Console Output

Started by upstream project "cannoli" build number 2203
originally caused by:
 Started by timer
Running as SYSTEM
[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/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 2.7.4'
 > git fetch --tags --progress https://github.com/bigdatagenomics/cannoli.git +refs/heads/*:refs/remotes/origin/* # timeout=10
Checking out Revision eb0243314c3e4d2a95eb16db3531e26c1aec164f (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f eb0243314c3e4d2a95eb16db3531e26c1aec164f # timeout=10
Commit message: "remove adam-shade dependency"
 > git rev-list --no-walk eb0243314c3e4d2a95eb16db3531e26c1aec164f # 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/jenkins573685055359622240.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/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
++ mktemp -d -t cannoliTestMvnXXXXXXX
+ CANNOLI_MVN_TMP_DIR=/tmp/cannoliTestMvnKPcLzvd

# 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/cannoliTestMvnKPcLzvd: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 ${BASH_SOURCE[0]} 
+++ dirname /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/jenkins-test
++ cd /home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
++ pwd
+ DIR=/home/jenkins/workspace/cannoli/HADOOP_VERSION/3.2.1/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
PROJECT_ROOT=${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>" ${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=0.12.0-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 0.12.0-SNAPSHOT on Spark 3.0.1 Scala 2.12 and Hadoop 3.2.1'
Testing Cannoli version 0.12.0-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 0.12.0-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 55 .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 0.12.0-SNAPSHOT                     [2/5]
[INFO] --------------------------------[ jar ]---------------------------------
Downloading from sonatype-nexus-snapshots: https://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark3_2.12/0.34.0-SNAPSHOT/maven-metadata.xml
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[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 1615484379984
[INFO] prepare-compile in 0 s
[INFO] compile in 1 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 1615484382825
[INFO] prepare-compile in 0 s
[INFO] compile in 1 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.LocalBuilderTest
[INFO] Tests run: 18, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.081 s - in org.bdgenomics.cannoli.builder.LocalBuilderTest
[INFO] Running org.bdgenomics.cannoli.builder.DockerBuilderTest
[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.bdgenomics.cannoli.builder.DockerBuilderTest
[INFO] Running org.bdgenomics.cannoli.builder.CommandBuildersTest
[INFO] Tests run: 4, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.bdgenomics.cannoli.builder.CommandBuildersTest
[INFO] Running org.bdgenomics.cannoli.builder.SingularityBuilderTest
[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 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_2.12-0.12.0-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_2.12-0.12.0-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] ----------< org.bdgenomics.cannoli:cannoli-core-spark3_2.12 >-----------
[INFO] Building Cannoli_2.12: Core 0.12.0-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_2.12:3.0.1 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 1615484390447
[ERROR] /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:23: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.ADAMContext._
[ERROR]                            ^
[ERROR] /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:24: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.variant.{ VariantContextDataset, VCFInFormatter, VCFOutFormatter }
[ERROR]                            ^
[ERROR] /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:68: error: not found: type VariantContextDataset
[ERROR]     sc: SparkContext) extends CannoliFn[VariantContextDataset, VariantContextDataset](sc) {
[ERROR]                                         ^
[ERROR] /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:68: error: not found: type VariantContextDataset
[ERROR]     sc: SparkContext) extends CannoliFn[VariantContextDataset, VariantContextDataset](sc) {
[ERROR]                                                                ^
[ERROR] /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:70: error: not found: type VariantContextDataset
[ERROR]   override def apply(variants: VariantContextDataset): VariantContextDataset = {
[ERROR]                                                        ^
[ERROR] /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:70: error: not found: type VariantContextDataset
[ERROR]   override def apply(variants: VariantContextDataset): VariantContextDataset = {
[ERROR]                                ^
[ERROR] /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:89: error: not found: value VCFInFormatter
[ERROR]     implicit val tFormatter = VCFInFormatter
[ERROR]                               ^
[ERROR] /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:90: error: not found: type VCFOutFormatter
[ERROR]     implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration, stringency)
[ERROR]                                   ^
[ERROR] /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:92: error: not found: type VariantContextDataset
[ERROR]     variants.pipe[VariantContext, VariantContextProduct, VariantContextDataset, VCFInFormatter](
[ERROR]                                                          ^
[ERROR] /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:92: error: not found: type VCFInFormatter
[ERROR]     variants.pipe[VariantContext, VariantContextProduct, VariantContextDataset, VCFInFormatter](
[ERROR]                                                                                 ^
[ERROR] /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: error: not found: value cmd
[ERROR]       cmd = builder.build(),
[ERROR]       ^
[ERROR] /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: error: ambiguous reference to overloaded definition,
[ERROR] both method files in class CannoliFn of type (pathName: String, filter: org.apache.hadoop.fs.PathFilter)Seq[String]
[ERROR] and  method files in class CannoliFn of type (pathName: String)Seq[String]
[ERROR] match expected type ?
