SuccessConsole Output

Skipping 310 KB.. Full Log
7CWJ6SCJEgYhn6zEskT9nMS8dP3gkqLMvHTriiIGKaihyfl5xfk5qXrOEBpkDgMEMDIxMFQUlDCw2+gXFyTm2QEAI9P8iI4AAAA=
- generate observations for a read with an insertion under diploid model
- generate observations for a read with a deletion under diploid model
2018-01-01 05:57:14 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
DiscoveredVariantSuite:
- round trip conversion to/from variant
SquareOffReferenceModelSuite:
- don't trim a snp
- trim a mnp
- trim an insertion
- don't trim a deletion
2018-01-01 05:57:15 WARN  Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf.
- extract variants finds sites with a called alt
- find genotype if variant is present
- don't find genotype if variant is not present
- excise a genotype from a reference block
- square off a site with data from multiple samples
2018-01-01 05:57:16 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
DiscoverVariantsSuite:
- no variants in unaligned read
- no variants in rdd with unaligned read
- no variants in read that is a perfect sequence match
2018-01-01 05:57:17 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- no variants in rdd with sequence match reads
- find snp in read with a 1bp sequence mismatch
2018-01-01 05:57:17 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- find one snp in reads with 1bp sequence mismatch
- find insertion in read
2018-01-01 05:57:18 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- find insertion in reads
- find deletion in read
2018-01-01 05:57:19 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- find deletion in reads
2018-01-01 05:57:19 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- find variants in alignment record rdd
- break TT->CA mnp into two snps
ObservationOperatorSuite:
- zero operators are empty
- non-zero operators are non-empty
- cannot build mismatch with wrong ref length
- collapsing a non repeated set of operators should eliminate 0 ops
- collapsing a repeated set of operators with mixed match/mismatch
- collapse a set of operators with repeats
- collapse a set of operators with repeats and clips
- make a cigar and md tag from a single sequence match
- make a cigar and md tag from a single sequence mismatch
- make a cigar and md tag from a single multi-base sequence match
- make a cigar and md tag from a single deletion
- make a cigar and md tag from a single insertion
- make a cigar for a match followed by a deletion
- make a cigar for an insertion flanked by matches
- make a cigar for a match followed by a mismatch
- make a cigar for a multi-base mismatch flanked by matches
- make a cigar for a match after a clip
- make a cigar for a mismatch after a clip
- extract reference from a single snp
- extract reference from a single deletion
- extract reference from a single insertion
- extract reference from a soft clipped sequence
- extract reference from a hard clipped sequence
- extract reference from a match flanked deletion
- extract reference from a match flanked insertion
- read must be mapped to extract alignment operators
- extracting alignment operators will fail if cigar is unset
- extracting alignment operators will fail if cigar is *
- extracting alignment operators will fail if MD tag is unset
- extract alignment operators from a perfect read
- extract alignment operators from a read with a single mismatch
- extract alignment operators from a read with a single deletion
- extract alignment operators from a read with a single insertion
LogUtilsSuite:
- test our nifty log summer
- can we compute the sum of logs correctly?
- can we compute the additive inverse of logs correctly?
ObservationSuite:
- cannot create an observation with empty likelihoods
- cannot create an observation with 1-length likelihoods
- cannot create an observation with mismatching likelihood lengths
- forward strand must be >= 0
- forward strand cannot exceed coverage
- square map-q must be >= 0
- coverage is strictly positive
- invert an observation
- null an observation
RealignmentBlockSuite:
- folding over a clip returns the clip operator, soft clip
- folding over a clip returns the clip operator, hard clip
- folding over a canonical block returns the original alignment
- violate an invariant of the fold function, part 1
- violate an invariant of the fold function, part 2
- apply the fold function on a realignable block
- having a clip in the middle of a read is illegal
- can't have two soft clips back to back
- a read that is an exact sequence match is canonical
- hard clip before soft clip is ok at start of read
- hard clip after soft clip is ok at end of read
- a read with a single snp is canonical
- a read containing an indel with exact flanks is wholly realignable
- a read containing an indel with exact flanks is wholly realignable, with soft clipped bases
- a read containing an indel with longer flanks can be split into multiple blocks
