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Posted to issues@spark.apache.org by "Shivaram Venkataraman (JIRA)" <ji...@apache.org> on 2015/05/06 06:20:01 UTC
[jira] [Updated] (SPARK-6834) Failed with error: ‘invalid package name’ Error in as.name(name) : attempt to use zero-length variable name
[ https://issues.apache.org/jira/browse/SPARK-6834?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Shivaram Venkataraman updated SPARK-6834:
-----------------------------------------
Target Version/s: 1.5.0 (was: 1.4.0)
> Failed with error: ‘invalid package name’ Error in as.name(name) : attempt to use zero-length variable name
> -----------------------------------------------------------------------------------------------------------
>
> Key: SPARK-6834
> URL: https://issues.apache.org/jira/browse/SPARK-6834
> Project: Spark
> Issue Type: Bug
> Components: SparkR
> Affects Versions: 1.4.0
> Reporter: Shivaram Venkataraman
>
> Context: trying to interface SparkR with foreach. Foreach is an abstraction over several parallel backends. This would enable execution on spark cluster of > 50 R packages including very popular caret and plyr. Simple foreach examples work. caret unfortunately does not.
> I have a repro but it is somewhat complex (it is the main example of model fitting in caret on their website though, not something made on purpose to make SparkR fail). If I find anything more straightforward, I will comment here. Reproduced in an R --vanilla session, but I can uninstall all of my packages, so I may have missed some deps.
> Reproduce with:
> install.packages(c("caret", "foreach", "devtools", "mlbench", "gbm", "survival", "splines"))
> library(caret)
> library(foreach)
> library(devtools)
> install_github("RevolutionAnalytics/doParallelSpark", subdir = "pkg")
> library(doParallelSpark)
> registerDoParallelSpark()
> library(mlbench)
> data(Sonar)
> set.seed(998)
> inTraining <- createDataPartition(Sonar$Class, p = .75, list = FALSE)
> training <- Sonar[ inTraining,]
> testing <- Sonar[-inTraining,]
> fitControl <- trainControl(## 10-fold CV
> method = "repeatedcv",
> number = 10,
> ## repeated ten times
> repeats = 10)
> set.seed(825)
> gbmFit1 <- train(Class ~ ., data = training,
> method = "gbm",
> trControl = fitControl,
> ## This last option is actually one
> ## for gbm() that passes through
> verbose = FALSE)
> Stack trace
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Error in as.name(name) : attempt to use zero-length variable name
> Calls: source ... withVisible -> eval -> eval -> getNamespace -> as.name
> Execution halted
> 15/03/26 14:32:30 ERROR Executor: Exception in task 0.0 in stage 3.0 (TID 5)
> org.apache.spark.SparkException: R computation failed with
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Error in as.name(name) : attempt to use zero-length variable name
> Calls: source ... withVisible -> eval -> eval -> getNamespace -> as.name
> Execution halted
> at edu.berkeley.cs.amplab.sparkr.BaseRRDD.compute(RRDD.scala:80)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:229)
> at edu.berkeley.cs.amplab.sparkr.BaseRRDD.compute(RRDD.scala:32)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:229)
> at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
> at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
> at org.apache.spark.scheduler.Task.run(Task.scala:54)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:177)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at java.lang.Thread.run(Thread.java:745)
> 15/03/26 14:32:30 WARN TaskSetManager: Lost task 0.0 in stage 3.0 (TID 5, localhost): org.apache.spark.SparkException: R computation failed with
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Error in as.name(name) : attempt to use zero-length variable name
> Calls: source ... withVisible -> eval -> eval -> getNamespace -> as.name
> Execution halted
> edu.berkeley.cs.amplab.sparkr.BaseRRDD.compute(RRDD.scala:80)
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> org.apache.spark.rdd.RDD.iterator(RDD.scala:229)
> edu.berkeley.cs.amplab.sparkr.BaseRRDD.compute(RRDD.scala:32)
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> org.apache.spark.rdd.RDD.iterator(RDD.scala:229)
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
> org.apache.spark.scheduler.Task.run(Task.scala:54)
> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:177)
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> java.lang.Thread.run(Thread.java:745)
> 15/03/26 14:32:30 ERROR TaskSetManager: Task 0 in stage 3.0 failed 1 times; aborting job
> collect on 33 failed with java.lang.reflect.InvocationTargetException
> java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at edu.berkeley.cs.amplab.sparkr.SparkRBackendHandler.handleMethodCall(SparkRBackendHandler.scala:111)
> at edu.berkeley.cs.amplab.sparkr.SparkRBackendHandler.channelRead0(SparkRBackendHandler.scala:58)
> at edu.berkeley.cs.amplab.sparkr.SparkRBackendHandler.channelRead0(SparkRBackendHandler.scala:19)
> at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333)
> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319)
> at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333)
> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319)
> at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:163)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:333)
> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:319)
> at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:787)
> at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:130)
> at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:511)
> at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:468)
> at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:382)
> at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:354)
> at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116)
> at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:137)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: 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 5, localhost): org.apache.spark.SparkException: R computation failed with
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Failed with error: ‘invalid package name’
> Error in as.name(name) : attempt to use zero-length variable name
> Calls: source ... withVisible -> eval -> eval -> getNamespace -> as.name
> Execution halted
> edu.berkeley.cs.amplab.sparkr.BaseRRDD.compute(RRDD.scala:80)
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> org.apache.spark.rdd.RDD.iterator(RDD.scala:229)
> edu.berkeley.cs.amplab.sparkr.BaseRRDD.compute(RRDD.scala:32)
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:262)
> org.apache.spark.rdd.RDD.iterator(RDD.scala:229)
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
> org.apache.spark.scheduler.Task.run(Task.scala:54)
> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:177)
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> java.lang.Thread.run(Thread.java:745)
> Driver stacktrace:
> at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1185)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1174)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1173)
> at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
> at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
> at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1173)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:688)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:688)
> at scala.Option.foreach(Option.scala:236)
> at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:688)
> at org.apache.spark.scheduler.DAGSchedulerEventProcessActor$$anonfun$receive$2.applyOrElse(DAGScheduler.scala:1391)
> at akka.actor.ActorCell.receiveMessage(ActorCell.scala:498)
> at akka.actor.ActorCell.invoke(ActorCell.scala:456)
> at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:237)
> at akka.dispatch.Mailbox.run(Mailbox.scala:219)
> at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:386)
> at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
> at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
> at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
> at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
> Error: returnStatus == 0 is not TRUE
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