SuccessConsole Output

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OP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added.
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[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
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[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/test/scala added.
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[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-parent_2.11 ---
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
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Downloaded: http://oss.sonatype.org/content/repositories/snapshots/org/bdgenomics/adam/adam-core-spark2_2.11/0.23.0-SNAPSHOT/adam-core-spark2_2.11-0.23.0-20171219.152300-589.jar (3366 KB at 2479.8 KB/sec)
Downloading: http://people.apache.org/repo/m2-snapshot-repository/org/bdgenomics/utils/utils-serialization-spark2_2.11/0.2.13/utils-serialization-spark2_2.11-0.2.13.jar
               
Downloading: http://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-serialization-spark2_2.11/0.2.13/utils-serialization-spark2_2.11-0.2.13.jar
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Downloaded: http://repo.maven.apache.org/maven2/org/bdgenomics/utils/utils-serialization-spark2_2.11/0.2.13/utils-serialization-spark2_2.11-0.2.13.jar (5 KB at 27.8 KB/sec)
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 20 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala:-1: info: compiling
[INFO] Compiling 15 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/classes at 1513766970808
[WARNING] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure
[WARNING]       case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector)
[WARNING]               ^
[WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala:-1: info: compiling
[INFO] Compiling 5 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/test-classes at 1513766980097
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 ---
Discovery starting.
Discovery completed in 473 milliseconds.
Run starting. Expected test count is: 16
NormalizationSuite:
2017-12-20 02:49:48 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2017-12-20 02:49:50 WARN  Executor:66 - 1 block locks were not released by TID = 5:
[rdd_0_1]
2017-12-20 02:49:50 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_0_3]
- mean centers data by columns
- zScores data by rows
2017-12-20 02:49:51 WARN  Executor:66 - 1 block locks were not released by TID = 11:
[rdd_3_3]
2017-12-20 02:49:51 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_3_1]
2017-12-20 02:49:51 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2017-12-20 02:49:51 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2017-12-20 02:49:51 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
2017-12-20 02:49:51 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
2017-12-20 02:49:52 WARN  Executor:66 - 1 block locks were not released by TID = 23:
[rdd_3_3]
2017-12-20 02:49:52 WARN  Executor:66 - 1 block locks were not released by TID = 21:
[rdd_3_1]
- removes top k components of data
2017-12-20 02:49:52 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:49:53 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2017-12-20 02:49:53 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:49:53 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
2017-12-20 02:49:53 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
2017-12-20 02:49:53 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:49:53 WARN  Executor:66 - 1 block locks were not released by TID = 35:
[rdd_23_0]
2017-12-20 02:49:53 WARN  Executor:66 - 1 block locks were not released by TID = 41:
[rdd_23_0]
2017-12-20 02:49:54 WARN  Executor:66 - 1 block locks were not released by TID = 44:
[rdd_4_0]
- produces same results with fixed k
2017-12-20 02:49:54 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:49:54 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2017-12-20 02:49:54 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_7_0]
2017-12-20 02:49:54 WARN  Executor:66 - 1 block locks were not released by TID = 13:
[rdd_7_0]
2017-12-20 02:49:54 WARN  Executor:66 - 1 block locks were not released by TID = 18:
[rdd_4_0]
- filters and centers SVD results
2017-12-20 02:49:54 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:49:55 WARN  Executor:66 - 1 block locks were not released by TID = 8:
[rdd_1_0]
2017-12-20 02:49:55 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_10_0]
2017-12-20 02:49:55 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_10_0]
2017-12-20 02:49:55 WARN  Executor:66 - 1 block locks were not released by TID = 24:
[rdd_21_0]
2017-12-20 02:49:55 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:49:56 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:49:56 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:49:56 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:49:57 WARN  Executor:66 - 1 block locks were not released by TID = 99:
[rdd_64_0]
- filters and normalizes read depth data
HMMSuite:
2017-12-20 02:49:57 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:49:57 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Generates transition matrix for array of distances
- Handles contig boundaries in computing transition matrix
2017-12-20 02:49:57 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:49:57 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Discovers CNVs
DecaSuite:
2017-12-20 02:49:59 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:49:59 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- read XHMM matrix
2017-12-20 02:49:59 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:49:59 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2017-12-20 02:49:59 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_9_0]
2017-12-20 02:49:59 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_9_0]
- write XHMM matrix
CoverageSuite:
- Finds correct first target
- computes coverage for targets
- counts fragments not just reads
- counts imperfectly paired fragments
- incorporates CIGAR into fragment analysis
Run completed in 15 seconds, 242 milliseconds.