- a read containing an indel with longer flanks on both sides can be split into multiple blocks
- properly handle a read that starts with a long soft clip
JointAnnotatorCallerSuite:
- discard reference site
- calculate MAF for all called genotypes
- calculate MAF ignoring uncalled genotypes
- roll up variant annotations from a single genotype
- roll up variant annotations across multiple genotypes
- recalling genotypes is a no-op for no calls and complex hets
- recall a genotype so that the state changes
- allele frequency being outside of (0.0, 1.0) just computes posteriors
- compute variant quality from a single genotype
- compute variant quality from multiple genotypes
2018-01-01 05:57:20 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
PrefilterReadsSuite:
- filter on read uniqueness
- filter unmapped reads
- filter autosomal chromosomes with grc names
- filter sex chromosomes with grc names
- filter mitochondrial chromosome with a grc names
- filter autosomal chromosomes with hg names
- filter sex chromosomes with hg names
- filter mitochondrial chromosome with a hg names
- filter autosomal chromosomes from generator
- filter autosomal + sex chromosomes from generator
- filter all chromosomes from generator
- update a read whose mate is mapped to a filtered contig
- filter reads mapped to autosomal chromosomes from generator
- filter reads mapped to autosomal + sex chromosomes from generator
- filter reads mapped to all chromosomes from generator
- filter reads uniquely mapped to autosomal chromosomes from generator
- filter reads uniquely mapped to autosomal + sex chromosomes from generator
- filter reads uniquely mapped to all chromosomes from generator
- filter rdd of reads mapped to autosomal chromosomes from generator
2018-01-01 05:57:20 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- filter rdd of reads mapped to autosomal + sex chromosomes from generator
2018-01-01 05:57:20 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- filter rdd of reads mapped to all chromosomes from generator
2018-01-01 05:57:20 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- filter rdd of reads uniquely mapped to autosomal chromosomes from generator
2018-01-01 05:57:21 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- filter rdd of reads uniquely mapped to autosomal + sex chromosomes from generator
2018-01-01 05:57:21 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
- filter rdd of reads uniquely mapped to all chromosomes from generator
Run completed in 24 minutes, 32 seconds.
Total number of tests run: 276
Suites: completed 22, aborted 0
Tests: succeeded 276, failed 0, canceled 0, ignored 1, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-core-spark2_2.10 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-core-spark2_2.10 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-cli-spark2_2.10 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ avocado-cli-spark2_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-cli-spark2_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ avocado-cli-spark2_2.10 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-cli-spark2_2.10 ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-cli-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-cli-spark2_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.10:0.2.13 requires scala version: 2.10.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 8 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scala-2.10.4/classes at 1514815047576
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-cli-spark2_2.10 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scala-2.10.4/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-cli-spark2_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-cli-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-cli-spark2_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.10:0.2.13 requires scala version: 2.10.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 2 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scala-2.10.4/test-classes at 1514815052666
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-cli-spark2_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-cli-spark2_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-cli-spark2_2.10 ---
Discovery starting.
Discovery completed in 122 milliseconds.
Run starting. Expected test count is: 2
ReassembleSuite:
- k-mer length must be positive
MergeDiscoveredSuite:
2018-01-01 05:57:37 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
2018-01-01 05:57:37 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2018-01-01 05:57:41 WARN  DatasetBoundVariantRDD:148 - Saving directly as Parquet from SQL. Options other than compression codec are ignored.
2018-01-01 05:57:41 WARN  Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf.
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
- merge variants discovered from two samples
Run completed in 10 seconds, 421 milliseconds.
