[ADAM-2044] Update Spark version to 2.4.3, add move to Scala 2.12 script #2056

heuermh · 2018-09-21T16:42:40Z

Fixes #2044, fixes #2146, fixes #2114, fixes #2098, fixes #2091, fixes #2058

AmplabJenkins · 2018-09-21T16:44:05Z

Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains d43d7a0 # timeout=10Checking out Revision d43d7a0 (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f d43d7a0e351486160c94b3b812a35283c544809dFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.3,2.11,2.2.2,ubuntuTriggering ADAM-prb ? 2.6.2,2.11,2.2.2,ubuntuADAM-prb ? 2.7.3,2.11,2.2.2,ubuntu completed with result FAILUREADAM-prb ? 2.6.2,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-09-28T15:11:42Z

Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 4a64b40 # timeout=10Checking out Revision 4a64b40 (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 4a64b40d237ca102e09b7d3ac46c14036e6de5f3First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,2.2.2,ubuntuTriggering ADAM-prb ? 2.7.3,2.11,2.2.2,ubuntuADAM-prb ? 2.6.2,2.11,2.2.2,ubuntu completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2018-09-28T16:34:03Z

Appears that a new release of bdg-utils may be required with bump to Parquet version 1.8.3

$ mvn test
...
*** RUN ABORTED ***
  java.lang.NoSuchFieldError: BROTLI
  at org.apache.parquet.hadoop.metadata.CompressionCodecName.<clinit>(CompressionCodecName.java:31)
  at org.bdgenomics.adam.rdd.JavaSaveArgs$.$lessinit$greater$default$4(GenomicRDD.scala:78)
  at org.bdgenomics.adam.rdd.SortedGenomicRDDSuite$$anonfun$8.apply$mcV$sp(SortedGenomicRDDSuite.scala:316)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:102)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
  at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
  at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85)
  at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
  at org.scalatest.Transformer.apply(Transformer.scala:22)
  at org.scalatest.Transformer.apply(Transformer.scala:20)
  at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166)
  at org.scalatest.Suite$class.withFixture(Suite.scala:1122)
  at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
  at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
  at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
  at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
  at org.bdgenomics.adam.rdd.SortedGenomicRDDSuite.org$scalatest$BeforeAndAfter$$super$runTest(SortedGenomicRDDSuite.scala:30)

AmplabJenkins · 2018-09-28T16:40:40Z

Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 3cecfcb # timeout=10Checking out Revision 3cecfcb (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 3cecfcb376081b31eb7635b9129a10316497c576First time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,2.2.2,ubuntuTriggering ADAM-prb ? 2.7.3,2.11,2.2.2,ubuntuADAM-prb ? 2.6.2,2.11,2.2.2,ubuntu completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-09-28T16:50:31Z

Test FAILed.
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Build result: FAILURE

[...truncated 3 lines...]Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 85506a7 # timeout=10Checking out Revision 85506a7 (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 85506a75fa0eb7a8c80b613a41248e4e24f0220bFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.6.2,2.11,2.2.2,ubuntuTriggering ADAM-prb ? 2.7.3,2.11,2.2.2,ubuntuADAM-prb ? 2.6.2,2.11,2.2.2,ubuntu completed with result FAILUREADAM-prb ? 2.7.3,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2018-09-30T02:56:56Z

Per the most recent failures, it appears that we now have a conflict between parquet 1.8.3 used in adam and 1.10.0 used in Spark 2.4.0. Bumping the parquet version to 1.10.0 hits the error described further in issue #2058.