Total number of tests run: 16
Suites: completed 5, aborted 0
Tests: succeeded 16, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-core_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 20 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-core_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala:-1: info: compiling
[INFO] Compiling 15 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scala-2.11.8/scoverage-classes at 1513767003502
[WARNING] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/main/scala/org/bdgenomics/deca/util/MLibUtils.scala:63: warning: non-variable type argument Int in type pattern breeze.linalg.SliceVector[Int,Double] is unchecked since it is eliminated by erasure
[WARNING]       case v: SliceVector[Int, Double] => breezeVectorToMLlib(v.toDenseVector)
[WARNING]               ^
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[WARNING] [warn] Could not instrument [EmptyTree$/null]. No pos.
[INFO] [info] Instrumentation completed [1282 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/scoverage-data]
[WARNING] warning: there were 14 deprecation warnings; re-run with -deprecation for details
[WARNING] two warnings found
[INFO] prepare-compile in 0 s
[INFO] compile in 8 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-core_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-core_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-core_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 17 resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-core_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[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) @ deca-core_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-core_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-core_2.11 ---
Discovery starting.
Discovery completed in 490 milliseconds.
Run starting. Expected test count is: 16
NormalizationSuite:
2017-12-20 02:50:14 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2017-12-20 02:50:16 WARN  Executor:66 - 1 block locks were not released by TID = 5:
[rdd_0_1]
2017-12-20 02:50:16 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_0_3]
- mean centers data by columns
- zScores data by rows
2017-12-20 02:50:17 WARN  Executor:66 - 1 block locks were not released by TID = 11:
[rdd_3_3]
2017-12-20 02:50:17 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_3_1]
2017-12-20 02:50:17 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
2017-12-20 02:50:17 WARN  BLAS:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
2017-12-20 02:50:17 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
2017-12-20 02:50:17 WARN  LAPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
2017-12-20 02:50:18 WARN  Executor:66 - 1 block locks were not released by TID = 21:
[rdd_3_1]
2017-12-20 02:50:18 WARN  Executor:66 - 1 block locks were not released by TID = 23:
[rdd_3_3]
- removes top k components of data
2017-12-20 02:50:18 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:50:18 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2017-12-20 02:50:18 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:50:18 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
2017-12-20 02:50:18 WARN  ARPACK:61 - Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
2017-12-20 02:50:19 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:50:19 WARN  Executor:66 - 1 block locks were not released by TID = 35:
[rdd_23_0]
2017-12-20 02:50:19 WARN  Executor:66 - 1 block locks were not released by TID = 41:
[rdd_23_0]
2017-12-20 02:50:19 WARN  Executor:66 - 1 block locks were not released by TID = 44:
[rdd_4_0]
- produces same results with fixed k
2017-12-20 02:50:19 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:50:20 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2017-12-20 02:50:20 WARN  Executor:66 - 1 block locks were not released by TID = 7:
[rdd_7_0]
2017-12-20 02:50:20 WARN  Executor:66 - 1 block locks were not released by TID = 13:
[rdd_7_0]
2017-12-20 02:50:20 WARN  Executor:66 - 1 block locks were not released by TID = 18:
[rdd_4_0]
- filters and centers SVD results
2017-12-20 02:50:20 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:50:20 WARN  Executor:66 - 1 block locks were not released by TID = 8:
[rdd_1_0]
2017-12-20 02:50:20 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_10_0]
2017-12-20 02:50:21 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_10_0]
2017-12-20 02:50:21 WARN  Executor:66 - 1 block locks were not released by TID = 24:
[rdd_21_0]
2017-12-20 02:50:21 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:50:21 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:50:21 WARN  RowMatrix:66 - The input data is not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:50:22 WARN  RowMatrix:66 - The input data was not directly cached, which may hurt performance if its parent RDDs are also uncached.