Total number of tests run: 2
Suites: completed 3, aborted 0
Tests: succeeded 2, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-cli-spark2_2.10 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-cli-spark2_2.10 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ avocado-cli-spark2_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-cli-spark2_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ avocado-cli-spark2_2.10 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] No files needs to be copied to output directory. Up to date: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/java-templates added.
[INFO] 
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[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ avocado-cli-spark2_2.10 ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-cli-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-cli-spark2_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.10:0.2.13 requires scala version: 2.10.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/annotations:-1: info: compiling
[INFO] Compiling 8 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scala-2.10.4/scoverage-classes at 1514815067466
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [362 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-cli-spark2_2.10 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scala-2.10.4/scoverage-classes
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ avocado-cli-spark2_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-cli-spark2_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-cli-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-cli-spark2_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.10:0.2.13 requires scala version: 2.10.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-cli-spark2_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-cli-spark2_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-cli-spark2_2.10 ---
Discovery starting.
Discovery completed in 122 milliseconds.
Run starting. Expected test count is: 2
ReassembleSuite:
- k-mer length must be positive
MergeDiscoveredSuite:
2018-01-01 05:57:53 WARN  SparkContext:66 - Support for Scala 2.10 is deprecated as of Spark 2.1.0
2018-01-01 05:57:53 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2018-01-01 05:57:57 WARN  DatasetBoundVariantRDD:148 - Saving directly as Parquet from SQL. Options other than compression codec are ignored.
2018-01-01 05:57:58 WARN  Utils:66 - Truncated the string representation of a plan since it was too large. This behavior can be adjusted by setting 'spark.debug.maxToStringFields' in SparkEnv.conf.
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
- merge variants discovered from two samples
Run completed in 10 seconds, 241 milliseconds.
Total number of tests run: 2
Suites: completed 3, aborted 0
Tests: succeeded 2, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-cli-spark2_2.10 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ avocado-cli-spark2_2.10 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO] [scoverage] Generating aggregated cobertura XML report...
[INFO] [scoverage] Generating aggregated scoverage XML report...
[INFO] [scoverage] Generating aggregated scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado: A Variant Caller, Distributed 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- coveralls-maven-plugin:3.0.1:report (default-cli) @ avocado-parent-spark2_2.10 ---
[INFO] Starting Coveralls job for jenkins (3700 / https://amplab.cs.berkeley.edu/jenkins/job/avocado/HADOOP_VERSION=2.3.0,SCALAVER=2.10,SPARK_VERSION=2.0.0,label=centos/3700/)
[INFO] Using repository token <secret>
[INFO] Git commit fa192c0 in master
[INFO] Writing Coveralls data to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/target/coveralls.json...
[INFO] Processing coverage report from /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/target/cobertura.xml
[INFO] Successfully wrote Coveralls data in 139ms
[INFO] Gathered code coverage metrics for 44 source files with 10108 lines of code:
[INFO] - 1591 relevant lines
[INFO] - 1293 covered lines
[INFO] - 298 missed lines
[INFO] Submitting Coveralls data to API
[INFO] Successfully submitted Coveralls data in 1206ms for Job #3700.4
[INFO] https://coveralls.io/jobs/32438670
[INFO] *** It might take hours for Coveralls to update the actual coverage numbers for a job
[INFO]     If you see question marks in the report, please be patient
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed ............ SUCCESS [1.637s]
[INFO] avocado-core: Core variant calling algorithms ..... SUCCESS [49:26.287s]
[INFO] avocado-cli: Command line interface for a distributed variant caller  SUCCESS [41.233s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 50:13.556s
[INFO] Finished at: Mon Jan 01 05:58:06 PST 2018
[INFO] Final Memory: 71M/1477M
[INFO] ------------------------------------------------------------------------

