-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 3.2.1 ]] # 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 3.0.1 ]] # print versions echo "Testing Cannoli version ${VERSION} on Spark ${SPARK_VERSION} Scala ${SCALA_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing Cannoli version 0.13.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 3.2.1' Testing Cannoli version 0.13.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 3.2.1 # build the distribution package and the integration tests mvn -U \ clean \ package \ -Dhadoop.version=${HADOOP_VERSION} + mvn -U clean package -Dhadoop.version=3.2.1 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 0.13.0-SNAPSHOT [1/5] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark3_2.12 --- [INFO] Modified 0 of 56 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-parent-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-parent-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-parent-spark3_2.12 --- [INFO] No source files found [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark3_2.12 >--------- [INFO] Building Cannoli_2.12: Builder 0.13.0-SNAPSHOT [2/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/scala added. [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-resources-plugin:3.1.0:resources (default-resources) @ cannoli-builder-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-builder-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/java:-1: info: compiling [INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/classes at 1617920839223 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-builder-spark3_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-builder-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-builder-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-builder-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/java:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/test-classes at 1617920843139 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-builder-spark3_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 4 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/test-classes [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running org.bdgenomics.cannoli.builder.DockerBuilderTest [INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 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.LocalBuilderTest [INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.bdgenomics.cannoli.builder.LocalBuilderTest [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] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-builder-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-builder-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-builder-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-builder-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 10 documentable templates /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark3_2.12 >----------- [INFO] Building Cannoli_2.12: Core 0.13.0-SNAPSHOT [3/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala added. [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-resources-plugin:3.1.0:resources (default-resources) @ cannoli-core-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-core-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala:-1: info: compiling [INFO] Compiling 27 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/scala-2.12.10/classes at 1617920854235 [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/CannoliFn.scala:76: warning: method isDirectory in class FileSystem is deprecated: see corresponding Javadoc for more information. [WARNING] val paths = if (fs.isDirectory(path)) { [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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] cmd = builder.build(), [WARNING] ^ [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala/org/bdgenomics/cannoli/Vep.scala:120: 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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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] 52 warnings found [INFO] prepare-compile in 0 s [INFO] compile in 10 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-core-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-core-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-core-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/scala-2.12.10/test-classes at 1617920864802 [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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-spark3_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-spark3_2.12 --- [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-core-spark3_2.12 --- Discovery starting. Discovery completed in 199 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 877 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] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-core-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-core-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-core-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-core-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 54 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark3_2.12 >----------- [INFO] Building Cannoli_2.12: CLI 0.13.0-SNAPSHOT [4/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark3_2.12 --- [INFO] Modified 0 of 27 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-cli-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates:-1: info: compiling [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala:-1: info: compiling [INFO] Compiling 26 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.10/classes at 1617920885824 [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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 9 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-cli-spark3_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.10/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-cli-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-cli-spark3_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-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/test/scala:-1: info: compiling [INFO] Compiling 2 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/scala-2.12.10/test-classes at 1617920896039 [WARNING] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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 6 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ cannoli-cli-spark3_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-spark3_2.12 --- [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark3_2.12 --- Discovery starting. Discovery completed in 277 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: 2021-04-08 15:28:26 WARN Utils:69 - Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.10.21 instead (on interface igb0) 2021-04-08 15:28:26 WARN Utils:69 - Set SPARK_LOCAL_IP if you need to bind to another address 2021-04-08 15:28:26 WARN NativeCodeLoader:60 - 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 7 seconds, 881 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] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-cli-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-cli-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-cli-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-cli-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 78 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark3_2.12 >--------- [INFO] Building Cannoli_2.12: Assembly 0.13.0-SNAPSHOT [5/5] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added. [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-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-assembly-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [INFO] /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/scala-2.12.10/classes at 1617920923969 [INFO] prepare-compile in 0 s [INFO] compile in 2 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ cannoli-assembly-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-assembly-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-assembly-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [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-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-assembly-spark3_2.12 --- [INFO] No tests to run. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-assembly-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-assembly-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-assembly-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-assembly-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-shade-plugin:3.2.0:shade (default) @ cannoli-assembly-spark3_2.12 --- [INFO] Including org.bdgenomics.cannoli:cannoli-cli-spark3_2.12:jar:0.13.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli-spark3_2.12:jar:0.34.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark3_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-spark3_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-spark3_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-spark3_2.12:jar:0.34.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_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-spark3_2.12:jar:0.34.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.34.0 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-spark3_2.12:jar:0.13.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.cannoli:cannoli-builder-spark3_2.12:jar:0.13.0-SNAPSHOT in the shaded jar. [WARNING] parquet-avro-1.10.1.jar, adam-core-spark3_2.12-0.34.0.jar define 3 overlapping classes: [WARNING] - org.apache.parquet.avro.AvroSchemaConverter$2 [WARNING] - org.apache.parquet.avro.AvroSchemaConverter [WARNING] - org.apache.parquet.avro.AvroSchemaConverter$1 [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar with /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-shaded.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Cannoli_2.12 0.13.0-SNAPSHOT: [INFO] [INFO] Cannoli_2.12 ....................................... SUCCESS [ 3.570 s] [INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 14.853 s] [INFO] Cannoli_2.12: Core ................................. SUCCESS [ 32.044 s] [INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 39.455 s] [INFO] Cannoli_2.12: Assembly ............................. SUCCESS [ 13.388 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 01:43 min [INFO] Finished at: 2021-04-08T15:28:56-07:00 [INFO] ------------------------------------------------------------------------ # make verbose again set -x -v + set -x -v # we are done with maven, so clean up the maven temp dir find ${CANNOLI_MVN_TMP_DIR} + find /tmp/cannoliTestMvnFkY0bVI /tmp/cannoliTestMvnFkY0bVI /tmp/cannoliTestMvnFkY0bVI/7699547963812984980 /tmp/cannoliTestMvnFkY0bVI/7699547963812984980/.double.ifq.crc /tmp/cannoliTestMvnFkY0bVI/7699547963812984980/double.ifq /tmp/cannoliTestMvnFkY0bVI/1656453237139662109 /tmp/cannoliTestMvnFkY0bVI/1656453237139662109/.test.ifq.bz2.crc /tmp/cannoliTestMvnFkY0bVI/1656453237139662109/test.ifq.bz2 /tmp/cannoliTestMvnFkY0bVI/4294587919899176245 /tmp/cannoliTestMvnFkY0bVI/4294587919899176245/test.ifq.gz /tmp/cannoliTestMvnFkY0bVI/4294587919899176245/.test.ifq.gz.crc /tmp/cannoliTestMvnFkY0bVI/1996807754860339042 /tmp/cannoliTestMvnFkY0bVI/1996807754860339042/.test.ifq.crc /tmp/cannoliTestMvnFkY0bVI/1996807754860339042/test.ifq /tmp/cannoliTestMvnFkY0bVI/4678621877995220847 /tmp/cannoliTestMvnFkY0bVI/4678621877995220847/.test.bam.crc /tmp/cannoliTestMvnFkY0bVI/4678621877995220847/test.bam rm -rf ${CANNOLI_MVN_TMP_DIR} + rm -rf /tmp/cannoliTestMvnFkY0bVI find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/cannoliTestMvnFkY0bVI:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' ./scripts/format-source + ./scripts/format-source +++ dirname ./scripts/format-source ++ cd ./scripts ++ pwd + DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts + pushd /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/.. ~/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu ~/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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 0.13.0-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 56 .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 0.13.0-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 0.13.0-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 0.13.0-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 27 .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 0.13.0-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 0.13.0-SNAPSHOT: [INFO] [INFO] Cannoli_2.12 ....................................... SUCCESS [ 3.060 s] [INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 0.018 s] [INFO] Cannoli_2.12: Core ................................. SUCCESS [ 0.693 s] [INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 0.374 s] [INFO] Cannoli_2.12: Assembly ............................. SUCCESS [ 0.020 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 4.450 s [INFO] Finished at: 2021-04-08T15:29:02-07:00 [INFO] ------------------------------------------------------------------------ + popd ~/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu if test -n "$(git status --porcelain)" then echo "Please run './scripts/format-source'" exit 1 fi ++ git status --porcelain + test -n '' echo + echo echo "All the tests passed" + echo 'All the tests passed' All the tests passed echo + echo + 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-spark3_2.12 >---------- [INFO] Building Cannoli_2.12 0.13.0-SNAPSHOT [1/6] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark3_2.12 --- [INFO] Modified 0 of 56 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-parent-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-parent-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-parent-spark3_2.12 --- [INFO] No source files found [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-parent-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-parent-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-parent-spark3_2.12 --- [INFO] No source files found [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-parent-spark3_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-parent-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-parent-spark3_2.12/0.13.0-SNAPSHOT/cannoli-parent-spark3_2.12-0.13.0-SNAPSHOT.pom [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-parent-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark3_2.12/0.13.0-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-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (629 B at 746 B/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark3_2.12/0.13.0-SNAPSHOT/cannoli-parent-spark3_2.12-0.13.0-20210408.222910-13.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-spark3_2.12/0.13.0-SNAPSHOT/cannoli-parent-spark3_2.12-0.13.0-20210408.222910-13.pom (21 kB at 32 kB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark3_2.12/maven-metadata.xml Progress (1): 411 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark3_2.12/maven-metadata.xml (411 B at 2.6 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark3_2.12/0.13.0-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-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (629 B at 1.2 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark3_2.12/maven-metadata.xml Progress (1): 411 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-parent-spark3_2.12/maven-metadata.xml (411 B at 804 B/s) [INFO] [INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark3_2.12 >--------- [INFO] Building Cannoli_2.12: Builder 0.13.0-SNAPSHOT [2/6] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/scala added. [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-resources-plugin:3.1.0:resources (default-resources) @ cannoli-builder-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-builder-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [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-builder-spark3_2.12 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 7 source files to /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/scala-2.12.10/classes [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-builder-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-builder-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-builder-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [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-builder-spark3_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-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-builder-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-builder-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-builder-spark3_2.12 --- [INFO] Loading source files for package org.bdgenomics.cannoli.builder... Constructing Javadoc information... Standard Doclet version 1.8.0_282 Building tree for all the packages and classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/CommandBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/CommandBuilders.