2017-12-20 02:50:22 WARN  Executor:66 - 1 block locks were not released by TID = 99:
[rdd_64_0]
- filters and normalizes read depth data
HMMSuite:
2017-12-20 02:50:23 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:50:23 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Generates transition matrix for array of distances
- Handles contig boundaries in computing transition matrix
2017-12-20 02:50:23 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:50:23 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- Discovers CNVs
DecaSuite:
2017-12-20 02:50:25 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:50:25 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
- read XHMM matrix
2017-12-20 02:50:25 WARN  Executor:66 - 1 block locks were not released by TID = 0:
[rdd_1_0]
2017-12-20 02:50:25 WARN  Executor:66 - 1 block locks were not released by TID = 6:
[rdd_1_0]
2017-12-20 02:50:25 WARN  Executor:66 - 1 block locks were not released by TID = 9:
[rdd_9_0]
2017-12-20 02:50:26 WARN  Executor:66 - 1 block locks were not released by TID = 15:
[rdd_9_0]
- write XHMM matrix
CoverageSuite:
- Finds correct first target
- computes coverage for targets
- counts fragments not just reads
- counts imperfectly paired fragments
- incorporates CIGAR into fragment analysis
Run completed in 15 seconds, 327 milliseconds.
Total number of tests run: 16
Suites: completed 5, aborted 0
Tests: succeeded 16, failed 0, canceled 0, ignored 0, pending 0
All tests passed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-core_2.11 ---
[INFO] [scoverage] Generating cobertura XML report...
[INFO] [scoverage] Generating scoverage XML report...
[INFO] [scoverage] Generating scoverage HTML report...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[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/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes at 1513767040295
[INFO] prepare-compile in 0 s
[INFO] compile in 4 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala:-1: info: compiling
[INFO] Compiling 1 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/test-classes at 1513767045745
[INFO] prepare-compile in 0 s
[INFO] compile in 3 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:testCompile (default-testCompile) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 ---
Discovery starting.
Discovery completed in 118 milliseconds.
Run starting. Expected test count is: 0
DecaMainSuite:
- no op to test setup !!! IGNORED !!!
Run completed in 184 milliseconds.
Total number of tests run: 0
Suites: completed 2, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 1, pending 0
No tests were executed.
[INFO] 
[INFO] >>> scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[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/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:pre-compile (default-cli) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- maven-resources-plugin:2.6:resources (default-resources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/annotations:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/scoverage-classes at 1513767050111
[INFO] [info] Cleaning datadir [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scoverage-data]
[INFO] [info] Beginning coverage instrumentation
[INFO] [info] Instrumentation completed [312 statements]
[INFO] [info] Wrote instrumentation file [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scoverage-data/scoverage.coverage.xml]
[INFO] [info] Will write measurement data to [/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scoverage-data]
[INFO] prepare-compile in 0 s
[INFO] compile in 6 s
[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/scoverage-classes
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:post-compile (default-cli) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[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) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 ---
Discovery starting.
Discovery completed in 122 milliseconds.
Run starting. Expected test count is: 0
DecaMainSuite:
- no op to test setup !!! IGNORED !!!
Run completed in 191 milliseconds.
Total number of tests run: 0
Suites: completed 2, aborted 0
Tests: succeeded 0, failed 0, canceled 0, ignored 1, pending 0
No tests were executed.
[INFO] 
[INFO] <<< scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 <<<
[INFO] 
[INFO] --- scoverage-maven-plugin:1.1.1:report (default-cli) @ deca-cli_2.11 ---
[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] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.554s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [1:09.449s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [28.022s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1:40.241s
[INFO] Finished at: Wed Dec 20 02:50:58 PST 2017
[INFO] Final Memory: 68M/1489M
[INFO] ------------------------------------------------------------------------

# if those pass, build the distribution package
mvn -U \
    -P distribution \
    package \
    -DskipTests \
    -Dhadoop.version=${HADOOP_VERSION} \
    -Dspark.version=${SPARK_VERSION} \
    -DargLine=${DECA_MVN_TMP_DIR}
+ mvn -U -P distribution package -DskipTests -Dhadoop.version=2.6.0 -Dspark.version=2.0.0 -DargLine=/tmp/decaTestMvn98ARHK9
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.deca:deca-core_2.11:jar:0.1.1-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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-distribution_2.11:pom:0.1.1-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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 357, 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 361, 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 365, 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] deca: Distributed Exome CNV Analyzer
[INFO] deca-core: Core variant calling algorithms
[INFO] deca-cli: Command line interface for a distributed variant caller
[INFO] deca: distribution
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: Distributed Exome CNV Analyzer 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-parent_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-parent_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/src/main/scala added.