# if those pass, build the distribution package
mvn -U \
    -P distribution \
    package \
    -DskipTests \
    -Dhadoop.version=${HADOOP_VERSION} \
    -Dspark.version=${SPARK_VERSION} \
    -DargLine=${AVOCADO_MVN_TMP_DIR}
+ mvn -U -P distribution package -DskipTests -Dhadoop.version=2.3.0 -Dspark.version=2.0.0 -DargLine=/tmp/avocadoTestMvnOrg439X
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-core-spark2_2.10:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-cli-spark2_2.10:jar:0.0.3-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-distribution-spark2_2.10:pom:0.0.3-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent-spark2_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-parent-spark2_2.10:pom:0.0.3-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 336, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 344, column 25
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed
[INFO] avocado-core: Core variant calling algorithms
[INFO] avocado-cli: Command line interface for a distributed variant caller
[INFO] avocado: distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado: A Variant Caller, Distributed 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent-spark2_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent-spark2_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent-spark2_2.10 ---
[INFO] Modified 0 of 56 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-parent-spark2_2.10 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-parent-spark2_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-parent-spark2_2.10 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ avocado-parent-spark2_2.10 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ avocado-parent-spark2_2.10 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ avocado-parent-spark2_2.10 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-parent-spark2_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-parent-spark2_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ avocado-parent-spark2_2.10 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ avocado-parent-spark2_2.10 ---
[INFO] No source files found
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-core: Core variant calling algorithms 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-core-spark2_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-core-spark2_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-core-spark2_2.10 ---
[INFO] Modified 0 of 47 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-core-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-core-spark2_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.10:0.2.13 requires scala version: 2.10.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-core-spark2_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-core-spark2_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-core-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 26 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-core-spark2_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.10:0.2.13 requires scala version: 2.10.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-core-spark2_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-core-spark2_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-core-spark2_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ avocado-core-spark2_2.10 ---
[INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-core/target/avocado-core-spark2_2.10-0.0.3-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ avocado-core-spark2_2.10 ---
[INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-core/target/avocado-core-spark2_2.10-0.0.3-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ avocado-core-spark2_2.10 ---
[INFO] 
[INFO] --- maven-jar-plugin:2.4:test-jar (default) @ avocado-core-spark2_2.10 ---
[INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-core/target/avocado-core-spark2_2.10-0.0.3-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
Downloading: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-cli-spark2_2.10/0.23.0-SNAPSHOT/maven-metadata.xml
Downloading: http://people.apache.org/repo/m2-snapshot-repository/org/bdgenomics/adam/adam-cli-spark2_2.10/0.23.0-SNAPSHOT/maven-metadata.xml
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Downloading: http://people.apache.org/repo/m2-snapshot-repository/org/bdgenomics/adam/adam-apis-spark2_2.10/0.23.0-SNAPSHOT/maven-metadata.xml
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-cli-spark2_2.10 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ avocado-cli-spark2_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-cli-spark2_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ avocado-cli-spark2_2.10 ---
[INFO] Coping files with filtering to temporary directory.
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 1 resource
[INFO] Copied 1 files to output directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-cli-spark2_2.10 ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ avocado-cli-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-cli-spark2_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.10:0.2.13 requires scala version: 2.10.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 8 source files to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scala-2.10.4/classes at 1514815097717
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ avocado-cli-spark2_2.10 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/scala-2.10.4/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-cli-spark2_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ avocado-cli-spark2_2.10 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 2 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-cli-spark2_2.10 ---
[WARNING]  Expected all dependencies to require Scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.10:0.2.11 requires scala version: 2.10.4
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.10:0.2.13 requires scala version: 2.10.6
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ avocado-cli-spark2_2.10 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ avocado-cli-spark2_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ avocado-cli-spark2_2.10 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ avocado-cli-spark2_2.10 ---
[INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/avocado-cli-spark2_2.10-0.0.3-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ avocado-cli-spark2_2.10 ---
[INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/avocado-cli-spark2_2.10-0.0.3-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ avocado-cli-spark2_2.10 ---
[INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:2.9.1:javadoc' has not been previously called for the module: 'org.bdgenomics.avocado:avocado-core-spark2_2.10:jar:0.0.3-SNAPSHOT'. Trying to invoke it...
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[WARNING] Creating fake javadoc directory to prevent repeated invocations: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-core/target/apidocs
[ERROR] Error fetching link: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-core/target/apidocs/package-list. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.avocado.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_60