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/DockerBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/LocalBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/SingularityBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/package-frame.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/package-summary.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/package-tree.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/serialized-form.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/LocalBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/CommandBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/CommandBuilders.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/SingularityBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/org/bdgenomics/cannoli/builder/class-use/DockerBuilder.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/index-all.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/index.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-builder-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-builder-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-builder-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 10 documentable templates /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-builder-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-builder-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-builder-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-builder-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-builder-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 10 documentable templates /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-builder-spark3_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-builder-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-sources.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/builder/target/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-builder-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-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-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 7.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13.jar Progress (1): 4.1/10 kB Progress (1): 8.2/10 kB Progress (1): 10 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13.jar (10 kB at 19 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13.pom Progress (1): 987 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13.pom (987 B at 2.0 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13-sources.jar Progress (1): 4.1/11 kB Progress (1): 8.2/11 kB Progress (1): 11 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13-sources.jar (11 kB at 22 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13-javadoc.jar Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB 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 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13-javadoc.jar (1.2 MB at 1.4 MB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13-javadoc.jar Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB 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 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13-javadoc.jar (1.2 MB at 2.0 MB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13-javadoc.jar Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.1/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.2/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.3/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.4/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.5/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.6/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.7/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.8/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 0.9/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB Progress (1): 1.0/1.2 MB 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 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-SNAPSHOT/cannoli-builder-spark3_2.12-0.13.0-20210408.222926-13-javadoc.jar (1.2 MB at 2.0 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/maven-metadata.xml Progress (1): 412 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/maven-metadata.xml (412 B at 2.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/0.13.0-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-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 2.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/maven-metadata.xml Progress (1): 412 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-builder-spark3_2.12/maven-metadata.xml (412 B at 812 B/s) [INFO] [INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark3_2.12 >----------- [INFO] Building Cannoli_2.12: Core 0.13.0-SNAPSHOT [3/6] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala added. [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-resources-plugin:3.1.0:resources (default-resources) @ cannoli-core-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-core-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [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-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-core-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-core-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [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-spark3_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-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-core-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-core-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-core-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-core-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-core-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-core-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 54 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-core-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-core-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-core-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-core-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-core-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 54 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-core-spark3_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-core-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-sources.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-core-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-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-core-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 7.6 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13.jar Progress (1): 4.1/203 kB Progress (1): 8.2/203 kB Progress (1): 12/203 kB Progress (1): 16/203 kB Progress (1): 20/203 kB Progress (1): 25/203 kB Progress (1): 29/203 kB Progress (1): 33/203 kB Progress (1): 37/203 kB Progress (1): 41/203 kB Progress (1): 45/203 kB Progress (1): 49/203 kB Progress (1): 53/203 kB Progress (1): 57/203 kB Progress (1): 61/203 kB Progress (1): 66/203 kB Progress (1): 70/203 kB Progress (1): 74/203 kB Progress (1): 78/203 kB Progress (1): 82/203 kB Progress (1): 86/203 kB Progress (1): 90/203 kB Progress (1): 94/203 kB Progress (1): 98/203 kB Progress (1): 102/203 kB Progress (1): 106/203 kB Progress (1): 111/203 kB Progress (1): 115/203 kB Progress (1): 119/203 kB Progress (1): 123/203 kB Progress (1): 127/203 kB Progress (1): 131/203 kB Progress (1): 135/203 kB Progress (1): 139/203 kB Progress (1): 143/203 kB Progress (1): 147/203 kB Progress (1): 152/203 kB Progress (1): 156/203 kB Progress (1): 160/203 kB Progress (1): 164/203 kB Progress (1): 168/203 kB Progress (1): 172/203 kB Progress (1): 176/203 kB Progress (1): 180/203 kB Progress (1): 184/203 kB Progress (1): 188/203 kB Progress (1): 193/203 kB Progress (1): 197/203 kB Progress (1): 201/203 kB Progress (1): 203 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13.jar (203 kB at 290 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13.pom Progress (1): 2.7 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13.pom (2.7 kB at 5.