$ mvn test
...
- transform reads to variant rdd *** FAILED ***
  org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 3.0 failed 1 times, most recent failure: Lost task 0.0 in stage 3.0 (TID 3, localhost, executor driver): org.apache.avro.SchemaParseException: Can't redefine: list
	at org.apache.avro.Schema$Names.put(Schema.java:1128)
	at org.apache.avro.Schema$NamedSchema.writeNameRef(Schema.java:562)
	at org.apache.avro.Schema$RecordSchema.toJson(Schema.java:690)
	at org.apache.avro.Schema$ArraySchema.toJson(Schema.java:805)
	at org.apache.avro.Schema$UnionSchema.toJson(Schema.java:882)
	at org.apache.avro.Schema$RecordSchema.fieldsToJson(Schema.java:716)
	at org.apache.avro.Schema$RecordSchema.toJson(Schema.java:701)
	at org.apache.avro.Schema$UnionSchema.toJson(Schema.java:882)
	at org.apache.avro.Schema$RecordSchema.fieldsToJson(Schema.java:716)
	at org.apache.avro.Schema$RecordSchema.toJson(Schema.java:701)
	at org.apache.avro.Schema.toString(Schema.java:324)
	at org.apache.avro.SchemaCompatibility.checkReaderWriterCompatibility(SchemaCompatibility.java:68)
	at org.apache.parquet.avro.AvroRecordConverter.isElementType(AvroRecordConverter.java:866)
	at org.apache.parquet.avro.AvroIndexedRecordConverter$AvroArrayConverter.<init>(AvroIndexedRecordConverter.java:333)
	at org.apache.parquet.avro.AvroIndexedRecordConverter.newConverter(AvroIndexedRecordConverter.java:172)
	at org.apache.parquet.avro.AvroIndexedRecordConverter.<init>(AvroIndexedRecordConverter.java:94)
	at org.apache.parquet.avro.AvroIndexedRecordConverter.newConverter(AvroIndexedRecordConverter.java:168)
	at org.apache.parquet.avro.AvroIndexedRecordConverter.<init>(AvroIndexedRecordConverter.java:94)
	at org.apache.parquet.avro.AvroIndexedRecordConverter.<init>(AvroIndexedRecordConverter.java:66)
	at org.apache.parquet.avro.AvroCompatRecordMaterializer.<init>(AvroCompatRecordMaterializer.java:34)
	at org.apache.parquet.avro.AvroReadSupport.newCompatMaterializer(AvroReadSupport.java:144)
	at org.apache.parquet.avro.AvroReadSupport.prepareForRead(AvroReadSupport.java:136)
	at org.apache.parquet.hadoop.InternalParquetRecordReader.initialize(InternalParquetRecordReader.java:204)
	at org.apache.parquet.hadoop.ParquetRecordReader.initializeInternalReader(ParquetRecordReader.java:182)
	at org.apache.parquet.hadoop.ParquetRecordReader.initialize(ParquetRecordReader.java:140)
	at org.apache.spark.rdd.NewHadoopRDD$$anon$1.liftedTree1$1(NewHadoopRDD.scala:199)
	at org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>(NewHadoopRDD.scala:196)
	at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:151)
	at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:70)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
	at org.apache.spark.scheduler.Task.run(Task.scala:121)
	at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:402)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:408)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)