[ERROR]       files = builder.getFiles()
[ERROR]       ^
[ERROR] /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:23: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.ADAMContext._
[ERROR]                            ^
[ERROR] /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:24: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.read.{ AlignmentDataset, BAMInFormatter }
[ERROR]                            ^
[ERROR] /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:25: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.variant.{ VariantContextDataset, VCFOutFormatter }
[ERROR]                            ^
[ERROR] /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:72: error: not found: type AlignmentDataset
[ERROR]     sc: SparkContext) extends CannoliFn[AlignmentDataset, VariantContextDataset](sc) {
[ERROR]                                         ^
[ERROR] /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:72: error: not found: type VariantContextDataset
[ERROR]     sc: SparkContext) extends CannoliFn[AlignmentDataset, VariantContextDataset](sc) {
[ERROR]                                                           ^
[ERROR] /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:74: error: not found: type VariantContextDataset
[ERROR]   override def apply(alignments: AlignmentDataset): VariantContextDataset = {
[ERROR]                                                     ^
[ERROR] /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:74: error: not found: type AlignmentDataset
[ERROR]   override def apply(alignments: AlignmentDataset): VariantContextDataset = {
[ERROR]                                  ^
[ERROR] /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:102: error: not found: value BAMInFormatter
[ERROR]     implicit val tFormatter = BAMInFormatter
[ERROR]                               ^
[ERROR] /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:103: error: not found: type VCFOutFormatter
[ERROR]     implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration, stringency)
[ERROR]                                   ^
[ERROR] /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:105: error: not found: type VariantContextDataset
[ERROR]     alignments.pipe[VariantContext, VariantContextProduct, VariantContextDataset, BAMInFormatter](
[ERROR]                                                            ^
[ERROR] /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:105: error: not found: type BAMInFormatter
[ERROR]     alignments.pipe[VariantContext, VariantContextProduct, VariantContextDataset, BAMInFormatter](
[ERROR]                                                                                   ^
[ERROR] /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: error: not found: value cmd
[ERROR]       cmd = builder.build(),
[ERROR]       ^
[ERROR] /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: error: ambiguous reference to overloaded definition,
[ERROR] both method files in class CannoliFn of type (pathName: String, filter: org.apache.hadoop.fs.PathFilter)Seq[String]
[ERROR] and  method files in class CannoliFn of type (pathName: String)Seq[String]
[ERROR] match expected type ?