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13-sources.jar Progress (1): 4.1/53 kB Progress (1): 8.2/53 kB Progress (1): 12/53 kB Progress (1): 16/53 kB Progress (1): 20/53 kB Progress (1): 25/53 kB Progress (1): 29/53 kB Progress (1): 33/53 kB Progress (1): 37/53 kB Progress (1): 41/53 kB Progress (1): 45/53 kB Progress (1): 49/53 kB Progress (1): 53 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13-sources.jar (53 kB at 98 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13-javadoc.jar Progress (1): 0/1.4 MB Progress (1): 0/1.4 MB Progress (1): 0/1.4 MB Progress (1): 0/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13-javadoc.jar (1.4 MB at 2.1 MB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13-javadoc.jar Progress (1): 0/1.4 MB Progress (1): 0/1.4 MB Progress (1): 0/1.4 MB Progress (1): 0/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.1/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.2/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.3/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.4/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.5/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.6/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.7/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.8/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 0.9/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.0/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.1/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.2/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.3/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4/1.4 MB Progress (1): 1.4 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-SNAPSHOT/cannoli-core-spark3_2.12-0.13.0-20210408.222958-13-javadoc.jar (1.4 MB at 2.4 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/maven-metadata.xml Progress (1): 409 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/maven-metadata.xml (409 B at 2.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/0.13.0-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-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 2.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/maven-metadata.xml Progress (1): 409 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-core-spark3_2.12/maven-metadata.xml (409 B at 834 B/s) [INFO] [INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark3_2.12 >----------- [INFO] Building Cannoli_2.12: CLI 0.13.0-SNAPSHOT [4/6] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-cli-spark3_2.12 --- [INFO] Modified 0 of 27 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ cannoli-cli-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-cli-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [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-cli-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-cli-spark3_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-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [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-spark3_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-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ cannoli-cli-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-cli-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-cli-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-cli-spark3_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-spark3_2.12:jar:0.13.0-SNAPSHOT'. Trying to invoke it... [WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/core/target/apidocs [ERROR] Error fetching link: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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_282 Building tree for all the packages and classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/About.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-frame.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-summary.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/package-tree.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/constant-values.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/org/bdgenomics/cannoli/cli/class-use/About.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/overview-tree.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/index-all.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/deprecated-list.html... Building index for all classes... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/allclasses-frame.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/allclasses-noframe.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/index.html... Generating /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/apidocs/help-doc.html... [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-cli-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-cli-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-cli-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 78 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-cli-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:timestamp-property (timestamp-property) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- git-commit-id-plugin:2.2.2:revision (default) @ cannoli-cli-spark3_2.12 --- [INFO] [INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ cannoli-cli-spark3_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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/generated-sources/java-templates added. [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-cli-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-cli-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-cli-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] com.twitter:chill_2.12:0.9.5 requires scala version: 2.12.10 [WARNING] org.apache.spark:spark-network-common_2.12:3.0.2 requires scala version: 2.12.10 [WARNING] org.scala-lang.modules:scala-xml_2.12:1.2.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 78 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-cli-spark3_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-cli-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-sources.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/cli/target/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-cli-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-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-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 8.1 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13.jar Progress (1): 4.1/219 kB Progress (1): 8.2/219 kB Progress (1): 12/219 kB Progress (1): 16/219 kB Progress (1): 20/219 kB Progress (1): 25/219 kB Progress (1): 29/219 kB Progress (1): 33/219 kB Progress (1): 37/219 kB Progress (1): 41/219 kB Progress (1): 45/219 kB Progress (1): 49/219 kB Progress (1): 53/219 kB Progress (1): 57/219 kB Progress (1): 61/219 kB Progress (1): 66/219 kB Progress (1): 70/219 kB Progress (1): 74/219 kB Progress (1): 78/219 kB Progress (1): 82/219 kB Progress (1): 86/219 kB Progress (1): 90/219 kB Progress (1): 94/219 kB Progress (1): 98/219 kB Progress (1): 102/219 kB Progress (1): 106/219 kB Progress (1): 111/219 kB Progress (1): 115/219 kB Progress (1): 119/219 kB Progress (1): 123/219 kB Progress (1): 127/219 kB Progress (1): 131/219 kB Progress (1): 135/219 kB Progress (1): 139/219 kB Progress (1): 143/219 kB Progress (1): 147/219 kB Progress (1): 152/219 kB Progress (1): 156/219 kB Progress (1): 160/219 kB Progress (1): 164/219 kB Progress (1): 168/219 kB Progress (1): 172/219 kB Progress (1): 176/219 kB Progress (1): 180/219 kB Progress (1): 184/219 kB Progress (1): 188/219 kB Progress (1): 193/219 kB Progress (1): 197/219 kB Progress (1): 201/219 kB Progress (1): 205/219 kB Progress (1): 209/219 kB Progress (1): 213/219 kB Progress (1): 217/219 kB Progress (1): 219 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13.jar (219 kB at 301 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13.pom Progress (1): 3.7 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13.pom (3.7 kB at 7.