Building tree for all the packages and classes...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/About.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/package-frame.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/package-summary.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/package-tree.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/constant-values.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/class-use/About.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/org/bdgenomics/avocado/cli/package-use.html...
Building index for all the packages and classes...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/overview-tree.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/index-all.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/allclasses-frame.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/allclasses-noframe.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/index.html...
Generating /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/avocado-cli-spark2_2.10-0.0.3-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.4.3:shade (default) @ avocado-cli-spark2_2.10 ---
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.10:jar:0.2.11 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-avro:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-format:jar:2.3.0-incubating in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-misc-spark2_2.10:jar:0.2.11 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.10:jar:0.2.11 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.5.5 in the shaded jar.
[INFO] Including com.google.code.findbugs:annotations:jar:2.0.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.10.4 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.23 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-serialization-spark2_2.10:jar:0.2.11 in the shaded jar.
[INFO] Including org.bdgenomics.avocado:avocado-core-spark2_2.10:jar:0.0.3-SNAPSHOT in the shaded jar.
[INFO] Including commons-codec:commons-codec:jar:1.4 in the shaded jar.
[INFO] Including commons-logging:commons-logging:jar:1.1.3 in the shaded jar.
[INFO] Including org.apache.commons:commons-compress:jar:1.4.1 in the shaded jar.
[INFO] Including commons-io:commons-io:jar:1.3.2 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.10:jar:0.23.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.10:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.10:jar:0.2.13 in the shaded jar.
[INFO] Including org.hammerlab:genomic-loci_2.10:jar:1.4.4 in the shaded jar.
[INFO] Including org.hammerlab:args4s_2.10:jar:1.0.0 in the shaded jar.
[INFO] Including org.hammerlab:iterator_2.10:jar:1.0.0 in the shaded jar.
[INFO] Including org.spire-math:spire_2.10:jar:0.11.0 in the shaded jar.
[INFO] Including org.spire-math:spire-macros_2.10:jar:0.11.0 in the shaded jar.
[INFO] Including org.typelevel:machinist_2.10:jar:0.4.1 in the shaded jar.
[INFO] Including org.scalamacros:quasiquotes_2.10:jar:2.0.1 in the shaded jar.
[INFO] Including org.hammerlab:string-utils_2.10:jar:1.0.0 in the shaded jar.
[INFO] Including com.esotericsoftware.kryo:kryo:jar:2.24.0 in the shaded jar.
[INFO] Including com.esotericsoftware.minlog:minlog:jar:1.2 in the shaded jar.
[INFO] Including org.objenesis:objenesis:jar:2.1 in the shaded jar.
[INFO] Including org.bdgenomics.bdg-formats:bdg-formats:jar:0.11.3 in the shaded jar.
[INFO] Including it.unimi.dsi:fastutil:jar:6.6.5 in the shaded jar.
[INFO] Including org.apache.avro:avro:jar:1.8.0 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-core-asl:jar:1.9.13 in the shaded jar.
[INFO] Including org.codehaus.jackson:jackson-mapper-asl:jar:1.9.13 in the shaded jar.
[INFO] Including com.thoughtworks.paranamer:paranamer:jar:2.7 in the shaded jar.
[INFO] Including org.tukaani:xz:jar:1.5 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-scala_2.10:jar:1.8.2 in the shaded jar.
[INFO] Including org.seqdoop:hadoop-bam:jar:7.9.1 in the shaded jar.
[INFO] Including com.github.jsr203hadoop:jsr203hadoop:jar:1.0.3 in the shaded jar.
[INFO] Including com.github.samtools:htsjdk:jar:2.11.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-jexl:jar:2.1.1 in the shaded jar.
[INFO] Including gov.nih.nlm.ncbi:ngs-java:jar:1.2.4 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpclient:jar:4.5.2 in the shaded jar.
[INFO] Including org.apache.httpcomponents:httpcore:jar:4.4.4 in the shaded jar.
[INFO] Including com.google.guava:guava:jar:16.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-codegen-spark2_2.10:jar:0.23.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.10:jar:0.23.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.10:jar:0.23.0-SNAPSHOT in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.10:jar:4.1.0 in the shaded jar.
[INFO] Including com.google.inject:guice:jar:4.1.0 in the shaded jar.
[INFO] Including javax.inject:javax.inject:jar:1 in the shaded jar.
[INFO] Including aopalliance:aopalliance:jar:1.0 in the shaded jar.
[INFO] Including com.google.inject.extensions:guice-multibindings:jar:4.1.0 in the shaded jar.
[INFO] Including org.apache.commons:commons-math3:jar:3.4.1 in the shaded jar.
[INFO] Including com.google.code.findbugs:jsr305:jar:1.3.9 in the shaded jar.
[INFO] Including org.slf4j:slf4j-api:jar:1.7.16 in the shaded jar.
[INFO] Including org.xerial.snappy:snappy-java:jar:1.1.2.4 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-column:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-generator:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.7.0 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson:jar:1.7.0 in the shaded jar.
[INFO] Including org.scala-lang:scala-reflect:jar:2.10.6 in the shaded jar.
[WARNING] annotations-2.0.0.jar, jsr305-1.3.9.jar define 34 overlapping classes: 
[WARNING]   - javax.annotation.RegEx
[WARNING]   - javax.annotation.concurrent.Immutable
[WARNING]   - javax.annotation.meta.TypeQualifierDefault
[WARNING]   - javax.annotation.meta.TypeQualifier
[WARNING]   - javax.annotation.Syntax
[WARNING]   - javax.annotation.CheckForNull
[WARNING]   - javax.annotation.Nonnull
[WARNING]   - javax.annotation.CheckReturnValue
[WARNING]   - javax.annotation.meta.TypeQualifierNickname
[WARNING]   - javax.annotation.MatchesPattern
[WARNING]   - 24 more...
[WARNING] maven-shade-plugin has detected that some class files are
[WARNING] present in two or more JARs. When this happens, only one
[WARNING] single version of the class is copied to the uber jar.
[WARNING] Usually this is not harmful and you can skip these warnings,
[WARNING] otherwise try to manually exclude artifacts based on
[WARNING] mvn dependency:tree -Ddetail=true and the above output.
[WARNING] See http://maven.apache.org/plugins/maven-shade-plugin/
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/avocado-cli-spark2_2.10-0.0.3-SNAPSHOT.jar with /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-cli/target/avocado-cli-spark2_2.10-0.0.3-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado: distribution 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-distribution-spark2_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-distribution-spark2_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-distribution/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.3.2:exec (Generate Documentation) @ avocado-distribution-spark2_2.10 ---
! LaTeX Error: File `ifxetex.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Enter file name: 
! Emergency stop.
<read *> 
         