[ERROR]       files = builder.getFiles()
[ERROR]       ^
[ERROR] /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:23: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.ADAMContext._
[ERROR]                            ^
[ERROR] /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:24: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.variant.{
[ERROR]                            ^
[ERROR] /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:72: error: not found: type VariantContextDataset
[ERROR]     sc: SparkContext) extends CannoliFn[VariantContextDataset, VariantContextDataset](sc) {
[ERROR]                                         ^
[ERROR] /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:72: error: not found: type VariantContextDataset
[ERROR]     sc: SparkContext) extends CannoliFn[VariantContextDataset, VariantContextDataset](sc) {
[ERROR]                                                                ^
[ERROR] /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:74: error: not found: type VariantContextDataset
[ERROR]   override def apply(variantContexts: VariantContextDataset): VariantContextDataset = {
[ERROR]                                                               ^
[ERROR] /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:74: error: not found: type VariantContextDataset
[ERROR]   override def apply(variantContexts: VariantContextDataset): VariantContextDataset = {
[ERROR]                                       ^
[ERROR] /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:97: error: not found: value VCFInFormatter
[ERROR]     implicit val tFormatter = VCFInFormatter
[ERROR]                               ^
[ERROR] /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:98: error: not found: type VCFOutFormatter
[ERROR]     implicit val uFormatter = new VCFOutFormatter(sc.hadoopConfiguration, stringency)
[ERROR]                                   ^
[ERROR] /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:100: error: not found: type VariantContextDataset
[ERROR]     variantContexts.pipe[VariantContext, VariantContextProduct, VariantContextDataset, VCFInFormatter](
[ERROR]                                                                 ^
[ERROR] /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:100: error: not found: type VCFInFormatter
[ERROR]     variantContexts.pipe[VariantContext, VariantContextProduct, VariantContextDataset, VCFInFormatter](
[ERROR]                                                                                        ^
[ERROR] /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: error: not found: value cmd
[ERROR]       cmd = builder.build(),
[ERROR]       ^
[ERROR] /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: error: ambiguous reference to overloaded definition,
[ERROR] both method files in class CannoliFn of type (pathName: String, filter: org.apache.hadoop.fs.PathFilter)Seq[String]
[ERROR] and  method files in class CannoliFn of type (pathName: String)Seq[String]
[ERROR] match expected type ?
[ERROR]       files = builder.getFiles()
[ERROR]       ^
[ERROR] /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:21: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.ADAMContext._
[ERROR]                            ^
[ERROR] /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:22: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.feature.{
[ERROR]                            ^
[ERROR] /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:83: error: not found: type FeatureDataset
[ERROR]     sc: SparkContext) extends CannoliFn[FeatureDataset, FeatureDataset](sc) {
[ERROR]                                         ^
[ERROR] /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:83: error: not found: type FeatureDataset
[ERROR]     sc: SparkContext) extends CannoliFn[FeatureDataset, FeatureDataset](sc) {
[ERROR]                                                         ^
[ERROR] /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:85: error: not found: type FeatureDataset
[ERROR]   override def apply(features: FeatureDataset): FeatureDataset = {
[ERROR]                                                 ^
[ERROR] /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:85: error: not found: type FeatureDataset
[ERROR]   override def apply(features: FeatureDataset): FeatureDataset = {
[ERROR]                                ^
[ERROR] /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:114: error: not found: value BEDInFormatter
[ERROR]     implicit val tFormatter = BEDInFormatter
[ERROR]                               ^
[ERROR] /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:115: error: not found: type BEDOutFormatter
[ERROR]     implicit val uFormatter = new BEDOutFormatter
[ERROR]                                   ^
[ERROR] /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:117: error: not found: type FeatureDataset
[ERROR]     features.pipe[Feature, FeatureProduct, FeatureDataset, BEDInFormatter](
[ERROR]                                            ^
[ERROR] /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:117: error: not found: type BEDInFormatter
[ERROR]     features.pipe[Feature, FeatureProduct, FeatureDataset, BEDInFormatter](
[ERROR]                                                            ^
[ERROR] /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: error: not found: value cmd
[ERROR]       cmd = builder.build(),
[ERROR]       ^
[ERROR] /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: error: ambiguous reference to overloaded definition,
[ERROR] both method files in class CannoliFn of type (pathName: String, filter: org.apache.hadoop.fs.PathFilter)Seq[String]
[ERROR] and  method files in class CannoliFn of type (pathName: String)Seq[String]
[ERROR] match expected type ?