[INFO] 
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[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
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[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
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[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] Nothing to compile - all classes are up to date
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[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-core_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT-sources.jar
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[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/deca-core_2.11-0.1.1-SNAPSHOT-tests.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
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[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-cli_2.11 ---
[INFO] 
[INFO] --- git-commit-id-plugin:2.2.1:revision (default) @ deca-cli_2.11 ---
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[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-cli_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala added.
[INFO] 
[INFO] --- templating-maven-plugin:1.0.0:filter-sources (filter-src) @ deca-cli_2.11 ---
[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/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates added.
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
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[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
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[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[WARNING] Multiple versions of scala libraries detected!
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/main/scala:-1: info: compiling
[INFO] /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/generated-sources/java-templates:-1: info: compiling
[INFO] Compiling 10 source files to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes at 1513767068434
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[INFO] 
[INFO] --- maven-compiler-plugin:3.5.1:compile (default-compile) @ deca-cli_2.11 ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 1 source file to /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/scala-2.11.8/classes
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-cli_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/scala added.
[INFO] 
[INFO] --- maven-resources-plugin:2.6:testResources (default-testResources) @ deca-cli_2.11 ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] skip non existing resourceDirectory /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/src/test/resources
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-cli_2.11 ---
[WARNING]  Expected all dependencies to require Scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-metrics-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-cli-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-misc-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-serialization-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.bdgenomics.utils:utils-io-spark2_2.11:0.2.13 requires scala version: 2.11.8
[WARNING]  org.hammerlab:genomic-loci_2.11:1.4.4 requires scala version: 2.11.8
[WARNING]  org.hammerlab:args4s_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:iterator_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  org.hammerlab:string-utils_2.11:1.0.0 requires scala version: 2.11.8
[WARNING]  net.codingwell:scala-guice_2.11:4.1.0 requires scala version: 2.11.8
[WARNING]  com.twitter:chill_2.11:0.8.0 requires scala version: 2.11.7
[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) @ deca-cli_2.11 ---
[INFO] Nothing to compile - all classes are up to date
[INFO] 
[INFO] --- maven-surefire-plugin:2.7:test (default-test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- scalatest-maven-plugin:1.0:test (test) @ deca-cli_2.11 ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:2.4:jar (default-jar) @ deca-cli_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-cli_2.11 ---
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ deca-cli_2.11 ---
[INFO] The goal 'org.apache.maven.plugins:maven-javadoc-plugin:2.10.4:javadoc' has not been previously called for the module: 'org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-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/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/apidocs
[ERROR] Error fetching link: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-core/target/apidocs/package-list. Ignored it.
[INFO] 
Loading source files for package org.bdgenomics.deca.cli...
Constructing Javadoc information...
Standard Doclet version 1.8.0_60
Building tree for all the packages and classes...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/About.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-frame.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-summary.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-tree.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/constant-values.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/class-use/About.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/org/bdgenomics/deca/cli/package-use.html...
Building index for all the packages and classes...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/overview-tree.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/index-all.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/deprecated-list.html...
Building index for all classes...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/allclasses-frame.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/allclasses-noframe.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/index.html...
Generating /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/apidocs/help-doc.html...
[INFO] Building jar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-javadoc.jar
[INFO] 
[INFO] --- maven-shade-plugin:2.4.3:shade (default) @ deca-cli_2.11 ---
[INFO] Including net.fnothaft:jsr203-s3a:jar:0.0.1 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-cli-spark2_2.11:jar:0.2.13 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-column:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-common:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-encoding:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-hadoop:jar:1.8.1 in the shaded jar.
[INFO] Including org.apache.parquet:parquet-jackson: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_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-metrics-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including com.netflix.servo:servo-core:jar:0.12.12 in the shaded jar.
[INFO] Including org.scala-lang:scala-library:jar:2.11.8 in the shaded jar.
[INFO] Including args4j:args4j:jar:2.0.31 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-serialization-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.deca:deca-core_2.11:jar:0.1.1-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:2.4 in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-core-spark2_2.11:jar:0.23.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-io-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.bdgenomics.utils:utils-intervalrdd-spark2_2.11:jar:0.2.13 in the shaded jar.