l.10 \usepackage

pandoc: Error producing PDF
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-distribution-spark2_2.10 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ avocado-distribution-spark2_2.10 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ avocado-distribution-spark2_2.10 ---
[INFO] Test Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-distribution/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ avocado-distribution-spark2_2.10 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:2.2.1:jar-no-fork (attach-sources) @ avocado-distribution-spark2_2.10 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.9.1:jar (attach-javadocs) @ avocado-distribution-spark2_2.10 ---
[INFO] Not executing Javadoc as the project is not a Java classpath-capable package
[INFO] 
[INFO] >>> scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ avocado-distribution-spark2_2.10 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ avocado-distribution-spark2_2.10 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ avocado-distribution-spark2_2.10 ---
[INFO] Source directory: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-distribution/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.3.2:exec (Generate Documentation) @ avocado-distribution-spark2_2.10 ---
! LaTeX Error: File `ifxetex.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Enter file name: 
! Emergency stop.
<read *> 
         
l.10 \usepackage

pandoc: Error producing PDF
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ avocado-distribution-spark2_2.10 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ avocado-distribution-spark2_2.10 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.4.1:single (default) @ avocado-distribution-spark2_2.10 ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-distribution/target/avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT-bin.tar.gz
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/package-tree.html longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/package-frame.html longer than 100 characters.
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/package-summary.html longer than 100 characters.
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/package-use.html longer than 100 characters.
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/class-use/About.html longer than 100 characters.
[INFO] Building tar: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-distribution/target/avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT-bin.tar.bz2
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/package-tree.html longer than 100 characters.
[WARNING] Resulting tar file can only be processed successfully by GNU compatible tar commands
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/package-frame.html longer than 100 characters.
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/package-summary.html longer than 100 characters.
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/package-use.html longer than 100 characters.
[WARNING] Entry: avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT/javadocs/org/bdgenomics/avocado/cli/class-use/About.html longer than 100 characters.
[INFO] Building zip: /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/avocado-distribution/target/avocado-distribution-spark2_2.10-0.0.3-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed ............ SUCCESS [3.207s]
[INFO] avocado-core: Core variant calling algorithms ..... SUCCESS [5.266s]
[INFO] avocado-cli: Command line interface for a distributed variant caller  SUCCESS [17.695s]
[INFO] avocado: distribution ............................. SUCCESS [3.593s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 29.892s
[INFO] Finished at: Mon Jan 01 05:58:37 PST 2018
[INFO] Final Memory: 62M/1439M
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${AVOCADO_MVN_TMP_DIR}
+ find /tmp/avocadoTestMvnOrg439X
/tmp/avocadoTestMvnOrg439X
/tmp/avocadoTestMvnOrg439X/7774011887784205324
/tmp/avocadoTestMvnOrg439X/7774011887784205324/.trio.vcf.crc
/tmp/avocadoTestMvnOrg439X/7774011887784205324/trio.vcf
/tmp/avocadoTestMvnOrg439X/8304214418756111007
/tmp/avocadoTestMvnOrg439X/8304214418756111007/.trio.vcf.crc
/tmp/avocadoTestMvnOrg439X/8304214418756111007/trio.vcf
rm -rf ${AVOCADO_MVN_TMP_DIR}
+ rm -rf /tmp/avocadoTestMvnOrg439X

