Started by upstream project "ADAM-prb" build number 3157 originally caused by: GitHub pull request #2282 of commit e6332ef5bac0dc6ce37cb840631c62f3e67a8351, has merge conflicts. Running as SYSTEM [EnvInject] - Loading node environment variables. Building remotely on research-jenkins-worker-08 (ubuntu research-08) in workspace /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu The recommended git tool is: NONE No credentials specified 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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu # timeout=10 Using reference repository: /home/jenkins/gitcaches/adam.reference Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git --version # 'git version 2.7.4' > 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 e6332ef5bac0dc6ce37cb840631c62f3e67a8351 (detached) > git config core.sparsecheckout # timeout=10 > git checkout -f e6332ef5bac0dc6ce37cb840631c62f3e67a8351 # timeout=10 Commit message: "code format fix" > git rev-list --no-walk a895649d542ec33052f8626ea0be922d31f5ecb3 # timeout=10 [ubuntu] $ /bin/bash /tmp/jenkins814017707358950047.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 + 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 + /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/jenkins-test # make a tempdir for writing maven cruft to ADAM_MVN_TMP_DIR=$(mktemp -d -t adamTestMvnXXXXXXX) mktemp -d -t adamTestMvnXXXXXXX ++ mktemp -d -t adamTestMvnXXXXXXX + ADAM_MVN_TMP_DIR=/tmp/adamTestMvn1wolq6S # add this tempdir to the poms... find . -name pom.xml \ -exec sed -i.bak \ -e "s:sun.io.serialization.extendedDebugInfo=true:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${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/adamTestMvn1wolq6S: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 + 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 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 ${BASH_SOURCE[0]} +++ dirname /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts/jenkins-test ++ cd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts ++ pwd + DIR=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/label/ubuntu/scripts PROJECT_ROOT=${DIR}/.. + PROJECT_ROOT=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/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/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.2/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 3.2.1 ]] # 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 3.0.2 ]] 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 + '[' 2.12 == 2.11 ']' # move to Scala 2.12 if requested if [ ${SCALA_VERSION} == 2.12 ]; then set +e ./scripts/move_to_scala_2.12.sh set -e fi + '[' 2.12 == 2.12 ']' + set +e + ./scripts/move_to_scala_2.12.sh Scala version is already set to 2.12 (Scala artifacts have _2.12 version suffix in artifact name). Cowardly refusing to move to Scala 2.12 a second time... + set -e # move to Spark 2.x if requested if [ ${SPARK_VERSION} == 2.4.7 ]; then set +e ./scripts/move_to_spark_2.sh set -e fi + '[' 3.0.2 == 2.4.7 ']' # 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 + '[' 3.0.2 == 3.0.1 ']' # print versions echo "Testing ADAM version ${VERSION} on Spark ${SPARK_VERSION} and Hadoop ${HADOOP_VERSION}" + echo 'Testing ADAM version 0.33.0-SNAPSHOT on Spark 3.0.2 and Hadoop 3.2.1' Testing ADAM version 0.33.0-SNAPSHOT on Spark 3.0.2 and Hadoop 3.2.1 # first, build the sources, run the unit tests, and generate a coverage report mvn clean \ -Dhadoop.version=${HADOOP_VERSION} + mvn clean -Dhadoop.version=3.2.1 Java HotSpot(TM) 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_2.12 [pom] [INFO] ADAM_2.12: Shader workaround [jar] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils [jar] [INFO] ADAM_2.12: Core [jar] [INFO] ADAM_2.12: APIs for Java, Python [jar] [INFO] ADAM_2.12: CLI [jar] [INFO] ADAM_2.12: Assembly [jar] [INFO] [INFO] ------------< org.bdgenomics.adam:adam-parent-spark3_2.12 >------------- [INFO] Building ADAM_2.12 0.33.0-SNAPSHOT [1/7] [INFO] --------------------------------[ pom ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-parent-spark3_2.12 --- [INFO] [INFO] -------------< org.bdgenomics.adam:adam-shade-spark3_2.12 >------------- [INFO] Building ADAM_2.12: Shader workaround 0.33.0-SNAPSHOT [2/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-shade-spark3_2.12 --- [INFO] [INFO] ------------< org.bdgenomics.adam:adam-codegen-spark3_2.12 >------------ [INFO] Building ADAM_2.12: 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_2.12 --- [INFO] [INFO] -------------< org.bdgenomics.adam:adam-core-spark3_2.12 >-------------- [INFO] Building ADAM_2.12: Core 0.33.0-SNAPSHOT [4/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-core-spark3_2.12 --- [INFO] [INFO] -------------< org.bdgenomics.adam:adam-apis-spark3_2.12 >-------------- [INFO] Building ADAM_2.12: 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_2.12 --- [INFO] [INFO] --------------< org.bdgenomics.adam:adam-cli-spark3_2.12 >-------------- [INFO] Building ADAM_2.12: CLI 0.33.0-SNAPSHOT [6/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-cli-spark3_2.12 --- [INFO] [INFO] -----------< org.bdgenomics.adam:adam-assembly-spark3_2.12 >------------ [INFO] Building ADAM_2.12: Assembly 0.33.0-SNAPSHOT [7/7] [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ adam-assembly-spark3_2.12 --- [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for ADAM_2.12 0.33.0-SNAPSHOT: [INFO] [INFO] ADAM_2.12 .......................................... SUCCESS [ 0.314 s] [INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [ 0.049 s] [INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 0.010 s] [INFO] ADAM_2.12: Core .................................... SUCCESS [ 0.023 s] [INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 0.003 s] [INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 0.079 s] [INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 0.003 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ [INFO] Total time: 0.654 s [INFO] Finished at: 2021-02-28T02:41:39-08:00 [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 2282 ]] + COVERALLS_PRB_OPTION=-DpullRequest=2282 # coveralls token should not be visible set +x +v + set +x +v Coveralls token is not set. Exiting... Build step 'Execute shell' marked build as failure Recording test results ERROR: Step ‘Publish JUnit test result report’ failed: No test report files were found. Configuration error? [Set GitHub commit status (universal)] ERROR on repos [GHRepository@72f8a548[nodeId=MDEwOlJlcG9zaXRvcnkxNDU0MTUzMA==,description=ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.,homepage=http://bdgenomics.org/,name=adam,fork=false,archived=false,size=13492,milestones={},language=Scala,commits={},source=<null>,parent=<null>,isTemplate=<null>,url=https://api.github.com/repos/bigdatagenomics/adam,id=14541530,nodeId=<null>,createdAt=2013-11-19T23:47:57Z,updatedAt=2021-02-28T10:27:42Z]] (sha:e6332ef) with context:ADAM-prb/HADOOP_VERSION=3.2.1,SCALA_VERSION=2.12,SPARK_VERSION=3.0.2,label=ubuntu Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/e6332ef5bac0dc6ce37cb840631c62f3e67a8351 Finished: FAILURE