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https://issues.apache.org/jira/browse/TOREE-478?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
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antonkulaga updated TOREE-478:
------------------------------
Priority: Blocker (was: Major)
> Some dependencies do not resolve
> --------------------------------
>
> Key: TOREE-478
> URL: https://issues.apache.org/jira/browse/TOREE-478
> Project: TOREE
> Issue Type: Bug
> Affects Versions: 0.2.0
> Environment: Linux Mint, docker container based on latest
> jupyter/all-spark-notebook
> https://github.com/antonkulaga/bigdata-docker/blob/master/containers/spark-ml-notebook/Dockerfile
> Reporter: antonkulaga
> Priority: Blocker
>
> Whenever I try to import some libs, like:
> %AddDeps org.bdgenomics.adam adam-core-spark2_2.11 0.24.0 --transitive
> %AddDeps comp.bio.aging adam-playground_2.11 0.0.13 --repository
> https://dl.bintray.com/comp-bio-aging/main/
> And then start using them in a cell:
> import org.bdgenomics.adam.rdd.ADAMContext._
> val genage = sc.loadFasta("/path/to/my/fasta/file"))
> I get:
> lastException = null
> Name: org.apache.spark.SparkException
> Message: Job aborted due to stage failure: ClassNotFound with classloader:
> scala.reflect.internal.util.ScalaClassLoader$URLClassLoader@4c2a056b
> StackTrace: at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1590)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1589)
> at
> scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
> at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
> at
> org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1589)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
> at
> org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
> at scala.Option.foreach(Option.scala:257)
> at
> org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:831)
> at
> org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1823)
> at
> org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1772)
> at
> org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1761)
> at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
> at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:642)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:2034)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:2055)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:2074)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:2099)
> at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:939)
> at
> org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
> at
> org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
> at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
> at org.apache.spark.rdd.RDD.collect(RDD.scala:938)
> at
> org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentRDD$.apply(NucleotideContigFragmentRDD.scala:95)
> at
> org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadFasta$1.apply(ADAMContext.scala:2488)
> at
> org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadFasta$1.apply(ADAMContext.scala:2472)
> at scala.Option.fold(Option.scala:158)
> at org.apache.spark.rdd.Timer.time(Timer.scala:48)
> at org.bdgenomics.adam.rdd.ADAMContext.loadFasta(ADAMContext.scala:2472)
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