Started by upstream project "ADAM-prb" build number 3125 originally caused by: GitHub pull request #2277 of commit e66c072d7d639f98a575be17e9a61f53b07f6a99 automatically merged. [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-09 (ubuntu ubuntu-gpu research-09 ubuntu-avx2) in workspace /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu Wiping out workspace first. Cloning the remote Git repository Cloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/*:refs/remotes/origin/* # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/*:refs/remotes/origin/pr/* # timeout=15 Checking out Revision 0e441bf36dd7b15678ef14de38f63344773f9079 (origin/pr/2277/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 0e441bf36dd7b15678ef14de38f63344773f9079 First time build. Skipping changelog. [ubuntu] $ /bin/bash /tmp/hudson7637932407427483819.sh + set -e + unset SPARK_TESTING + export JAVA_HOME=/usr/lib/jvm/java-8-oracle + JAVA_HOME=/usr/lib/jvm/java-8-oracle + export CONDA_BIN=/home/anaconda/bin/ + CONDA_BIN=/home/anaconda/bin/ + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + set +x + /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to ADAM_MVN_TMP_DIR=$(mktemp -d -t adamTestMvnXXXXXXX) mktemp -d -t adamTestMvnXXXXXXX ++ mktemp -d -t adamTestMvnXXXXXXX + ADAM_MVN_TMP_DIR=/tmp/adamTestMvn4lVODAr # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${ADAM_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/adamTestMvn4lVODAr:g' '{}' ';' find . -name "*.bak" -exec rm -f {} \; + find . -name '*.bak' -exec rm -f '{}' ';' # variable declarations export PATH=${JAVA_HOME}/bin/:${PATH} + export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games + PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8" + export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' + MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8' DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd ) cd $( dirname ${BASH_SOURCE[0]} ) && pwd dirname ${BASH_SOURCE[0]} +++ dirname /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/scripts/.. VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g') grep "<version>" ${PROJECT_ROOT}/pom.xml | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g' ++ grep '<version>' /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/scripts/../pom.xml ++ head -2 ++ tail -1 ++ sed 's/ *<version>//g' ++ sed 's/<\/version>//g' + VERSION=0.33.0-SNAPSHOT # is the hadoop version set? if ! [[ ${HADOOP_VERSION} ]]; then echo "HADOOP_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.7.5 ]] # is the spark version set? if ! [[ ${SPARK_VERSION} ]]; then echo "SPARK_VERSION environment variable is not set." echo "Please set this variable before running." exit 1 fi + [[ -n 2.4.7 ]] set -e + set -e # move to Scala 2.11 if requested if [ ${SCALA_VERSION} == 2.11 ]; then set +e ./scripts/move_to_scala_2.11.sh set -e fi + '[' 2.11 == 2.11 ']' + set +e + ./scripts/move_to_scala_2.11.sh + set -e # move to Scala 2.12 if requested if [ ${SCALA_VERSION} == 2.12 ]; then set +e ./scripts/move_to_scala_2.12.sh set -e fi + '[' 2.11 == 2.12 ']' # move to Spark 2.x if requested if [ ${SPARK_VERSION} == 2.4.6 ]; then set +e ./scripts/move_to_spark_2.sh set -e fi + '[' 2.4.7 == 2.4.6 ']' # move to Spark 3.x if requested if [ ${SPARK_VERSION} == 3.0.1 ]; then set +e ./scripts/move_to_spark_3.sh set -e fi + '[' 2.4.7 == 3.0.1 ']' # print versions echo "Testing ADAM version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing ADAM version 0.33.0-SNAPSHOT on Spark 2.4.7 and Hadoop 2.7.5' Testing ADAM version 0.33.0-SNAPSHOT on Spark 2.4.7 and Hadoop 2.7.5 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${HADOOP_VERSION} + mvn clean -Dhadoop.version=2.7.5 OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] ADAM_2.11 [pom] [INFO] ADAM_2.11: Shader workaround [jar] [INFO] ADAM_2.11: Avro-to-Dataset codegen utils [jar] [INFO] ADAM_2.11: Core [jar] [INFO] ADAM_2.11: APIs for Java, Python [jar] [INFO] ADAM_2.11: CLI [jar] [INFO] ADAM_2.11: Assembly [jar] [INFO] [INFO] ------------< org.bdgenomics.adam:adam-parent-spark3_2.11 >------------- [INFO] Building ADAM_2.11 0.33.0-SNAPSHOT [1/7] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-parent-spark3_2.11 --- [INFO] [INFO] -------------< org.bdgenomics.adam:adam-shade-spark3_2.11 >------------- [INFO] Building ADAM_2.11: Shader workaround 0.33.0-SNAPSHOT [2/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-shade-spark3_2.11 --- [INFO] [INFO] ------------< org.bdgenomics.adam:adam-codegen-spark3_2.11 >------------ [INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.33.0-SNAPSHOT [3/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-codegen-spark3_2.11 --- [INFO] [INFO] -------------< org.bdgenomics.adam:adam-core-spark3_2.11 >-------------- [INFO] Building ADAM_2.11: Core 0.33.0-SNAPSHOT [4/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-core-spark3_2.11 --- [INFO] [INFO] -------------< org.bdgenomics.adam:adam-apis-spark3_2.11 >-------------- [INFO] Building ADAM_2.11: APIs for Java, Python 0.33.0-SNAPSHOT [5/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-apis-spark3_2.11 --- [INFO] [INFO] --------------< org.bdgenomics.adam:adam-cli-spark3_2.11 >-------------- [INFO] Building ADAM_2.11: CLI 0.33.0-SNAPSHOT [6/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-cli-spark3_2.11 --- [INFO] [INFO] -----------< org.bdgenomics.adam:adam-assembly-spark3_2.11 >------------ [INFO] Building ADAM_2.11: Assembly 0.33.0-SNAPSHOT [7/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-assembly-spark3_2.11 --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for ADAM_2.11 0.33.0-SNAPSHOT: [INFO] [INFO] ADAM_2.11 .......................................... SUCCESS [ 0.249 s] [INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [ 0.014 s] [INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [ 0.012 s] [INFO] ADAM_2.11: Core .................................... SUCCESS [ 0.019 s] [INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [ 0.004 s] [INFO] ADAM_2.11: CLI ..................................... SUCCESS [ 0.028 s] [INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 0.004 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.497 s [INFO] Finished at: 2020-10-19T20:04:33-07:00 [INFO] ------------------------------------------------------------------------ # if this is a pull request, we need to set the coveralls pr id if [[ ! -z $ghprbPullId ]]; then COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}" fi + [[ ! -z 2277 ]] + COVERALLS_PRB_OPTION=-DpullRequest=2277 # coveralls token should not be visible set +x +v + set +x +v OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0 [INFO] Scanning for projects... [INFO] ------------------------------------------------------------------------ [INFO] Reactor Build Order: [INFO] [INFO] ADAM_2.11 [pom] [INFO] ADAM_2.11: Shader workaround [jar] [INFO] ADAM_2.11: Avro-to-Dataset codegen utils [jar] [INFO] ADAM_2.11: Core [jar] [INFO] ADAM_2.11: APIs for Java, Python [jar] [INFO] ADAM_2.11: CLI [jar] [INFO] ADAM_2.11: Assembly [jar] [INFO] [INFO] ------------< org.bdgenomics.adam:adam-parent-spark3_2.11 >------------- [INFO] Building ADAM_2.11 0.33.0-SNAPSHOT [1/7] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark3_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark3_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark3_2.11 --- [INFO] Modified 0 of 242 .scala files [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-parent-spark3_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-parent-spark3_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-parent-spark3_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-parent-spark3_2.11 --- [INFO] Modified 0 of 242 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-parent-spark3_2.11 --- [INFO] Skipping SCoverage execution for project with packaging type 'pom' [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-parent-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-parent-spark3_2.11 --- [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-parent-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-parent-spark3_2.11 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-parent-spark3_2.11 --- [INFO] [INFO] -------------< org.bdgenomics.adam:adam-shade-spark3_2.11 >------------- [INFO] Building ADAM_2.11: Shader workaround 0.33.0-SNAPSHOT [2/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark3_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark3_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark3_2.11 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark3_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark3_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/src/main/java:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/target/2.11.12/classes at 1603163086306 [INFO] prepare-compile in 0 s [INFO] compile in 1 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark3_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/target/2.11.12/classes [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark3_2.11 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark3_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark3_2.11 --- [INFO] No tests to run. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-shade-spark3_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-shade-spark3_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-shade-spark3_2.11 --- [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark3_2.11 --- [INFO] Modified 0 of 0 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-shade-spark3_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-shade-spark3_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-shade-spark3_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/src/main/java:-1: info: compiling [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/target/generated-sources/annotations:-1: info: compiling [INFO] Compiling 1 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/target/2.11.12/scoverage-classes at 1603163089067 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [0 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 1 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-shade-spark3_2.11 --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 1 source file to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/target/2.11.12/scoverage-classes [INFO] [INFO] --- plexus-component-metadata:1.5.5:generate-metadata (default) @ adam-shade-spark3_2.11 --- [INFO] Discovered 1 component descriptors(s) [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-shade-spark3_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-shade-spark3_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-shade/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-shade-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-shade-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-shade-spark3_2.11 --- [INFO] No tests to run. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-shade-spark3_2.11 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-shade-spark3_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] ------------< org.bdgenomics.adam:adam-codegen-spark3_2.11 >------------ [INFO] Building ADAM_2.11: Avro-to-Dataset codegen utils 0.33.0-SNAPSHOT [3/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark3_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark3_2.11 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark3_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark3_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/target/2.11.12/classes at 1603163091050 [INFO] prepare-compile in 0 s [INFO] compile in 3 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark3_2.11 --- [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) @ adam-codegen-spark3_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark3_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark3_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark3_2.11 --- Discovery starting. Discovery completed in 62 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 94 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ adam-codegen-spark3_2.11 >>> [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-versions) @ adam-codegen-spark3_2.11 --- [INFO] [INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ adam-codegen-spark3_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ adam-codegen-spark3_2.11 --- [INFO] Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/main/scala added. [INFO] [INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark3_2.11 --- [INFO] Modified 0 of 4 .scala files [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ adam-codegen-spark3_2.11 --- [INFO] [INFO] --- maven-resources-plugin:3.1.0:resources (default-resources) @ adam-codegen-spark3_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/main/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-codegen-spark3_2.11 --- [INFO] /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/main/scala:-1: info: compiling [INFO] Compiling 4 source files to /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/target/2.11.12/scoverage-classes at 1603163095773 [INFO] [info] Cleaning datadir [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/target/scoverage-data] [INFO] [info] Beginning coverage instrumentation [INFO] [info] Instrumentation completed [0 statements] [INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/target/scoverage-data/scoverage.coverage.xml] [INFO] [info] Will write measurement data to [/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/target/scoverage-data] [INFO] prepare-compile in 0 s [INFO] compile in 4 s [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ adam-codegen-spark3_2.11 --- [INFO] Nothing to compile - all classes are up to date [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ adam-codegen-spark3_2.11 --- [INFO] [INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ adam-codegen-spark3_2.11 --- [INFO] Test Source directory: /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/test/scala added. [INFO] [INFO] --- maven-resources-plugin:3.1.0:testResources (default-testResources) @ adam-codegen-spark3_2.11 --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] skip non existing resourceDirectory /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/adam-codegen/src/test/resources [INFO] [INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ adam-codegen-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ adam-codegen-spark3_2.11 --- [INFO] No sources to compile [INFO] [INFO] --- maven-surefire-plugin:3.0.0-M3:test (default-test) @ adam-codegen-spark3_2.11 --- [INFO] Tests are skipped. [INFO] [INFO] --- scalatest-maven-plugin:2.0.0:test (test) @ adam-codegen-spark3_2.11 --- Discovery starting. Discovery completed in 74 milliseconds. Run