[ERROR]       files = builder.getFiles()
[ERROR]       ^
[ERROR] /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:23: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.ADAMContext._
[ERROR]                            ^
[ERROR] /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:24: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.read.{ AlignmentDataset, AnySAMOutFormatter }
[ERROR]                            ^
[ERROR] /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:25: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.sequence.{ FASTAInFormatter, SequenceDataset }
[ERROR]                            ^
[ERROR] /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:98: error: not found: type SequenceDataset
[ERROR]     sc: SparkContext) extends CannoliFn[SequenceDataset, AlignmentDataset](sc) {
[ERROR]                                         ^
[ERROR] /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:98: error: not found: type AlignmentDataset
[ERROR]     sc: SparkContext) extends CannoliFn[SequenceDataset, AlignmentDataset](sc) {
[ERROR]                                                          ^
[ERROR] /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:100: error: not found: type AlignmentDataset
[ERROR]   override def apply(sequences: SequenceDataset): AlignmentDataset = {
[ERROR]                                                   ^
[ERROR] /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:100: error: not found: type SequenceDataset
[ERROR]   override def apply(sequences: SequenceDataset): AlignmentDataset = {
[ERROR]                                 ^
[ERROR] /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:147: error: not found: value FASTAInFormatter
[ERROR]     implicit val tFormatter = FASTAInFormatter
[ERROR]                               ^
[ERROR] /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:148: error: not found: type AnySAMOutFormatter
[ERROR]     implicit val uFormatter = new AnySAMOutFormatter(ValidationStringency.valueOf(args.stringency))
[ERROR]                                   ^
[ERROR] /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:150: error: not found: type AlignmentDataset
[ERROR]     sequences.pipe[Alignment, AlignmentProduct, AlignmentDataset, FASTAInFormatter](
[ERROR]                                                 ^
[ERROR] /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:150: error: not found: type FASTAInFormatter
[ERROR]     sequences.pipe[Alignment, AlignmentProduct, AlignmentDataset, FASTAInFormatter](
[ERROR]                                                                   ^
[ERROR] /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: error: not found: value cmd
[ERROR]       cmd = builder.build(),
[ERROR]       ^
[ERROR] /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: error: ambiguous reference to overloaded definition,
[ERROR] both method files in class CannoliFn of type (pathName: String, filter: org.apache.hadoop.fs.PathFilter)Seq[String]
[ERROR] and  method files in class CannoliFn of type (pathName: String)Seq[String]
[ERROR] match expected type ?
[ERROR]       files = builder.getFiles()
[ERROR]       ^
[ERROR] /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:21: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.ADAMContext._
[ERROR]                            ^
[ERROR] /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:22: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.fragment.{ FragmentDataset, InterleavedFASTQInFormatter }
[ERROR]                            ^
[ERROR] /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:23: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.read.{ AlignmentDataset, AnySAMOutFormatter }
[ERROR]                            ^
[ERROR] /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:66: error: not found: type FragmentDataset
[ERROR]     sc: SparkContext) extends CannoliFn[FragmentDataset, AlignmentDataset](sc) {
[ERROR]                                         ^
[ERROR] /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:66: error: not found: type AlignmentDataset
[ERROR]     sc: SparkContext) extends CannoliFn[FragmentDataset, AlignmentDataset](sc) {
[ERROR]                                                          ^
[ERROR] /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:68: error: not found: type AlignmentDataset
[ERROR]   override def apply(fragments: FragmentDataset): AlignmentDataset = {
[ERROR]                                                   ^
[ERROR] /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:68: error: not found: type FragmentDataset
[ERROR]   override def apply(fragments: FragmentDataset): AlignmentDataset = {
[ERROR]                                 ^
[ERROR] /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:94: error: not found: value InterleavedFASTQInFormatter
[ERROR]     implicit val tFormatter = InterleavedFASTQInFormatter
[ERROR]                               ^
[ERROR] /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:95: error: not found: type AnySAMOutFormatter
[ERROR]     implicit val uFormatter = new AnySAMOutFormatter
[ERROR]                                   ^
[ERROR] /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:97: error: not found: type AlignmentDataset
[ERROR]     fragments.pipe[Alignment, AlignmentProduct, AlignmentDataset, InterleavedFASTQInFormatter](
[ERROR]                                                 ^
[ERROR] /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:97: error: not found: type InterleavedFASTQInFormatter
[ERROR]     fragments.pipe[Alignment, AlignmentProduct, AlignmentDataset, InterleavedFASTQInFormatter](
[ERROR]                                                                   ^
[ERROR] /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: error: not found: value cmd
[ERROR]       cmd = builder.build(),
[ERROR]       ^
[ERROR] /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: error: ambiguous reference to overloaded definition,
[ERROR] both method files in class CannoliFn of type (pathName: String, filter: org.apache.hadoop.fs.PathFilter)Seq[String]
[ERROR] and  method files in class CannoliFn of type (pathName: String)Seq[String]
[ERROR] match expected type ?