[INFO] Including org.hammerlab:genomic-loci_2.11:jar:1.4.4 in the shaded jar.
[INFO] Including org.hammerlab:args4s_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including org.hammerlab:iterator_2.11:jar:1.0.0 in the shaded jar.
[INFO] Including org.hammerlab:string-utils_2.11: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:7.9.0 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_2.11:jar:0.23.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-cli-spark2_2.11:jar:0.23.0-SNAPSHOT in the shaded jar.
[INFO] Including org.bdgenomics.adam:adam-apis-spark2_2.11:jar:0.23.0-SNAPSHOT in the shaded jar.
[INFO] Including net.codingwell:scala-guice_2.11: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.scala-lang:scala-reflect:jar:2.11.7 in the shaded jar.
[INFO] Including org.scalanlp:breeze_2.11:jar:0.12 in the shaded jar.
[INFO] Including org.scalanlp:breeze-macros_2.11:jar:0.12 in the shaded jar.
[INFO] Including com.github.fommil.netlib:core:jar:1.1.2 in the shaded jar.
[INFO] Including net.sourceforge.f2j:arpack_combined_all:jar:0.1 in the shaded jar.
[INFO] Including net.sf.opencsv:opencsv:jar:2.3 in the shaded jar.
[INFO] Including com.github.rwl:jtransforms:jar:2.4.0 in the shaded jar.
[INFO] Including junit:junit:jar:4.8.2 in the shaded jar.
[INFO] Including org.spire-math:spire_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including org.spire-math:spire-macros_2.11:jar:0.7.4 in the shaded jar.
[INFO] Including com.chuusai:shapeless_2.11:jar:2.0.0 in the shaded jar.
[INFO] Including org.scalanlp:breeze-natives_2.11:jar:0.12 in the shaded jar.
[INFO] Skipping pom dependency com.github.fommil.netlib:all:pom:1.1.2 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-osx-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:native_ref-java:jar:1.1 in the shaded jar.
[INFO] Including com.github.fommil:jniloader:jar:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-i686:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-win-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-win-i686:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_ref-linux-armhf:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-osx-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:native_system-java:jar:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-linux-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-linux-i686:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-linux-armhf:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-win-x86_64:jar:natives:1.1 in the shaded jar.
[INFO] Including com.github.fommil.netlib:netlib-native_system-win-i686:jar:natives:1.1 in the shaded jar.
[INFO] Replacing original artifact with shaded artifact.
[INFO] Replacing /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT.jar with /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-cli/target/deca-cli_2.11-0.1.1-SNAPSHOT-shaded.jar
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: distribution 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-distribution_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-distribution_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.3.2:exec (Generate Documentation) @ deca-distribution_2.11 ---
! 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 from TeX source
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-distribution_2.11 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ deca-distribution_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-test-source (add-test-source) @ deca-distribution_2.11 ---
[INFO] Test Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/src/test/scala added.
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:testCompile (scala-test-compile-first) @ deca-distribution_2.11 ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-source-plugin:3.0.1:jar-no-fork (attach-sources) @ deca-distribution_2.11 ---
[INFO] 
[INFO] --- maven-javadoc-plugin:2.10.4:jar (attach-javadocs) @ deca-distribution_2.11 ---
[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) @ deca-distribution_2.11 >>>
[INFO] 
[INFO] --- maven-enforcer-plugin:1.0:enforce (enforce-maven) @ deca-distribution_2.11 ---
[INFO] 
[INFO] --- build-helper-maven-plugin:1.10:add-source (add-source) @ deca-distribution_2.11 ---
[INFO] Source directory: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/src/main/scala added.