2018-09-29 21:39:47 ERROR TaskSetManager:70 - Task 0 in stage 3.0 failed 1 times; aborting job
  at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1866)
  at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
  at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
  at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1866)
  at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
  at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
  at scala.Option.foreach(Option.scala:257)
  at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2100)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2049)
  at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2038)
  at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
  at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
  at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126)
  at org.apache.spark.rdd.RDD.count(RDD.scala:1168)
  at org.bdgenomics.adam.rdd.read.AlignmentRecordRDDSuite$$anonfun$78.checkSave$6(AlignmentRecordRDDSuite.scala:1551)
  at org.bdgenomics.adam.rdd.read.AlignmentRecordRDDSuite$$anonfun$78.apply$mcV$sp(AlignmentRecordRDDSuite.scala:1579)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply$mcV$sp(SparkFunSuite.scala:102)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
  at org.bdgenomics.utils.misc.SparkFunSuite$$anonfun$sparkTest$1.apply(SparkFunSuite.scala:98)
  at org.scalatest.Transformer$$anonfun$apply$1.apply$mcV$sp(Transformer.scala:22)
  at org.scalatest.OutcomeOf$class.outcomeOf(OutcomeOf.scala:85)
  at org.scalatest.OutcomeOf$.outcomeOf(OutcomeOf.scala:104)
  at org.scalatest.Transformer.apply(Transformer.scala:22)
  at org.scalatest.Transformer.apply(Transformer.scala:20)
  at org.scalatest.FunSuiteLike$$anon$1.apply(FunSuiteLike.scala:166)
  at org.scalatest.Suite$class.withFixture(Suite.scala:1122)
  at org.scalatest.FunSuite.withFixture(FunSuite.scala:1555)
  at org.scalatest.FunSuiteLike$class.invokeWithFixture$1(FunSuiteLike.scala:163)
  at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.FunSuiteLike$$anonfun$runTest$1.apply(FunSuiteLike.scala:175)
  at org.scalatest.SuperEngine.runTestImpl(Engine.scala:306)
  at org.scalatest.FunSuiteLike$class.runTest(FunSuiteLike.scala:175)
  at org.bdgenomics.adam.util.ADAMFunSuite.org$scalatest$BeforeAndAfter$$super$runTest(ADAMFunSuite.scala:24)
  at org.scalatest.BeforeAndAfter$class.runTest(BeforeAndAfter.scala:200)
  at org.bdgenomics.adam.util.ADAMFunSuite.runTest(ADAMFunSuite.scala:24)
  at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208)
  at org.scalatest.FunSuiteLike$$anonfun$runTests$1.apply(FunSuiteLike.scala:208)
  at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:413)
  at org.scalatest.SuperEngine$$anonfun$traverseSubNodes$1$1.apply(Engine.scala:401)
  at scala.collection.immutable.List.foreach(List.scala:392)
  at org.scalatest.SuperEngine.traverseSubNodes$1(Engine.scala:401)
  at org.scalatest.SuperEngine.org$scalatest$SuperEngine$$runTestsInBranch(Engine.scala:396)
  at org.scalatest.SuperEngine.runTestsImpl(Engine.scala:483)
  at org.scalatest.FunSuiteLike$class.runTests(FunSuiteLike.scala:208)
  at org.scalatest.FunSuite.runTests(FunSuite.scala:1555)
  at org.scalatest.Suite$class.run(Suite.scala:1424)
  at org.scalatest.FunSuite.org$scalatest$FunSuiteLike$$super$run(FunSuite.scala:1555)
  at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.FunSuiteLike$$anonfun$run$1.apply(FunSuiteLike.scala:212)
  at org.scalatest.SuperEngine.runImpl(Engine.scala:545)
  at org.scalatest.FunSuiteLike$class.run(FunSuiteLike.scala:212)
  at org.bdgenomics.adam.util.ADAMFunSuite.org$scalatest$BeforeAndAfter$$super$run(ADAMFunSuite.scala:24)
  at org.scalatest.BeforeAndAfter$class.run(BeforeAndAfter.scala:241)
  at org.bdgenomics.adam.util.ADAMFunSuite.run(ADAMFunSuite.scala:24)
  at org.scalatest.tools.SuiteRunner.run(SuiteRunner.scala:55)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2563)
  at org.scalatest.tools.Runner$$anonfun$doRunRunRunDaDoRunRun$3.apply(Runner.scala:2557)
  at scala.collection.immutable.List.foreach(List.scala:392)
  at org.scalatest.tools.Runner$.doRunRunRunDaDoRunRun(Runner.scala:2557)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1044)
  at org.scalatest.tools.Runner$$anonfun$runOptionallyWithPassFailReporter$2.apply(Runner.scala:1043)
  at org.scalatest.tools.Runner$.withClassLoaderAndDispatchReporter(Runner.scala:2722)
  at org.scalatest.tools.Runner$.runOptionallyWithPassFailReporter(Runner.scala:1043)
  at org.scalatest.tools.Runner$.main(Runner.scala:860)
  at org.scalatest.tools.Runner.main(Runner.scala)
  Cause: org.apache.avro.SchemaParseException: Can't redefine: list
  at org.apache.avro.Schema$Names.put(Schema.java:1128)
  at org.apache.avro.Schema$NamedSchema.writeNameRef(Schema.java:562)
  at org.apache.avro.Schema$RecordSchema.toJson(Schema.java:690)
  at org.apache.avro.Schema$ArraySchema.toJson(Schema.java:805)
  at org.apache.avro.Schema$UnionSchema.toJson(Schema.java:882)
  at org.apache.avro.Schema$RecordSchema.fieldsToJson(Schema.java:716)
  at org.apache.avro.Schema$RecordSchema.toJson(Schema.java:701)
  at org.apache.avro.Schema$UnionSchema.toJson(Schema.java:882)
  at org.apache.avro.Schema$RecordSchema.fieldsToJson(Schema.java:716)
  at org.apache.avro.Schema$RecordSchema.toJson(Schema.java:701)
  at org.apache.avro.Schema.toString(Schema.java:324)
  at org.apache.avro.SchemaCompatibility.checkReaderWriterCompatibility(SchemaCompatibility.java:68)
  at org.apache.parquet.avro.AvroRecordConverter.isElementType(AvroRecordConverter.java:866)
  at org.apache.parquet.avro.AvroIndexedRecordConverter$AvroArrayConverter.<init>(AvroIndexedRecordConverter.java:333)
  at org.apache.parquet.avro.AvroIndexedRecordConverter.newConverter(AvroIndexedRecordConverter.java:172)
  at org.apache.parquet.avro.AvroIndexedRecordConverter.<init>(AvroIndexedRecordConverter.java:94)
  at org.apache.parquet.avro.AvroIndexedRecordConverter.newConverter(AvroIndexedRecordConverter.java:168)
  at org.apache.parquet.avro.AvroIndexedRecordConverter.<init>(AvroIndexedRecordConverter.java:94)
  at org.apache.parquet.avro.AvroIndexedRecordConverter.<init>(AvroIndexedRecordConverter.java:66)
  at org.apache.parquet.avro.AvroCompatRecordMaterializer.<init>(AvroCompatRecordMaterializer.java:34)
  at org.apache.parquet.avro.AvroReadSupport.newCompatMaterializer(AvroReadSupport.java:144)
  at org.apache.parquet.avro.AvroReadSupport.prepareForRead(AvroReadSupport.java:136)
  at org.apache.parquet.hadoop.InternalParquetRecordReader.initialize(InternalParquetRecordReader.java:204)
  at org.apache.parquet.hadoop.ParquetRecordReader.initializeInternalReader(ParquetRecordReader.java:182)
  at org.apache.parquet.hadoop.ParquetRecordReader.initialize(ParquetRecordReader.java:140)
  at org.apache.spark.rdd.NewHadoopRDD$$anon$1.liftedTree1$1(NewHadoopRDD.scala:199)
  at org.apache.spark.rdd.NewHadoopRDD$$anon$1.<init>(NewHadoopRDD.scala:196)
  at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:151)
  at org.apache.spark.rdd.NewHadoopRDD.compute(NewHadoopRDD.scala:70)
  at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
  at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
  at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
  at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
  at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
  at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
  at org.apache.spark.scheduler.Task.run(Task.scala:121)
  at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:402)
  at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
  at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:408)
  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
  at java.lang.Thread.run(Thread.java:748)

