FailedConsole Output

Started by upstream project "cannoli" build number 2117
originally caused by:
 Started by GitHub push by heuermh
[EnvInject] - Loading node environment variables.
Building remotely on research-jenkins-worker-09 (ubuntu ubuntu-gpu research-09 ubuntu-avx2) in workspace /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu
 > 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 fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/heads/*:refs/remotes/origin/*
Checking out Revision a6388e24c69eecbed2bd84d67d345889f82ee14a (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f a6388e24c69eecbed2bd84d67d345889f82ee14a
 > git rev-list 6181d15e66926de29d9486f7b325f27f7676d5d9 # 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/hudson3456573938640944740.sh
+ set -e
+ export JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ JAVA_HOME=/usr/lib/jvm/java-8-oracle
+ export CONDA_BIN=/home/anaconda/bin/
+ CONDA_BIN=/home/anaconda/bin/
+ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ set +x
+ /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test

# make a tempdir for writing maven cruft to
CANNOLI_MVN_TMP_DIR=$(mktemp -d -t cannoliTestMvnXXXXXXX)
mktemp -d -t cannoliTestMvnXXXXXXX
++ mktemp -d -t cannoliTestMvnXXXXXXX
+ CANNOLI_MVN_TMP_DIR=/tmp/cannoliTestMvnqCy04pZ

# 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/cannoliTestMvnqCy04pZ:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

# variable declarations
export PATH=${JAVA_HOME}/bin/:${PATH}
+ export PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
+ PATH=/usr/lib/jvm/java-8-oracle/bin/:/usr/lib/jvm/java-8-oracle/bin/:/home/anaconda/bin/:/home/jenkins/tools/hudson.tasks.Maven_MavenInstallation/Maven_3.6.3/bin/:/home/jenkins/gems/bin:/usr/local/go/bin:/home/jenkins/go-projects/bin:/home/jenkins/anaconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
export MAVEN_OPTS="-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8"
+ export 'MAVEN_OPTS=-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
+ MAVEN_OPTS='-Xmx1536m -XX:MaxPermSize=1g -Dfile.encoding=utf-8'
DIR=$( cd $( dirname ${BASH_SOURCE[0]} ) && pwd )
 cd $( dirname ${BASH_SOURCE[0]} ) && pwd 
 dirname ${BASH_SOURCE[0]} 
+++ dirname /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts
PROJECT_ROOT=${DIR}/..
+ PROJECT_ROOT=/home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/..
VERSION=$(grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g')
grep "<version>" ${PROJECT_ROOT}/pom.xml  | head -2 | tail -1 | sed 's/ *<version>//g' | sed 's/<\/version>//g'
++ grep '<version>' /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/scripts/../pom.xml
++ head -2
++ tail -1
++ sed 's/ *<version>//g'
++ sed 's/<\/version>//g'
+ VERSION=0.11.0-SNAPSHOT

# is the hadoop version set?
if ! [[ ${HADOOP_VERSION} ]];
then
    echo "HADOOP_VERSION environment variable is not set."
    echo "Please set this variable before running."
    exit 1
fi
+ [[ -n 2.7.5 ]]

# is the scala version set?
if ! [[ ${SCALA_VERSION} ]];
then
    echo "SCALA_VERSION environment variable is not set."
    echo "Please set this variable before running."
    exit 1
fi
+ [[ -n 2.11 ]]

# 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 2.4.6 ]]

# print versions
echo "Testing Cannoli version ${VERSION} on Spark ${SPARK_VERSION} Scala ${SCALA_VERSION} and Hadoop ${HADOOP_VERSION}"
+ echo 'Testing Cannoli version 0.11.0-SNAPSHOT on Spark 2.4.6 Scala 2.11 and Hadoop 2.7.5'
Testing Cannoli version 0.11.0-SNAPSHOT on Spark 2.4.6 Scala 2.11 and Hadoop 2.7.5

# move to Scala 2.11 if requested
if [ ${SCALA_VERSION} == 2.11 ];
then
    set +e
    ./scripts/move_to_scala_2.11.sh
    set -e
fi
+ '[' 2.11 == 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} == 2.4.7 ];
then
    set +e
    ./scripts/move_to_spark_2.sh
    set -e
fi
+ '[' 2.4.6 == 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
+ '[' 2.4.6 == 3.0.1 ']'