starting. Expected test count is: 0 DiscoverySuite: Run completed in 107 milliseconds. Total number of tests run: 0 Suites: completed 1, aborted 0 Tests: succeeded 0, failed 0, canceled 0, ignored 0, pending 0 No tests were executed. [INFO] [INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ adam-codegen-spark3_2.11 <<< [INFO] [INFO] [INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ adam-codegen-spark3_2.11 --- [INFO] [scoverage] Generating cobertura XML report... [INFO] [scoverage] Generating scoverage XML report... [INFO] [scoverage] Generating scoverage HTML report... [INFO] [INFO] -------------< org.bdgenomics.adam:adam-core-spark3_2.11 >-------------- [INFO] Building ADAM_2.11: Core 0.33.0-SNAPSHOT [4/7] [INFO] --------------------------------[ jar ]--------------------------------- Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-misc-spark3_2.11/0.3.0/utils-misc-spark3_2.11-0.3.0.pom [WARNING] The POM for org.bdgenomics.utils:utils-misc-spark3_2.11:jar:tests:0.3.0 is missing, no dependency information available [WARNING] The POM for org.bdgenomics.utils:utils-misc-spark3_2.11:jar:0.3.0 is missing, no dependency information available Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-io-spark3_2.11/0.3.0/utils-io-spark3_2.11-0.3.0.pom [WARNING] The POM for org.bdgenomics.utils:utils-io-spark3_2.11:jar:0.3.0 is missing, no dependency information available Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-cli-spark3_2.11/0.3.0/utils-cli-spark3_2.11-0.3.0.pom [WARNING] The POM for org.bdgenomics.utils:utils-cli-spark3_2.11:jar:0.3.0 is missing, no dependency information available Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-intervalrdd-spark3_2.11/0.3.0/utils-intervalrdd-spark3_2.11-0.3.0.pom [WARNING] The POM for org.bdgenomics.utils:utils-intervalrdd-spark3_2.11:jar:0.3.0 is missing, no dependency information available Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/3.0.1/spark-core_2.11-3.0.1.pom [WARNING] The POM for org.apache.spark:spark-core_2.11:jar:3.0.1 is missing, no dependency information available Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-sql_2.11/3.0.1/spark-sql_2.11-3.0.1.pom [WARNING] The POM for org.apache.spark:spark-sql_2.11:jar:3.0.1 is missing, no dependency information available Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-misc-spark3_2.11/0.3.0/utils-misc-spark3_2.11-0.3.0-tests.jar Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-cli-spark3_2.11/0.3.0/utils-cli-spark3_2.11-0.3.0.jar Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-io-spark3_2.11/0.3.0/utils-io-spark3_2.11-0.3.0.jar Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-misc-spark3_2.11/0.3.0/utils-misc-spark3_2.11-0.3.0.jar Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-intervalrdd-spark3_2.11/0.3.0/utils-intervalrdd-spark3_2.11-0.3.0.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-core_2.11/3.0.1/spark-core_2.11-3.0.1.jar Downloading from central: https://repo.maven.apache.org/maven2/org/apache/spark/spark-sql_2.11/3.0.1/spark-sql_2.11-3.0.1.jar [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for ADAM_2.11 0.33.0-SNAPSHOT: [INFO] [INFO] ADAM_2.11 .......................................... SUCCESS [ 10.287 s] [INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [ 5.146 s] [INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [ 9.975 s] [INFO] ADAM_2.11: Core .................................... FAILURE [ 2.112 s] [INFO] ADAM_2.11: APIs for Java, Python ................... SKIPPED [INFO] ADAM_2.11: CLI ..................................... SKIPPED [INFO] ADAM_2.11: Assembly ................................ SKIPPED [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 27.796 s [INFO] Finished at: 2020-10-19T20:05:02-07:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal on project adam-core-spark3_2.11: Could not resolve dependencies for project org.bdgenomics.adam:adam-core-spark3_2.11:jar:0.33.0-SNAPSHOT: The following artifacts could not be resolved: org.bdgenomics.utils:utils-misc-spark3_2.11:jar:tests:0.3.0, org.bdgenomics.utils:utils-misc-spark3_2.11:jar:0.3.0, org.bdgenomics.utils:utils-io-spark3_2.11:jar:0.3.0, org.bdgenomics.utils:utils-cli-spark3_2.11:jar:0.3.0, org.bdgenomics.utils:utils-intervalrdd-spark3_2.11:jar:0.3.0, org.apache.spark:spark-core_2.11:jar:3.0.1, org.apache.spark:spark-sql_2.11:jar:3.0.1: Could not find artifact org.bdgenomics.utils:utils-misc-spark3_2.11:jar:tests:0.3.0 in central (https://repo.maven.apache.org/maven2) -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException [ERROR] [ERROR] After correcting the problems, you can resume the build with the command [ERROR] mvn <args> -rf :adam-core-spark3_2.11 Build step 'Execute shell' marked build as failure Recording test results Publishing Scoverage XML and HTML report... ERROR: cannot find scoverage report Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/0e441bf36dd7b15678ef14de38f63344773f9079 Finished: FAILURE