CRAN Package Check Results for Package SparkR

Last updated on 2020-05-24 23:47:56 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.4.5 24.07 113.94 138.01 OK
r-devel-linux-x86_64-debian-gcc 2.4.5 20.63 88.71 109.34 OK
r-devel-linux-x86_64-fedora-clang 2.4.5 177.96 OK
r-devel-linux-x86_64-fedora-gcc 2.4.5 168.48 OK
r-devel-windows-ix86+x86_64 2.4.5 59.00 133.00 192.00 OK
r-patched-linux-x86_64 2.4.5 24.12 114.27 138.39 OK
r-patched-solaris-x86 2.4.5 210.10 OK
r-release-linux-x86_64 2.4.5 24.60 114.19 138.79 OK
r-release-osx-x86_64 2.4.5 WARN
r-release-windows-ix86+x86_64 2.4.5 43.00 185.00 228.00 OK
r-oldrel-osx-x86_64 2.4.5 OK
r-oldrel-windows-ix86+x86_64 2.4.5 37.00 174.00 211.00 OK

Check Details

Version: 2.4.5
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘sparkr-vignettes.Rmd’ using rmarkdown
    
    Attaching package: 'SparkR'
    
    The following objects are masked from 'package:stats':
    
     cov, filter, lag, na.omit, predict, sd, var, window
    
    The following objects are masked from 'package:base':
    
     as.data.frame, colnames, colnames<-, drop, endsWith, intersect,
     rank, rbind, sample, startsWith, subset, summary, transform, union
    
    Picked up _JAVA_OPTIONS: -XX:-UsePerfData
    Picked up _JAVA_OPTIONS: -XX:-UsePerfData
    20/05/12 15:36:03 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
    Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
    Setting default log level to "WARN".
    To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
    
    [Stage 0:> (0 + 1) / 1]
    
    
    [Stage 1:> (0 + 1) / 1]20/05/12 15:36:27 ERROR Executor: Exception in task 0.0 in stage 1.0 (TID 1)
    java.net.SocketTimeoutException: Accept timed out
     at java.net.PlainSocketImpl.socketAccept(Native Method)
     at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:409)
     at java.net.ServerSocket.implAccept(ServerSocket.java:545)
     at java.net.ServerSocket.accept(ServerSocket.java:513)
     at org.apache.spark.api.r.RRunner$.createRWorker(RRunner.scala:383)
     at org.apache.spark.api.r.RRunner.compute(RRunner.scala:69)
     at org.apache.spark.api.r.BaseRRDD.compute(RRDD.scala:54)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
     at org.apache.spark.scheduler.Task.run(Task.scala:123)
     at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
     at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
     at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
     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)
    20/05/12 15:36:27 WARN TaskSetManager: Lost task 0.0 in stage 1.0 (TID 1, localhost, executor driver): java.net.SocketTimeoutException: Accept timed out
     at java.net.PlainSocketImpl.socketAccept(Native Method)
     at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:409)
     at java.net.ServerSocket.implAccept(ServerSocket.java:545)
     at java.net.ServerSocket.accept(ServerSocket.java:513)
     at org.apache.spark.api.r.RRunner$.createRWorker(RRunner.scala:383)
     at org.apache.spark.api.r.RRunner.compute(RRunner.scala:69)
     at org.apache.spark.api.r.BaseRRDD.compute(RRDD.scala:54)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
     at org.apache.spark.scheduler.Task.run(Task.scala:123)
     at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
     at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
     at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
     at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
     at java.lang.Thread.run(Thread.java:748)
    
    20/05/12 15:36:27 ERROR TaskSetManager: Task 0 in stage 1.0 failed 1 times; aborting job
    20/05/12 15:36:27 ERROR RBackendHandler: dfToCols on org.apache.spark.sql.api.r.SQLUtils failed
    java.lang.reflect.InvocationTargetException
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:498)
     at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167)
     at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108)
     at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40)
     at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352)
     at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352)
     at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352)
     at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:328)
     at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:302)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352)
     at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1422)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:931)
     at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:163)
     at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:700)
     at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:635)
     at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:552)
     at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:514)
     at io.netty.util.concurrent.SingleThreadEventExecutor$6.run(SingleThreadEventExecutor.java:1044)
     at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
     at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
     at java.lang.Thread.run(Thread.java:748)
    Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1.0 failed 1 times, most recent failure: Lost task 0.0 in stage 1.0 (TID 1, localhost, executor driver): java.net.SocketTimeoutException: Accept timed out
     at java.net.PlainSocketImpl.socketAccept(Native Method)
     at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:409)
     at java.net.ServerSocket.implAccept(ServerSocket.java:545)
     at java.net.ServerSocket.accept(ServerSocket.java:513)
     at org.apache.spark.api.r.RRunner$.createRWorker(RRunner.scala:383)
     at org.apache.spark.api.r.RRunner.compute(RRunner.scala:69)
     at org.apache.spark.api.r.BaseRRDD.compute(RRDD.scala:54)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
     at org.apache.spark.scheduler.Task.run(Task.scala:123)
     at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
     at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
     at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
     at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
     at java.lang.Thread.run(Thread.java:748)
    