[INFO] 
[INFO] --- exec-maven-plugin:1.3.2:exec (Generate Documentation) @ deca-distribution_2.11 ---
! 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 from TeX source
[INFO] 
[INFO] <<< scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.11 <<<
[INFO] 
[INFO] --- scala-maven-plugin:3.2.2:doc-jar (attach-scaladocs) @ deca-distribution_2.11 ---
[INFO] No source files found
[INFO] 
[INFO] --- maven-assembly-plugin:2.4.1:single (default) @ deca-distribution_2.11 ---
[INFO] Reading assembly descriptor: src/main/assembly/assembly.xml
[INFO] Building tar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/target/deca-distribution_2.11-0.1.1-SNAPSHOT-bin.tar.gz
[INFO] Building tar: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/target/deca-distribution_2.11-0.1.1-SNAPSHOT-bin.tar.bz2
[INFO] Building zip: /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/deca-distribution/target/deca-distribution_2.11-0.1.1-SNAPSHOT-bin.zip
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [2.637s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [4.557s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [22.950s]
[INFO] deca: distribution ................................ SUCCESS [1.874s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 32.153s
[INFO] Finished at: Wed Dec 20 02:51:31 PST 2017
[INFO] Final Memory: 66M/1106M
[INFO] ------------------------------------------------------------------------

# we are done with maven, so clean up the maven temp dir
find ${DECA_MVN_TMP_DIR}
+ find /tmp/decaTestMvn98ARHK9
/tmp/decaTestMvn98ARHK9
/tmp/decaTestMvn98ARHK9/1513766987712-0
/tmp/decaTestMvn98ARHK9/1513766987712-0/test.txt
/tmp/decaTestMvn98ARHK9/1513766987712-0/.test.txt.crc
/tmp/decaTestMvn98ARHK9/1513767013662-0
/tmp/decaTestMvn98ARHK9/1513767013662-0/test.txt
/tmp/decaTestMvn98ARHK9/1513767013662-0/.test.txt.crc
rm -rf ${DECA_MVN_TMP_DIR}
+ rm -rf /tmp/decaTestMvn98ARHK9

find . -name pom.xml \
    -exec sed -i.bak \
    -e "s:sun.io.serialization.extendedDebugInfo=true -Djava.io.tmpdir=${DECA_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/decaTestMvn98ARHK9:sun.io.serialization.extendedDebugInfo=true:g' '{}' ';'
find . -name "*.bak" -exec rm -f {} \;
+ find . -name '*.bak' -exec rm -f '{}' ';'

./scripts/format-source
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts
+ pushd /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/scripts/..
~/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos ~/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/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.deca:deca-core_2.11:jar:0.1.1-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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-cli_2.11:jar:0.1.1-SNAPSHOT
[WARNING] 'dependencies.dependency.exclusions.exclusion.artifactId' for org.apache.hadoop:hadoop-client:jar with value '*' does not match a valid id pattern. @ line 180, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 357, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 361, 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.deca:deca-parent_2.11:0.1.1-SNAPSHOT, /home/jenkins/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos/pom.xml, line 365, column 25
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.bdgenomics.deca:deca-parent_2.11:pom:0.1.1-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 357, 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 361, 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 365, 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] deca: Distributed Exome CNV Analyzer
[INFO] deca-core: Core variant calling algorithms
[INFO] deca-cli: Command line interface for a distributed variant caller
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca: Distributed Exome CNV Analyzer 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-parent_2.11 ---
[INFO] Modified 0 of 30 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-parent_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-core: Core variant calling algorithms 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-core_2.11 ---
[INFO] Modified 0 of 20 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-core_2.11 ---
[INFO] Updating license headers...
[INFO]                                                                         
[INFO] ------------------------------------------------------------------------
[INFO] Building deca-cli: Command line interface for a distributed variant caller 0.1.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ deca-cli_2.11 ---
[INFO] Modified 0 of 10 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ deca-cli_2.11 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] deca: Distributed Exome CNV Analyzer .............. SUCCESS [1.521s]
[INFO] deca-core: Core variant calling algorithms ........ SUCCESS [0.307s]
[INFO] deca-cli: Command line interface for a distributed variant caller  SUCCESS [0.102s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2.232s
[INFO] Finished at: Wed Dec 20 02:51:35 PST 2017
[INFO] Final Memory: 17M/1113M
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/deca-prb/HADOOP_VERSION/2.6.0/SCALAVER/2.11/SPARK_VERSION/2.0.0/label/centos
if test -n "$(git status --porcelain | grep -v -e html -e pdf)"
then
    echo "Please run './scripts/format-source'"
    exit 1
fi
++ git status --porcelain
++ grep -v -e html -e pdf
+ test -n ''

echo
+ echo

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

Recording test results
Publishing Scoverage XML and HTML report...
Finished: SUCCESS