AmplabJenkins · 2018-12-28T04:33:30Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #2056 of commit 222252e.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse 222252e^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 222252e # timeout=10Checking out Revision 222252e (origin/pr/2056/head) > git config core.sparsecheckout # timeout=10 > git checkout -f 222252e4f5851e0c94b74fac9e008192d4941ebcFirst time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2018-12-28T19:22:21Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #2056 of commit 1262416.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse 1262416^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 1262416 # timeout=10Checking out Revision 1262416 (origin/pr/2056/head) > git config core.sparsecheckout # timeout=10 > git checkout -f 1262416 > git rev-list 222252e # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.2,ubuntuADAM-prb ? 2.7.5,2.11,2.2.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-03-01T18:36:39Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #2056 of commit f2cd5b0 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains fe0dafe # timeout=10Checking out Revision fe0dafe (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f fe0dafed5ce81eac3e581d216809a1199998a5c7First time build. Skipping changelog.Triggering ADAM-prb ? 2.7.5,2.11,2.2.3,ubuntuADAM-prb ? 2.7.5,2.11,2.2.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2019-03-01T18:36:47Z

Rebased to fix merge; squashed commit from #2107

heuermh · 2019-03-01T18:38:11Z

Jenkins, retest this please

AmplabJenkins · 2019-03-01T18:53:27Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #2056 of commit f2cd5b0 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains fe0dafe # timeout=10Checking out Revision fe0dafe (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f fe0dafe > git rev-list fe0dafe # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.3,ubuntuADAM-prb ? 2.7.5,2.11,2.2.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-03-11T02:51:18Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #2056 of commit c0fc042 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 153873f # timeout=10Checking out Revision 153873f (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 153873f > git rev-list fe0dafe # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.3,ubuntuADAM-prb ? 2.7.5,2.11,2.2.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2019-03-11T02:57:07Z