[ERROR]       files = builder.getFiles()
[ERROR]       ^
[ERROR] /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:22: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.ADAMContext._
[ERROR]                            ^
[ERROR] /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:23: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.fragment.{ FragmentDataset, InterleavedFASTQInFormatter }
[ERROR]                            ^
[ERROR] /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:24: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.read.{ AlignmentDataset, AnySAMOutFormatter }
[ERROR]                            ^
[ERROR] /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:70: error: not found: type FragmentDataset
[ERROR]     sc: SparkContext) extends CannoliFn[FragmentDataset, AlignmentDataset](sc) {
[ERROR]                                         ^
[ERROR] /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:70: error: not found: type AlignmentDataset
[ERROR]     sc: SparkContext) extends CannoliFn[FragmentDataset, AlignmentDataset](sc) {
[ERROR]                                                          ^
[ERROR] /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:72: error: not found: type AlignmentDataset
[ERROR]   override def apply(fragments: FragmentDataset): AlignmentDataset = {
[ERROR]                                                   ^
[ERROR] /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:72: error: not found: type FragmentDataset
[ERROR]   override def apply(fragments: FragmentDataset): AlignmentDataset = {
[ERROR]                                 ^
[ERROR] /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:110: error: not found: value InterleavedFASTQInFormatter
[ERROR]     implicit val tFormatter = InterleavedFASTQInFormatter
[ERROR]                               ^
[ERROR] /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:111: error: not found: type AnySAMOutFormatter
[ERROR]     implicit val uFormatter = new AnySAMOutFormatter
[ERROR]                                   ^
[ERROR] /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:113: error: not found: type AlignmentDataset
[ERROR]     fragments.pipe[Alignment, AlignmentProduct, AlignmentDataset, InterleavedFASTQInFormatter](
[ERROR]                                                 ^
[ERROR] /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:113: error: not found: type InterleavedFASTQInFormatter
[ERROR]     fragments.pipe[Alignment, AlignmentProduct, AlignmentDataset, InterleavedFASTQInFormatter](
[ERROR]                                                                   ^
[ERROR] /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: error: not found: value cmd
[ERROR]       cmd = builder.build(),
[ERROR]       ^
[ERROR] /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: error: ambiguous reference to overloaded definition,
[ERROR] both method files in class CannoliFn of type (pathName: String, filter: org.apache.hadoop.fs.PathFilter)Seq[String]
[ERROR] and  method files in class CannoliFn of type (pathName: String)Seq[String]
[ERROR] match expected type ?