# first, build the sources, run the unit tests, and generate a coverage report
mvn clean \
    -Dhadoop.version=${HADOOP_VERSION}
+ mvn clean -Dhadoop.version=2.7.5
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Cannoli_2.11                                                       [pom]
[INFO] Cannoli_2.11: Builder                                              [jar]
[INFO] Cannoli_2.11: Core                                                 [jar]
[INFO] Cannoli_2.11: CLI                                                  [jar]
[INFO] Cannoli_2.11: Assembly                                             [jar]
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark3_2.11 >----------
[INFO] Building Cannoli_2.11 0.11.0-SNAPSHOT                              [1/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-parent-spark3_2.11 ---
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark3_2.11 >---------
[INFO] Building Cannoli_2.11: Builder 0.11.0-SNAPSHOT                     [2/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-builder-spark3_2.11 ---
[INFO] 
[INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark3_2.11 >-----------
[INFO] Building Cannoli_2.11: Core 0.11.0-SNAPSHOT                        [3/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-core-spark3_2.11 ---
[INFO] 
[INFO] -----------< org.bdgenomics.cannoli:cannoli-cli-spark3_2.11 >-----------
[INFO] Building Cannoli_2.11: CLI 0.11.0-SNAPSHOT                         [4/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-cli-spark3_2.11 ---
[INFO] 
[INFO] --------< org.bdgenomics.cannoli:cannoli-assembly-spark3_2.11 >---------
[INFO] Building Cannoli_2.11: Assembly 0.11.0-SNAPSHOT                    [5/5]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:3.1.0:clean (default-clean) @ cannoli-assembly-spark3_2.11 ---
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.11 0.11.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.11 ....................................... SUCCESS [  0.216 s]
[INFO] Cannoli_2.11: Builder .............................. SUCCESS [  0.003 s]
[INFO] Cannoli_2.11: Core ................................. SUCCESS [  0.007 s]
[INFO] Cannoli_2.11: CLI .................................. SUCCESS [  0.027 s]
[INFO] Cannoli_2.11: Assembly ............................. SUCCESS [  0.010 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.434 s
[INFO] Finished at: 2020-10-20T08:32:01-07:00
[INFO] ------------------------------------------------------------------------

# if this is a pull request, we need to set the coveralls pr id
if [[ ! -z $ghprbPullId ]];
then
    COVERALLS_PRB_OPTION="-DpullRequest=${ghprbPullId}"
fi
+ [[ ! -z '' ]]

# coveralls token should not be visible
set +x +v
+ set +x +v
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Cannoli_2.11                                                       [pom]
[INFO] Cannoli_2.11: Builder                                              [jar]
[INFO] Cannoli_2.11: Core                                                 [jar]
[INFO] Cannoli_2.11: CLI                                                  [jar]
[INFO] Cannoli_2.11: Assembly                                             [jar]
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-parent-spark3_2.11 >----------
[INFO] Building Cannoli_2.11 0.11.0-SNAPSHOT                              [1/5]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark3_2.11 ---
[INFO] Modified 0 of 54 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ cannoli-parent-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark3_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) > [scoverage]test @ cannoli-parent-spark3_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-maven) @ cannoli-parent-spark3_2.11 ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.2:enforce (enforce-java) @ cannoli-parent-spark3_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-source (add-source) @ cannoli-parent-spark3_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ cannoli-parent-spark3_2.11 ---
[INFO] Modified 0 of 54 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ cannoli-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) @ cannoli-parent-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ cannoli-parent-spark3_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ cannoli-parent-spark3_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/cannoli/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.6/label/ubuntu/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ cannoli-parent-spark3_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) < [scoverage]test @ cannoli-parent-spark3_2.11 <<<
[INFO] 
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ cannoli-parent-spark3_2.11 ---
[INFO] 
[INFO] ---------< org.bdgenomics.cannoli:cannoli-builder-spark3_2.11 >---------
[INFO] Building Cannoli_2.11: Builder 0.11.0-SNAPSHOT                     [2/5]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core-spark3_2.11/0.32.0/adam-core-spark3_2.11-0.32.0.pom
[WARNING] The POM for org.bdgenomics.adam:adam-core-spark3_2.11:jar:0.32.0 is missing, no dependency information available
Downloading from central: https://repo.maven.apache.org/maven2/org/bdgenomics/adam/adam-core-spark3_2.11/0.32.0/adam-core-spark3_2.11-0.32.0.jar
[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] Skipping Cannoli_2.11
[INFO] This project has been banned from the build due to previous failures.
[INFO] ------------------------------------------------------------------------
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.11 0.11.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.11 ....................................... SUCCESS [  2.892 s]
[INFO] Cannoli_2.11: Builder .............................. FAILURE [  0.612 s]
[INFO] Cannoli_2.11: Core ................................. SKIPPED
[INFO] Cannoli_2.11: CLI .................................. SKIPPED
[INFO] Cannoli_2.11: Assembly ............................. SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  3.775 s
[INFO] Finished at: 2020-10-20T08:32:06-07:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal on project cannoli-builder-spark3_2.11: Could not resolve dependencies for project org.bdgenomics.cannoli:cannoli-builder-spark3_2.11:jar:0.11.0-SNAPSHOT: Could not find artifact org.bdgenomics.adam:adam-core-spark3_2.11:jar:0.32.0 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 :cannoli-builder-spark3_2.11
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?
Publishing Scoverage XML and HTML report...
ERROR: cannot find scoverage report
Sending e-mails to: heuermh@gmail.com fnothaft@berkeley.edu
Finished: FAILURE