Jenkins, retest this please

AmplabJenkins · 2019-03-11T03:08:49Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #2056 of commit c0fc042 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 153873f # timeout=10Checking out Revision 153873f (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 153873f > git rev-list 153873f # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.2.3,ubuntuADAM-prb ? 2.7.5,2.11,2.2.3,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2019-04-26T20:25:55Z

Rebased, bumped Spark dependency to 2.4.2. Still fails unit tests

AmplabJenkins · 2019-04-26T20:31:06Z

Test FAILed.
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Build result: FAILURE

GitHub pull request #2056 of commit bd5b6e0 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 6faa666 # timeout=10Checking out Revision 6faa666 (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 6faa666 > git rev-list 153873f # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-04-26T22:26:59Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #2056 of commit e1d3cec automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains ddc6f13 # timeout=10Checking out Revision ddc6f13 (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f ddc6f13 > git rev-list 6faa666 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2019-04-26T22:28:26Z

Jenkins, retest this please

heuermh · 2019-04-27T02:17:46Z

Several new compile errors under Scala 2.12

$ ./scripts/move_to_scala_2.12.sh
...
$ mvn clean install
...
[INFO] --- scala-maven-plugin:3.2.2:compile (scala-compile-first) @ adam-core-spark2_2.12 ---
[INFO] working/adam/adam-core/src/main/java:-1: info: compiling
[INFO] working/adam/adam-core/src/main/scala:-1: info: compiling
[INFO] working/adam/adam-core/target/generated-sources/src/main/scala:-1: info: compiling
[INFO] Compiling 136 source files to working/adam/adam-core/target/2.12.6/classes at 1556331645761
[ERROR] working/adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala:3339: error: type mismatch;
[ERROR]  found   : Serializable
[ERROR]  required: org.apache.spark.rdd.RDD[org.bdgenomics.formats.avro.AlignmentRecord]
[ERROR]         loadBam(pathName, stringency).transform(RepairPartitions(_))
[ERROR]                                                                  ^
[ERROR] adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:912: error: value mapPartitionsWithIndex is not a member of Serializable
[ERROR]       newRdd.transform(_.mapPartitionsWithIndex(filterPartition))
[ERROR]                          ^
[ERROR] working/adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:912: error: missing argument list for method filterPartition
[ERROR] Unapplied methods are only converted to functions when a function type is expected.
[ERROR] You can make this conversion explicit by writing `filterPartition _` or `filterPartition(_,_)` instead of `filterPartition`.
[ERROR]       newRdd.transform(_.mapPartitionsWithIndex(filterPartition))
[ERROR]                                                 ^
[ERROR] working/adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3342: error: missing parameter type for expanded function ((x$55: <error>) => x$55.cache())
[ERROR]     transformDataset(_.cache())
[ERROR]                      ^
[ERROR] working/adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala:3346: error: missing parameter type for expanded function ((x$56: <error>) => x$56.persist(sl))
[ERROR]     transformDataset(_.persist(sl))
[ERROR]                      ^
[ERROR] working/adam/adam-core/src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentDataset.scala:431: error: reference to asScalaBuffer is ambiguous;
[ERROR] it is imported twice in the same scope by
[ERROR] import scala.collection.JavaConverters._
[ERROR] and import scala.collection.JavaConversions._
[ERROR]     extractRegions(asScalaBuffer(regions)).toJavaRDD()
[ERROR]                    ^
...
[ERROR] 56 errors found

AmplabJenkins · 2019-04-29T21:04:50Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #2056 of commit 30327b0 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 2948c4a # timeout=10Checking out Revision 2948c4a (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 2948c4a > git rev-list ddc6f13 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-04-29T22:13:43Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
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Build result: FAILURE

GitHub pull request #2056 of commit eba500c automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 0086fa9 # timeout=10Checking out Revision 0086fa9 (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 0086fa9 > git rev-list 2948c4a # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-04-29T23:17:21Z

Test FAILed.
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https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2973/

Build result: FAILURE

GitHub pull request #2056 of commit 874a4f5 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains c4f4ace # timeout=10Checking out Revision c4f4ace (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f c4f4ace > git rev-list 0086fa9 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-04-30T00:05:40Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2974/

Build result: FAILURE

GitHub pull request #2056 of commit 3a771ac automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains e03b030 # timeout=10Checking out Revision e03b030 (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f e03b030 > git rev-list c4f4ace # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2019-04-30T00:07:21Z

Jenkins, retest this please

AmplabJenkins · 2019-04-30T00:33:53Z

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2975/
Test PASSed.

heuermh · 2019-04-30T02:07:01Z

Please review.