    Driver stacktrace:
     at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1891)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1879)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1878)
     at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
     at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
     at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1878)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)
     at scala.Option.foreach(Option.scala:257)
     at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:927)
     at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2112)
     at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2061)
     at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2050)
     at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
     at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:738)
     at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
     at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
     at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
     at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:365)
     at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
     at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3389)
     at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2788)
     at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2788)
     at org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3370)
     at org.apache.spark.sql.execution.SQLExecution$$anonfun$withNewExecutionId$1.apply(SQLExecution.scala:80)
     at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:127)
     at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:75)
     at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3369)
     at org.apache.spark.sql.Dataset.collect(Dataset.scala:2788)
     at org.apache.spark.sql.api.r.SQLUtils$.dfToCols(SQLUtils.scala:181)
     at org.apache.spark.sql.api.r.SQLUtils.dfToCols(SQLUtils.scala)
     ... 37 more
    Caused by: java.net.SocketTimeoutException: Accept timed out
     at java.net.PlainSocketImpl.socketAccept(Native Method)
     at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:409)
     at java.net.ServerSocket.implAccept(ServerSocket.java:545)
     at java.net.ServerSocket.accept(ServerSocket.java:513)
     at org.apache.spark.api.r.RRunner$.createRWorker(RRunner.scala:383)
     at org.apache.spark.api.r.RRunner.compute(RRunner.scala:69)
     at org.apache.spark.api.r.BaseRRDD.compute(RRDD.scala:54)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
     at org.apache.spark.scheduler.Task.run(Task.scala:123)
     at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
     at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
     at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
     at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
     ... 1 more
    Quitting from lines 97-98 (sparkr-vignettes.Rmd)
    Error: processing vignette 'sparkr-vignettes.Rmd' failed with diagnostics:
    org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1.0 failed 1 times, most recent failure: Lost task 0.0 in stage 1.0 (TID 1, localhost, executor driver): java.net.SocketTimeoutException: Accept timed out
     at java.net.PlainSocketImpl.socketAccept(Native Method)
     at java.net.AbstractPlainSocketImpl.accept(AbstractPlainSocketImpl.java:409)
     at java.net.ServerSocket.implAccept(ServerSocket.java:545)
     at java.net.ServerSocket.accept(ServerSocket.java:513)
     at org.apache.spark.api.r.RRunner$.createRWorker(RRunner.scala:383)
     at org.apache.spark.api.r.RRunner.compute(RRunner.scala:69)
     at org.apache.spark.api.r.BaseRRDD.compute(RRDD.scala:54)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:52)
     at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:346)
     at org.apache.spark.rdd.RDD.iterator(RDD.scala:310)
     at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
     at org.apache.spark.scheduler.Task.run(Task.scala:123)
     at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408)
     at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
     at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414)
     at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
     at java.lang.Thread.run(Thread.java:748)
    
    Driver stacktrace:
     at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1891)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1879)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1878)
     at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
     at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
     at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1878)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:927)
     at scala.Option.foreach(Option.scala:257)
     at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:927)
     at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2112)
     at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2061)
     at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2050)
     at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
     at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:738)
     at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
     at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
     at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
     at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:365)
     at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
     at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3389)
     at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2788)
     at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2788)
     at org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3370)
     at org.apache.spark.sql.execution.SQLExecution$$anonfun$withNewExecutionId$1.apply(SQLExecution.scala:80)
     at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:127)
     at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:75)
     at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3369)
     at org.apache.spark.sql.Dataset.collect(Dataset.scala:2788)
     at org.apache.spark.sql.api.r.SQLUtils$.dfToCols(SQLUtils.scala:181)
     at org.apache.spark.sql.api.r.SQLUtils.dfToCols(SQLUtils.scala)
     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
     at java.lang.reflect.Method.invoke(Method.java:498)
     at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167)
     at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108)
     at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40)
     at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352)
     at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352)
     at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352)
     at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:328)
     at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:302)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352)
     at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1422)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374)
     at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360)
     at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:931)
     at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:163)
     at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:700)
     at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:635)
     at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:552)
     at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:514)
     at io.netty.util.concurrent.SingleThreadEventExecutor$6.run(SingleThreadEventExecutor.java:1044)
     a
    --- failed re-building ‘sparkr-vignettes.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘sparkr-vignettes.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64