[ERROR]       files = builder.getFiles()
[ERROR]       ^
[ERROR] /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:22: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.ADAMContext._
[ERROR]                            ^
[ERROR] /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:23: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.fragment.{ FragmentDataset, InterleavedFASTQInFormatter }
[ERROR]                            ^
[ERROR] /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:25: error: object rdd is not a member of package org.bdgenomics.adam
[ERROR] import org.bdgenomics.adam.rdd.read.{ AlignmentDataset, AnySAMOutFormatter }
[ERROR]                            ^
[ERROR] /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:67: error: not found: type FragmentDataset
[ERROR]     sc: SparkContext) extends CannoliFn[FragmentDataset, AlignmentDataset](sc) {
[ERROR]                                         ^
[ERROR] /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:67: error: not found: type AlignmentDataset
[ERROR]     sc: SparkContext) extends CannoliFn[FragmentDataset, AlignmentDataset](sc) {
[ERROR]                                                          ^
[ERROR] /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:69: error: not found: type AlignmentDataset
[ERROR]   override def apply(fragments: FragmentDataset): AlignmentDataset = {
[ERROR]                                                   ^
[ERROR] /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:69: error: not found: type FragmentDataset
[ERROR]   override def apply(fragments: FragmentDataset): AlignmentDataset = {
[ERROR]                                 ^
[ERROR] /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:136: error: not found: value InterleavedFASTQInFormatter
[ERROR]     implicit val tFormatter = InterleavedFASTQInFormatter
[ERROR]                               ^
[ERROR] /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:137: error: not found: type AnySAMOutFormatter
[ERROR]     implicit val uFormatter = new AnySAMOutFormatter
[ERROR]                                   ^
[ERROR] /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:139: error: not found: type AlignmentDataset
[ERROR]     val alignments = fragments.pipe[Alignment, AlignmentProduct, AlignmentDataset, InterleavedFASTQInFormatter](
[ERROR]                                                                  ^
[ERROR] /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:139: error: not found: type InterleavedFASTQInFormatter
[ERROR]     val alignments = fragments.pipe[Alignment, AlignmentProduct, AlignmentDataset, InterleavedFASTQInFormatter](
[ERROR]                                                                                    ^
[ERROR] /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: error: not found: value cmd
[ERROR]       cmd = builder.build(),
[ERROR]       ^
[ERROR] 306 errors found
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Cannoli_2.12 0.12.0-SNAPSHOT:
[INFO] 
[INFO] Cannoli_2.12 ....................................... SUCCESS [  2.231 s]
[INFO] Cannoli_2.12: Builder .............................. SUCCESS [ 20.030 s]
[INFO] Cannoli_2.12: Core ................................. FAILURE [  5.065 s]
[INFO] Cannoli_2.12: CLI .................................. SKIPPED
[INFO] Cannoli_2.12: Assembly ............................. SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  27.474 s
[INFO] Finished at: 2021-03-11T09:39:54-08:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal net.alchim31.maven:scala-maven-plugin:3.2.2:compile (scala-compile-first) on project cannoli-core-spark3_2.12: wrap: org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1) -> [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/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <args> -rf :cannoli-core-spark3_2.12
Build step 'Execute shell' marked build as failure
Recording test results
[Checks API] No suitable checks publisher found.
Sending e-mails to: heuermh@gmail.com fnothaft@berkeley.edu
ERROR: Couldn't connect to host, port: 127.0.0.1, 25; timeout 60000
com.sun.mail.util.MailConnectException: Couldn't connect to host, port: 127.0.0.1, 25; timeout 60000;
  nested exception is:
	java.net.ConnectException: Connection refused (Connection refused)
	at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2210)
	at com.sun.mail.smtp.SMTPTransport.protocolConnect(SMTPTransport.java:722)
	at javax.mail.Service.connect(Service.java:342)
	at javax.mail.Service.connect(Service.java:222)
	at javax.mail.Service.connect(Service.java:171)
	at javax.mail.Transport.send0(Transport.java:230)
	at javax.mail.Transport.send(Transport.java:100)
	at hudson.tasks.MailSender.run(MailSender.java:130)
	at hudson.tasks.Mailer.perform(Mailer.java:176)
	at hudson.tasks.Mailer.perform(Mailer.java:139)
	at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
	at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:741)
	at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:690)
	at hudson.model.Build$BuildExecution.post2(Build.java:186)
	at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:635)
	at hudson.model.Run.execute(Run.java:1919)
	at hudson.matrix.MatrixRun.run(MatrixRun.java:153)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:428)
Caused by: java.net.ConnectException: Connection refused (Connection refused)
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:607)
	at com.sun.mail.util.SocketFetcher.createSocket(SocketFetcher.java:333)
	at com.sun.mail.util.SocketFetcher.getSocket(SocketFetcher.java:214)
	at com.sun.mail.smtp.SMTPTransport.openServer(SMTPTransport.java:2160)
	... 18 more
Finished: FAILURE