Note Spark 2.4.2 was released with the binary distribution defaulting to Scala 2.12 in error. Thus we should probably wait to merge this pull request (and related bdg-utils 0.2.15 release) on the release of 2.4.3, which should be coming soon and will fix this error. Otherwise it will be difficult to update the Jenkins build configuration.

AmplabJenkins · 2019-05-09T14:58:06Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2977/

Build result: FAILURE

GitHub pull request #2056 of commit 488ac7c automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 12a124f # timeout=10Checking out Revision 12a124f (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 12a124f > git rev-list e03b030 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

AmplabJenkins · 2019-05-09T16:41:42Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2978/

Build result: FAILURE

GitHub pull request #2056 of commit 94e124e automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 869e000 # timeout=10Checking out Revision 869e000 (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 869e000 > git rev-list 12a124f # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2019-05-09T16:42:46Z

Jenkins, retest this please

AmplabJenkins · 2019-05-09T16:50:11Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2979/

Build result: FAILURE

GitHub pull request #2056 of commit 94e124e automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 869e000 # timeout=10Checking out Revision 869e000 (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 869e000 > git rev-list 869e000 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2019-05-09T18:42:40Z

Jenkins, retest this please

AmplabJenkins · 2019-05-09T19:08:56Z

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2980/
Test PASSed.

heuermh · 2019-05-09T19:16:09Z

adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformVariants.scala

@@ -127,7 +130,7 @@ class TransformVariants(val args: TransformVariantsArgs)
      stringency = stringency)

    if (args.outputPath.endsWith(".vcf")) {
-      maybeSort(maybeCoalesce(variants.toVariantContexts)).saveAsVcf(args, stringency)
+      maybeSort(maybeCoalesce(variants).toVariantContexts).saveAsVcf(args, stringency)


Note this change may have performance implications, I couldn't figure out how to maintain the generic signature for maybeCoalesce

heuermh · 2019-05-09T21:24:50Z

Ping @akmorrow13 @fnothaft @jpdna for review.

This now works for me with Scala 2.12 against Spark 2.4.3 in local and clustered mode. I'll squash commits after review.

akmorrow13 · 2019-05-09T22:45:27Z

adam-assembly/pom.xml

+          <relocations>
+            <relocation>
+              <pattern>org.apache.parquet.avro</pattern>
+              <shadedPattern>org.bdgenomics.adam.shaded.org.apache.parquet.avro</shadedPattern>


Whats the shade for again?

Mostly, you don't want to know. 😉

Since parquet-mr won't include the pull request with the fix we need for some time, I've had to hack up an older version from source to add the fix, build it in adam, then shade parquet-avro to another package, while excluding the version in the external jar that does not contain the fix, with an extension to maven-shade-plugin to do so correctly.

akmorrow13 · 2019-05-10T16:24:50Z

scripts/move_to_scala_2.11.sh

-find . -name "pom.xml" -exec sed -e "s/2.10.6/2.11.12/g" \
-    -e "s/2.10/2.11/g" \
+find . -name "pom.xml" -exec sed -e "s/2.12.8/2.11.12/g" \
+    -e "s/2.12/2.11/g" \


I don't think these files are being referenced in jenkins-test anymore. Do we want to run jenkins-test on scala 2.11 and 2.12?