# and move our poms back to their original values
# this will allow us to pass our porcelain test at the end
if [ ${SPARK_VERSION} == 2.0.0 ];
then
    
    echo "Rewriting POM.xml files back to Spark 1."
    ./scripts/move_to_spark_1.sh
fi
+ '[' 2.0.0 == 2.0.0 ']'
+ echo 'Rewriting POM.xml files back to Spark 1.'
Rewriting POM.xml files back to Spark 1.
+ ./scripts/move_to_spark_1.sh
if [ ${SCALAVER} == 2.11 ];
then
    echo "Rewriting POM.xml files back to Scala 2.10."
    ./scripts/move_to_scala_2.10.sh
fi
+ '[' 2.10 == 2.11 ']'

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${AVOCADO_MVN_TMP_DIR}:sun.io.serialization.extendedDebugInfo=true:g" \
    {} \;
+ find . -name pom.xml -exec sed -i.bak -e 's:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=/tmp/avocadoTestMvnOrg439X:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

if test -n "$(git status --porcelain)"
then
    echo "Applying move_to_xyz script marred a pom.xml file."
    echo "Exiting..."
    exit 1
fi
++ git status --porcelain
+ test -n ''

./scripts/format-source
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/scripts
+ pushd /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/scripts/..
~/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos ~/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos
+ mvn org.scalariform:scalariform-maven-plugin:format license:format
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-core_2.10:jar:0.0.3-SNAPSHOT
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 66, column 15
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 134, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-cli_2.10:jar:0.0.3-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 176, column 23
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 336, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ org.bdgenomics.avocado:avocado-parent_2.10:0.0.3-SNAPSHOT, /home/jenkins/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 344, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.avocado:avocado-parent_2.10:pom:0.0.3-SNAPSHOT
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 336, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 340, column 25
[WARNING] 'dependencyManagement.dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 344, column 25
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed
[INFO] avocado-core: Core variant calling algorithms
[INFO] avocado-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado: A Variant Caller, Distributed 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-parent_2.10 ---
[INFO] Modified 0 of 56 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ avocado-parent_2.10 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-core: Core variant calling algorithms 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-core_2.10 ---
[INFO] Modified 0 of 47 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ avocado-core_2.10 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building avocado-cli: Command line interface for a distributed variant caller 0.0.3-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ avocado-cli_2.10 ---
[INFO] Modified 0 of 9 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ avocado-cli_2.10 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] avocado: A Variant Caller, Distributed ............ SUCCESS [2.485s]
[INFO] avocado-core: Core variant calling algorithms ..... SUCCESS [0.826s]
[INFO] avocado-cli: Command line interface for a distributed variant caller  SUCCESS [0.082s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 3.712s
[INFO] Finished at: Mon Jan 01 05:58:42 PST 2018
[INFO] Final Memory: 16M/1114M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/avocado/HADOOP_VERSION/2.3.0/SCALAVER/2.10/SPARK_VERSION/2.0.0/label/centos
if test -n "$(git status --porcelain)"
then
    echo "Please run './scripts/format-source'"
    exit 1
fi
++ git status --porcelain
+ test -n ''

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

+ '[' 2.0.0 == 1.6.1 ']'
+ '[' 2.0.0 == 2.0.0 ']'
+ '[' 2.3.0 == 2.6.0 ']'
Recording test results
Sending e-mails to: fnothaft@berkeley.edu
Finished: SUCCESS