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13-sources.jar Progress (1): 4.1/45 kB Progress (1): 8.2/45 kB Progress (1): 12/45 kB Progress (1): 16/45 kB Progress (1): 20/45 kB Progress (1): 25/45 kB Progress (1): 29/45 kB Progress (1): 33/45 kB Progress (1): 37/45 kB Progress (1): 41/45 kB Progress (1): 45 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13-sources.jar (45 kB at 87 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13-javadoc.jar Progress (1): 0/1.6 MB Progress (1): 0/1.6 MB Progress (1): 0/1.6 MB Progress (1): 0/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 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): 1.4/1.6 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 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13-javadoc.jar (1.6 MB at 2.4 MB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13-javadoc.jar Progress (1): 0/1.6 MB Progress (1): 0/1.6 MB Progress (1): 0/1.6 MB Progress (1): 0/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 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): 1.4/1.6 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 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13-javadoc.jar (1.6 MB at 2.6 MB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13-javadoc.jar Progress (1): 0/1.6 MB Progress (1): 0/1.6 MB Progress (1): 0/1.6 MB Progress (1): 0/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.1/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.2/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.3/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.4/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.5/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.6/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.7/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.8/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 0.9/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.0/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.1/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.2/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 MB Progress (1): 1.3/1.6 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): 1.4/1.6 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 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-SNAPSHOT/cannoli-cli-spark3_2.12-0.13.0-20210408.223034-13-javadoc.jar (1.6 MB at 2.7 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/maven-metadata.xml Progress (1): 408 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/maven-metadata.xml (408 B at 2.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/0.13.0-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-spark3_2.12/0.13.0-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-spark3_2.12/maven-metadata.xml Progress (1): 408 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-cli-spark3_2.12/maven-metadata.xml (408 B at 817 B/s) [INFO] [INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark3_2.12 >--------- [INFO] Building Cannoli_2.12: Assembly 0.13.0-SNAPSHOT [5/6] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added. [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-resources-plugin:3.1.0:resources (default-resources) @ cannoli-assembly-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-assembly-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [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-spark3_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-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ cannoli-assembly-spark3_2.12 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-assembly-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [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-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ cannoli-assembly-spark3_2.12 --- [INFO] Tests are skipped. [INFO] [INFO] --- maven-jar-plugin:3.1.2:jar (default-jar) @ cannoli-assembly-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-assembly-spark3_2.12 --- [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-sources.jar [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-assembly-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-assembly-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-assembly-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-assembly-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-assembly-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-assembly-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-assembly-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-assembly-spark3_2.12 --- [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! [WARNING] Expected all dependencies to require Scala version: 2.12.10 [WARNING] org.bdgenomics.utils:utils-misc-spark3_2.12:0.3.0 requires scala version: 2.12.8 [WARNING] Multiple versions of scala libraries detected! model contains 6 documentable templates [INFO] Building jar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-shade-plugin:3.2.0:shade (default) @ cannoli-assembly-spark3_2.12 --- [INFO] Including org.bdgenomics.cannoli:cannoli-cli-spark3_2.12:jar:0.13.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-cli-spark3_2.12:jar:0.34.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-misc-spark3_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-spark3_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-spark3_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-spark3_2.12:jar:0.34.0 in the shaded jar. [INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark3_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-spark3_2.12:jar:0.34.0 in the shaded jar. [INFO] Including org.bdgenomics.adam:adam-apis-spark3_2.12:jar:0.34.0 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-spark3_2.12:jar:0.13.0-SNAPSHOT in the shaded jar. [INFO] Including org.bdgenomics.cannoli:cannoli-builder-spark3_2.12:jar:0.13.0-SNAPSHOT in the shaded jar. [WARNING] parquet-avro-1.10.1.jar, adam-core-spark3_2.12-0.34.0.jar define 3 overlapping classes: [WARNING] - org.apache.parquet.avro.AvroSchemaConverter$2 [WARNING] - org.apache.parquet.avro.AvroSchemaConverter [WARNING] - org.apache.parquet.avro.AvroSchemaConverter$1 [WARNING] maven-shade-plugin has detected that some class files are [WARNING] present in two or more JARs. When this happens, only one [WARNING] single version of the class is copied to the uber jar. [WARNING] Usually this is not harmful and you can skip these warnings, [WARNING] otherwise try to manually exclude artifacts based on [WARNING] mvn dependency:tree -Ddetail=true and the above output. [WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/ [INFO] Replacing original artifact with shaded artifact. [INFO] Replacing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar with /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-shaded.jar [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-assembly-spark3_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-assembly-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-sources.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-sources.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/assembly/target/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-assembly-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-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-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (1.2 kB at 7.2 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13.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 MB Progress (1): 7.7/46 MB Progress (1): 8.2/46 MB Progress (1): 8.6/46 MB Progress (1): 9.1/46 MB Progress (1): 9.5/46 MB Progress (1): 10/46 MB Progress (1): 10/46 MB Progress (1): 11/46 MB Progress (1): 11/46 MB Progress (1): 12/46 MB Progress (1): 12/46 MB Progress (1): 13/46 MB Progress (1): 13/46 MB Progress (1): 14/46 MB Progress (1): 14/46 MB Progress (1): 15/46 MB Progress (1): 15/46 MB Progress (1): 15/46 MB Progress (1): 16/46 MB Progress (1): 16/46 MB Progress (1): 17/46 MB Progress (1): 17/46 MB Progress (1): 18/46 MB Progress (1): 18/46 MB Progress (1): 19/46 MB Progress (1): 19/46 MB Progress (1): 20/46 MB Progress (1): 20/46 MB Progress (1): 20/46 MB Progress (1): 21/46 MB Progress (1): 21/46 MB Progress (1): 22/46 MB Progress (1): 22/46 MB Progress (1): 23/46 MB Progress (1): 23/46 MB Progress (1): 24/46 MB Progress (1): 24/46 MB Progress (1): 25/46 MB Progress (1): 25/46 MB Progress (1): 25/46 MB Progress (1): 26/46 MB Progress (1): 26/46 MB Progress (1): 27/46 MB Progress (1): 27/46 MB Progress (1): 28/46 MB Progress (1): 28/46 MB Progress (1): 29/46 MB Progress (1): 29/46 MB Progress (1): 30/46 MB Progress (1): 30/46 MB Progress (1): 30/46 MB Progress (1): 31/46 MB Progress (1): 31/46 MB Progress (1): 32/46 MB Progress (1): 32/46 MB Progress (1): 33/46 MB Progress (1): 33/46 MB Progress (1): 34/46 MB Progress (1): 34/46 MB Progress (1): 35/46 MB Progress (1): 35/46 MB Progress (1): 35/46 MB Progress (1): 36/46 MB Progress (1): 36/46 MB Progress (1): 37/46 MB Progress (1): 37/46 MB Progress (1): 38/46 MB Progress (1): 38/46 MB Progress (1): 39/46 MB Progress (1): 39/46 MB Progress (1): 40/46 MB Progress (1): 40/46 MB Progress (1): 40/46 MB Progress (1): 41/46 MB Progress (1): 41/46 MB Progress (1): 42/46 MB Progress (1): 42/46 MB Progress (1): 43/46 MB Progress (1): 43/46 MB Progress (1): 44/46 MB Progress (1): 44/46 MB Progress (1): 45/46 MB Progress (1): 45/46 MB Progress (1): 45/46 MB Progress (1): 46 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13.jar (46 MB at 15 MB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13.pom Progress (1): 2.1 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13.pom (2.1 kB at 4.0 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13-sources.jar Progress (1): 3.3 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13-sources.jar (3.3 kB at 6.7 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13-javadoc.jar Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13-javadoc.jar (1.1 MB at 1.8 MB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13-javadoc.jar Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.1/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.2/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.3/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.4/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.5/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.6/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.7/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.8/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 0.9/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.0/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1/1.1 MB Progress (1): 1.1 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-SNAPSHOT/cannoli-assembly-spark3_2.12-0.13.0-20210408.223052-13-javadoc.jar (1.1 MB at 1.9 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/maven-metadata.xml Progress (1): 413 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/maven-metadata.xml (413 B at 2.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/0.13.0-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-assembly-spark3_2.12/0.13.0-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-assembly-spark3_2.12/maven-metadata.xml Progress (1): 413 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-assembly-spark3_2.12/maven-metadata.xml (413 B at 675 B/s) [INFO] [INFO] ------< org.bdgenomics.cannoli:cannoli-distribution-spark3_2.12 >------- [INFO] Building Cannoli_2.12: Distribution 0.13.0-SNAPSHOT [6/6] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-distribution-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-distribution-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-distribution-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-distribution-spark3_2.12 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-distribution-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-distribution-spark3_2.12 --- [INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/src/test/scala added. [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-distribution-spark3_2.12 --- [INFO] No sources to compile [INFO] [INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ cannoli-distribution-spark3_2.12 --- [INFO] [INFO] --- maven-javadoc-plugin:3.1.0:jar (attach-javadocs) @ cannoli-distribution-spark3_2.12 --- [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) > generate-sources @ cannoli-distribution-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-distribution-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-distribution-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-distribution-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) < generate-sources @ cannoli-distribution-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ cannoli-distribution-spark3_2.12 --- [INFO] No source files found [INFO] [INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) > generate-sources @ cannoli-distribution-spark3_2.12 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-distribution-spark3_2.12 --- [INFO] [INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-distribution-spark3_2.12 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-distribution-spark3_2.12 --- [INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/src/main/scala added. [INFO] [INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) < generate-sources @ cannoli-distribution-spark3_2.12 <<< [INFO] [INFO] [INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-javadocs) @ cannoli-distribution-spark3_2.12 --- [INFO] No source files found [INFO] [INFO] --- maven-assembly-plugin:3.1.0:single (default) @ cannoli-distribution-spark3_2.12 --- [INFO] Reading assembly descriptor: src/main/assembly/assembly.xml [INFO] Building tar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT-bin.tar.gz [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/lib/source-code-pro-v6-latin-regular.woff longer than 100 characters. [WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/VtNormalizeArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BcftoolsMpileup.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BedtoolsIntersect.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SingleEndBowtie2.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BcftoolsCallArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/FreebayesArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SamtoolsMpileup.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SingleEndBowtie2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliReadDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BedtoolsIntersectArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/MagicBlastArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliVariantContextDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliSequenceDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BcftoolsNormArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SamtoolsMpileupArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliFeatureDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SingleEndStarArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SingleEndStar.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliAlignmentDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BcftoolsMpileupArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliFragmentDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsMpileupArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SamtoolsMpileup$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/CannoliModule.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/InterleaveFastqArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/VtNormalizeArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SampleReads.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsMpileup.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SamtoolsMpileupArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/MagicBlast.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndBowtie2.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsMpileup$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsCallArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Freebayes.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BwaMem2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndStarArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndStar.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BwaMemArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/InterleaveFastq.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndBowtie2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SamtoolsMpileup.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Minimap2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/MagicBlast$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BlastnArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SampleReads$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SampleReadsArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Minimap2$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/VtNormalize.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/FreebayesArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsNorm.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BedtoolsIntersect.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/VtNormalize$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsCall$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BedtoolsIntersectArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BedtoolsIntersect$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsNorm$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndBowtie2$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsCall.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/MagicBlastArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Freebayes$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsNormArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Bowtie2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SnpEffArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndStar$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/InterleaveFastq$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BowtieArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/package-frame.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/class-use/About.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/package-use.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/package-tree.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/package-summary.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/repo/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/repo/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-sources.jar longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/repo/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar longer than 100 characters. [INFO] Building tar: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT-bin.tar.bz2 [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/lib/source-code-pro-v6-latin-regular.woff longer than 100 characters. [WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/VtNormalizeArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BcftoolsMpileup.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BedtoolsIntersect.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SingleEndBowtie2.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BcftoolsCallArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/FreebayesArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SamtoolsMpileup.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SingleEndBowtie2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliReadDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BedtoolsIntersectArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/MagicBlastArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliVariantContextDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliSequenceDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BcftoolsNormArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SamtoolsMpileupArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliFeatureDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SingleEndStarArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/SingleEndStar.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliAlignmentDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/BcftoolsMpileupArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/Cannoli$$CannoliFragmentDataset.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsMpileupArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SamtoolsMpileup$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/CannoliModule.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/InterleaveFastqArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/VtNormalizeArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SampleReads.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsMpileup.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SamtoolsMpileupArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/MagicBlast.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndBowtie2.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsMpileup$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsCallArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Freebayes.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BwaMem2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndStarArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndStar.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BwaMemArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/InterleaveFastq.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndBowtie2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SamtoolsMpileup.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Minimap2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/MagicBlast$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BlastnArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SampleReads$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SampleReadsArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Minimap2$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/VtNormalize.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/FreebayesArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsNorm.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BedtoolsIntersect.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/VtNormalize$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsCall$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BedtoolsIntersectArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BedtoolsIntersect$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsNorm$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndBowtie2$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsCall.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/MagicBlastArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Freebayes$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BcftoolsNormArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/Bowtie2Args.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SnpEffArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/SingleEndStar$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/InterleaveFastq$.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/scaladocs/org/bdgenomics/cannoli/cli/BowtieArgs.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/package-frame.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/class-use/About.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/package-use.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/package-tree.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/javadocs/org/bdgenomics/cannoli/cli/package-summary.html longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/repo/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT.jar longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/repo/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-sources.jar longer than 100 characters. [WARNING] Entry: cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT/repo/cannoli-assembly-spark3_2.12-0.13.0-SNAPSHOT-javadoc.jar longer than 100 characters. [INFO] Building zip: /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT-bin.zip [INFO] [INFO] --- maven-license-plugin:1.10.b1:check (default) @ cannoli-distribution-spark3_2.12 --- [INFO] Checking licenses... [INFO] [INFO] --- maven-install-plugin:3.0.0-M1:install (default-install) @ cannoli-distribution-spark3_2.12 --- [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/pom.xml to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT.pom [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT-bin.tar.gz to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT-bin.tar.gz [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT-bin.tar.bz2 to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT-bin.tar.bz2 [INFO] Installing /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/distribution/target/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT-bin.zip to /home/jenkins/.m2/repository/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-SNAPSHOT-bin.zip [INFO] [INFO] --- maven-deploy-plugin:3.0.0-M1:deploy (default-deploy) @ cannoli-distribution-spark3_2.12 --- Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.3 kB Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (1.3 kB at 7.6 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-20210408.223129-13.pom Progress (1): 1.2 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-20210408.223129-13.pom (1.2 kB at 2.3 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-20210408.223129-13-bin.tar.gz Progress (1): 0.4/44 MB Progress (1): 0.9/44 MB Progress (1): 1.3/44 MB Progress (1): 1.8/44 MB Progress (1): 2.2/44 MB Progress (1): 2.7/44 MB Progress (1): 3.1/44 MB Progress (1): 3.5/44 MB Progress (1): 4.0/44 MB Progress (1): 4.4/44 MB Progress (1): 4.9/44 MB Progress (1): 5.3/44 MB Progress (1): 5.8/44 MB Progress (1): 6.2/44 MB Progress (1): 6.6/44 MB Progress (1): 7.1/44 MB Progress (1): 7.5/44 MB Progress (1): 8.0/44 MB Progress (1): 8.4/44 MB Progress (1): 8.8/44 MB Progress (1): 9.3/44 MB Progress (1): 9.7/44 MB Progress (1): 10/44 MB Progress (1): 11/44 MB Progress (1): 11/44 MB Progress (1): 12/44 MB Progress (1): 12/44 MB Progress (1): 12/44 MB Progress (1): 13/44 MB Progress (1): 13/44 MB Progress (1): 14/44 MB Progress (1): 14/44 MB Progress (1): 15/44 MB Progress (1): 15/44 MB Progress (1): 15/44 MB Progress (1): 16/44 MB Progress (1): 16/44 MB Progress (1): 17/44 MB Progress (1): 17/44 MB Progress (1): 18/44 MB Progress (1): 18/44 MB Progress (1): 19/44 MB Progress (1): 19/44 MB Progress (1): 19/44 MB Progress (1): 20/44 MB Progress (1): 20/44 MB Progress (1): 21/44 MB Progress (1): 21/44 MB Progress (1): 22/44 MB Progress (1): 22/44 MB Progress (1): 23/44 MB Progress (1): 23/44 MB Progress (1): 23/44 MB Progress (1): 24/44 MB Progress (1): 24/44 MB Progress (1): 25/44 MB Progress (1): 25/44 MB Progress (1): 26/44 MB Progress (1): 26/44 MB Progress (1): 27/44 MB Progress (1): 27/44 MB Progress (1): 27/44 MB Progress (1): 28/44 MB Progress (1): 28/44 MB Progress (1): 29/44 MB Progress (1): 29/44 MB Progress (1): 30/44 MB Progress (1): 30/44 MB Progress (1): 31/44 MB Progress (1): 31/44 MB Progress (1): 31/44 MB Progress (1): 32/44 MB Progress (1): 32/44 MB Progress (1): 33/44 MB Progress (1): 33/44 MB Progress (1): 34/44 MB Progress (1): 34/44 MB Progress (1): 35/44 MB Progress (1): 35/44 MB Progress (1): 35/44 MB Progress (1): 36/44 MB Progress (1): 36/44 MB Progress (1): 37/44 MB Progress (1): 37/44 MB Progress (1): 38/44 MB Progress (1): 38/44 MB Progress (1): 38/44 MB Progress (1): 39/44 MB Progress (1): 39/44 MB Progress (1): 40/44 MB Progress (1): 40/44 MB Progress (1): 41/44 MB Progress (1): 41/44 MB Progress (1): 42/44 MB Progress (1): 42/44 MB Progress (1): 42/44 MB Progress (1): 43/44 MB Progress (1): 43/44 MB Progress (1): 44/44 MB Progress (1): 44/44 MB Progress (1): 44 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-20210408.223129-13-bin.tar.gz (44 MB at 15 MB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-20210408.223129-13-bin.tar.bz2 Progress (1): 0.4/44 MB Progress (1): 0.9/44 MB Progress (1): 1.3/44 MB Progress (1): 1.7/44 MB Progress (1): 2.2/44 MB Progress (1): 2.6/44 MB Progress (1): 3.0/44 MB Progress (1): 3.5/44 MB Progress (1): 3.9/44 MB Progress (1): 4.3/44 MB Progress (1): 4.8/44 MB Progress (1): 5.2/44 MB Progress (1): 5.6/44 MB Progress (1): 6.1/44 MB Progress (1): 6.5/44 MB Progress (1): 6.9/44 MB Progress (1): 7.4/44 MB Progress (1): 7.8/44 MB Progress (1): 8.2/44 MB Progress (1): 8.7/44 MB Progress (1): 9.1/44 MB Progress (1): 9.6/44 MB Progress (1): 10.0/44 MB Progress (1): 10/44 MB Progress (1): 11/44 MB Progress (1): 11/44 MB Progress (1): 12/44 MB Progress (1): 12/44 MB Progress (1): 13/44 MB Progress (1): 13/44 MB Progress (1): 13/44 MB Progress (1): 14/44 MB Progress (1): 14/44 MB Progress (1): 15/44 MB Progress (1): 15/44 MB Progress (1): 16/44 MB Progress (1): 16/44 MB Progress (1): 16/44 MB Progress (1): 17/44 MB Progress (1): 17/44 MB Progress (1): 18/44 MB Progress (1): 18/44 MB Progress (1): 19/44 MB Progress (1): 19/44 MB Progress (1): 20/44 MB Progress (1): 20/44 MB Progress (1): 20/44 MB Progress (1): 21/44 MB Progress (1): 21/44 MB Progress (1): 22/44 MB Progress (1): 22/44 MB Progress (1): 23/44 MB Progress (1): 23/44 MB Progress (1): 23/44 MB Progress (1): 24/44 MB Progress (1): 24/44 MB Progress (1): 25/44 MB Progress (1): 25/44 MB Progress (1): 26/44 MB Progress (1): 26/44 MB Progress (1): 26/44 MB Progress (1): 27/44 MB Progress (1): 27/44 MB Progress (1): 28/44 MB Progress (1): 28/44 MB Progress (1): 29/44 MB Progress (1): 29/44 MB Progress (1): 30/44 MB Progress (1): 30/44 MB Progress (1): 30/44 MB Progress (1): 31/44 MB Progress (1): 31/44 MB Progress (1): 32/44 MB Progress (1): 32/44 MB Progress (1): 33/44 MB Progress (1): 33/44 MB Progress (1): 33/44 MB Progress (1): 34/44 MB Progress (1): 34/44 MB Progress (1): 35/44 MB Progress (1): 35/44 MB Progress (1): 36/44 MB Progress (1): 36/44 MB Progress (1): 36/44 MB Progress (1): 37/44 MB Progress (1): 37/44 MB Progress (1): 38/44 MB Progress (1): 38/44 MB Progress (1): 39/44 MB Progress (1): 39/44 MB Progress (1): 40/44 MB Progress (1): 40/44 MB Progress (1): 40/44 MB Progress (1): 41/44 MB Progress (1): 41/44 MB Progress (1): 42/44 MB Progress (1): 42/44 MB Progress (1): 43/44 MB Progress (1): 43/44 MB Progress (1): 43/44 MB Progress (1): 44 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-20210408.223129-13-bin.tar.bz2 (44 MB at 7.6 MB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-20210408.223129-13-bin.zip Progress (1): 0.4/44 MB Progress (1): 0.9/44 MB Progress (1): 1.3/44 MB Progress (1): 1.8/44 MB Progress (1): 2.2/44 MB Progress (1): 2.7/44 MB Progress (1): 3.1/44 MB Progress (1): 3.5/44 MB Progress (1): 4.0/44 MB Progress (1): 4.4/44 MB Progress (1): 4.9/44 MB Progress (1): 5.3/44 MB Progress (1): 5.8/44 MB Progress (1): 6.2/44 MB Progress (1): 6.6/44 MB Progress (1): 7.1/44 MB Progress (1): 7.5/44 MB Progress (1): 8.0/44 MB Progress (1): 8.4/44 MB Progress (1): 8.8/44 MB Progress (1): 9.3/44 MB Progress (1): 9.7/44 MB Progress (1): 10/44 MB Progress (1): 11/44 MB Progress (1): 11/44 MB Progress (1): 12/44 MB Progress (1): 12/44 MB Progress (1): 12/44 MB Progress (1): 13/44 MB Progress (1): 13/44 MB Progress (1): 14/44 MB Progress (1): 14/44 MB Progress (1): 15/44 MB Progress (1): 15/44 MB Progress (1): 15/44 MB Progress (1): 16/44 MB Progress (1): 16/44 MB Progress (1): 17/44 MB Progress (1): 17/44 MB Progress (1): 18/44 MB Progress (1): 18/44 MB Progress (1): 19/44 MB Progress (1): 19/44 MB Progress (1): 19/44 MB Progress (1): 20/44 MB Progress (1): 20/44 MB Progress (1): 21/44 MB Progress (1): 21/44 MB Progress (1): 22/44 MB Progress (1): 22/44 MB Progress (1): 23/44 MB Progress (1): 23/44 MB Progress (1): 23/44 MB Progress (1): 24/44 MB Progress (1): 24/44 MB Progress (1): 25/44 MB Progress (1): 25/44 MB Progress (1): 26/44 MB Progress (1): 26/44 MB Progress (1): 27/44 MB Progress (1): 27/44 MB Progress (1): 27/44 MB Progress (1): 28/44 MB Progress (1): 28/44 MB Progress (1): 29/44 MB Progress (1): 29/44 MB Progress (1): 30/44 MB Progress (1): 30/44 MB Progress (1): 31/44 MB Progress (1): 31/44 MB Progress (1): 31/44 MB Progress (1): 32/44 MB Progress (1): 32/44 MB Progress (1): 33/44 MB Progress (1): 33/44 MB Progress (1): 34/44 MB Progress (1): 34/44 MB Progress (1): 35/44 MB Progress (1): 35/44 MB Progress (1): 35/44 MB Progress (1): 36/44 MB Progress (1): 36/44 MB Progress (1): 37/44 MB Progress (1): 37/44 MB Progress (1): 38/44 MB Progress (1): 38/44 MB Progress (1): 38/44 MB Progress (1): 39/44 MB Progress (1): 39/44 MB Progress (1): 40/44 MB Progress (1): 40/44 MB Progress (1): 41/44 MB Progress (1): 41/44 MB Progress (1): 42/44 MB Progress (1): 42/44 MB Progress (1): 42/44 MB Progress (1): 43/44 MB Progress (1): 43/44 MB Progress (1): 44/44 MB Progress (1): 44/44 MB Progress (1): 44 MB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/cannoli-distribution-spark3_2.12-0.13.0-20210408.223129-13-bin.zip (44 MB at 9.3 MB/s) Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/maven-metadata.xml Progress (1): 417 B Downloaded from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/maven-metadata.xml (417 B at 2.5 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml Progress (1): 1.3 kB Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/0.13.0-SNAPSHOT/maven-metadata.xml (1.3 kB at 2.4 kB/s) Uploading to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/maven-metadata.xml Progress (1): 417 B Uploaded to sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/cannoli/cannoli-distribution-spark3_2.12/maven-metadata.xml (417 B at 837 B/s) [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Cannoli_2.12 0.13.0-SNAPSHOT: [INFO] [INFO] Cannoli_2.12 ....................................... SUCCESS [ 7.747 s] [INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 18.876 s] [INFO] Cannoli_2.12: Core ................................. SUCCESS [ 30.966 s] [INFO] Cannoli_2.12: CLI .................................. SUCCESS [ 36.512 s] [INFO] Cannoli_2.12: Assembly ............................. SUCCESS [ 20.746 s] [INFO] Cannoli_2.12: Distribution ......................... SUCCESS [ 45.363 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 02:40 min [INFO] Finished at: 2021-04-08T15:31:44-07:00 [INFO] ------------------------------------------------------------------------ Recording test results [Checks API] No suitable checks publisher found. Finished: SUCCESS