Chicken and egg unfortunately, Spark 2.4.x is required for Scala 2.12, and ADAM won't work on Scala 2.12 until this pull request

AmplabJenkins · 2019-05-11T17:36:04Z

Test FAILed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2981/

Build result: FAILURE

GitHub pull request #2056 of commit 9841310 automatically merged.Notifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'[EnvInject] - Loading node environment variables.Building remotely on amp-jenkins-worker-05 (centos spark-test) in workspace /home/jenkins/workspace/ADAM-prbWiping out workspace first.Cloning the remote Git repositoryCloning repository https://github.com/bigdatagenomics/adam.git > git init /home/jenkins/workspace/ADAM-prb # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git --version # timeout=10 > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/heads/:refs/remotes/origin/ # timeout=15 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/:refs/remotes/origin/ # timeout=10 > git config remote.origin.url https://github.com/bigdatagenomics/adam.git # timeout=10Fetching upstream changes from https://github.com/bigdatagenomics/adam.git > git fetch --tags --progress https://github.com/bigdatagenomics/adam.git +refs/pull/:refs/remotes/origin/pr/ # timeout=15 > git rev-parse origin/pr/2056/merge^{commit} # timeout=10 > git branch -a -v --no-abbrev --contains 1859f8c # timeout=10Checking out Revision 1859f8c (origin/pr/2056/merge) > git config core.sparsecheckout # timeout=10 > git checkout -f 1859f8c > git rev-list 869e000 # timeout=10Triggering ADAM-prb ? 2.7.5,2.11,2.3.2,ubuntuADAM-prb ? 2.7.5,2.11,2.3.2,ubuntu completed with result FAILURENotifying endpoint 'HTTP:https://webhooks.gitter.im/e/ac8bb6e9f53357bc8aa8'
Test FAILed.

heuermh · 2019-05-11T18:56:29Z

Jenkins, retest this please

AmplabJenkins · 2019-05-11T19:21:35Z

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2982/
Test PASSed.

heuermh changed the title ~~Update Spark version to 2.4.0-rc1, add move to Scala 2.12 script.~~ Update Spark version to 2.4.0-rc2, add move to Scala 2.12 script. Sep 28, 2018

heuermh force-pushed the spark-2.4.0 branch from 0fe8e09 to 222252e Compare December 28, 2018 04:03

heuermh changed the title ~~Update Spark version to 2.4.0-rc2, add move to Scala 2.12 script.~~ [ADAM-2044] Update Spark version to 2.4.0, add move to Scala 2.12 script Jan 6, 2019

heuermh added this to the 0.26.0 milestone Jan 6, 2019

heuermh modified the milestones: 0.26.0, 0.27.0 Feb 18, 2019

heuermh force-pushed the spark-2.4.0 branch from 1262416 to f2cd5b0 Compare March 1, 2019 18:35

heuermh mentioned this pull request Mar 1, 2019

[ADAM-2106] Update bdg-utils dependency version to 0.2.14 #2107

Closed

heuermh mentioned this pull request Mar 10, 2019

PARQUET-1441: SchemaParseException: Can't redefine: list in AvroIndexedRecordConverter apache/parquet-java#560

Merged

heuermh force-pushed the spark-2.4.0 branch from f2cd5b0 to c0fc042 Compare March 11, 2019 02:48

heuermh force-pushed the spark-2.4.0 branch from c0fc042 to bd5b6e0 Compare April 26, 2019 20:25

heuermh requested review from fnothaft and akmorrow13 April 30, 2019 02:02

heuermh changed the title ~~[ADAM-2044] Update Spark version to 2.4.0, add move to Scala 2.12 script~~ [ADAM-2044] Update Spark version to 2.4.3, add move to Scala 2.12 script May 1, 2019

heuermh commented May 9, 2019

View reviewed changes

akmorrow13 reviewed May 9, 2019

View reviewed changes

heuermh mentioned this pull request May 10, 2019

Update ADAM dependency version to 0.27.0 bigdatagenomics/deca#33

Open

akmorrow13 reviewed May 10, 2019

View reviewed changes

Update Spark version to 2.4.3, add move to Scala 2.12 script.

9841310

heuermh force-pushed the spark-2.4.0 branch from 94e124e to 9841310 Compare May 11, 2019 17:32

heuermh merged commit 4691c2c into bigdatagenomics:master May 11, 2019

heuermh deleted the spark-2.4.0 branch May 11, 2019 19:31

heuermh mentioned this pull request May 11, 2019

NoClassDefFoundError o.a.parquet.hadoop.metadata.CompressionCodecName #1742

Closed

[ADAM-2044] Update Spark version to 2.4.3, add move to Scala 2.12 script #2056

[ADAM-2044] Update Spark version to 2.4.3, add move to Scala 2.12 script #2056

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