./dev/make-distribution.sh --name custom-spark --pip --r --tgz -Psparkr
-Phive -Phive-thriftserver -Pmesos -Pyarn -Pkubernetes
<http://www.backbutton.co.uk/>
minor error Spark r test failed , I don't use r so it doesn't effect me.
***installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation
path
* DONE (SparkR)
++ cd /opt/spark/R/lib
++ jar cfM /opt/spark/R/lib/sparkr.zip SparkR
++ popd
++ cd /opt/spark/R/..
++ pwd
+ SPARK_HOME=/opt/spark
+ . /opt/spark/bin/load-spark-env.sh
++ '[' -z /opt/spark ']'
++ SPARK_ENV_SH=spark-env.sh
++ '[' -z '' ']'
++ export SPARK_ENV_LOADED=1
++ SPARK_ENV_LOADED=1
++ export SPARK_CONF_DIR=/opt/spark/conf
++ SPARK_CONF_DIR=/opt/spark/conf
++ SPARK_ENV_SH=/opt/spark/conf/spark-env.sh
++ [[ -f /opt/spark/conf/spark-env.sh ]]
++ set -a
++ . /opt/spark/conf/spark-env.sh
+++ export SPARK_LOCAL_IP=192.168.0.786
+++ SPARK_LOCAL_IP=192.168.0.786
++ set +a
++ export SPARK_SCALA_VERSION=2.12
++ SPARK_SCALA_VERSION=2.12
+ '[' -f /opt/spark/RELEASE ']'
+ SPARK_JARS_DIR=/opt/spark/assembly/target/scala-2.12/jars
+ '[' -d /opt/spark/assembly/target/scala-2.12/jars ']'
+ SPARK_HOME=/opt/spark
+ /usr/bin/R CMD build /opt/spark/R/pkg
* checking for file ‘/opt/spark/R/pkg/DESCRIPTION’ ... OK
* preparing ‘SparkR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- 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
20/06/24 10:23:54 WARN NativeCodeLoader: Unable to load native-hadoop
library for your platform... using builtin-java classes where applicable
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 9:=================================================> (88 + 1) /
100]
[Stage 13:=======================================> (147 + 1) /
200]
20/06/24 10:24:04 WARN Instrumentation: [79237008] regParam is zero, which
might cause numerical instability and overfitting.
20/06/24 10:24:04 WARN BLAS: Failed to load implementation from:
com.github.fommil.netlib.NativeSystemBLAS
20/06/24 10:24:04 WARN BLAS: Failed to load implementation from:
com.github.fommil.netlib.NativeRefBLAS
20/06/24 10:24:04 WARN LAPACK: Failed to load implementation from:
com.github.fommil.netlib.NativeSystemLAPACK
20/06/24 10:24:04 WARN LAPACK: Failed to load implementation from:
com.github.fommil.netlib.NativeRefLAPACK
20/06/24 10:24:09 WARN package: Truncated the string representation of a
plan since it was too large. This behavior can be adjusted by setting
'spark.sql.debug.maxToStringFields'.
[Stage 67:============> (45 + 1) /
200]
[Stage 67:=================> (62 + 1) /
200]
[Stage 67:======================> (80 + 1) /
200]
[Stage 67:==========================> (98 + 1) /
200]
[Stage 67:==============================> (114 + 1) /
200]
[Stage 67:===================================> (132 + 1) /
200]
[Stage 67:=======================================> (148 + 1) /
200]
[Stage 67:============================================> (166 + 1) /
200]
[Stage 67:=================================================> (184 + 1) /
200]
[Stage 69:============> (44 + 1) /
200]
[Stage 69:================> (61 + 1) /
200]
[Stage 69:=====================> (79 + 1) /
200]
[Stage 69:==========================> (97 + 1) /
200]
[Stage 69:===============================> (116 + 1) /
200]
[Stage 69:====================================> (134 + 1) /
200]
[Stage 69:=========================================> (152 + 1) /
200]
[Stage 69:=============================================> (169 + 1) /
200]
[Stage 69:==================================================> (187 + 1) /
200]
[Stage 70:> (0 + 1)
/ 5]
20/06/24 10:24:14 ERROR Executor: Exception in task 0.0 in stage 70.0 (TID
1148)
org.apache.spark.SparkException: R unexpectedly exited.
R worker produced errors: Error in FUN(X[[i]], ...) :
requireNamespace("e1071", quietly = TRUE) is not TRUE
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:144)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:137)
at
scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:128)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.hasNext(BaseRRunner.scala:113)
at scala.collection.Iterator.foreach(Iterator.scala:941)
at scala.collection.Iterator.foreach$(Iterator.scala:941)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.foreach(BaseRRunner.scala:102)
at
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
at
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>(TraversableOnce.scala:315)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>$(TraversableOnce.scala:313)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.to(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
at
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toBuffer(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
at
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toArray(BaseRRunner.scala:102)
at org.apache.spark.rdd.RDD.$anonfun$collect$2(RDD.scala:1030)
at
org.apache.spark.SparkContext.$anonfun$runJob$5(SparkContext.scala:2148)
at
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:127)
at
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:464)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:467)
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)
Caused by: java.io.EOFException
at java.io.DataInputStream.readInt(DataInputStream.java:392)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:98)
... 27 more
20/06/24 10:24:14 WARN TaskSetManager: Lost task 0.0 in stage 70.0 (TID
1148, 192.168.0.38, executor driver): org.apache.spark.SparkException: R
unexpectedly exited.
R worker produced errors: Error in FUN(X[[i]], ...) :
requireNamespace("e1071", quietly = TRUE) is not TRUE
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:144)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:137)
at
scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:128)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.hasNext(BaseRRunner.scala:113)
at scala.collection.Iterator.foreach(Iterator.scala:941)
at scala.collection.Iterator.foreach$(Iterator.scala:941)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.foreach(BaseRRunner.scala:102)
at
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
at
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>(TraversableOnce.scala:315)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>$(TraversableOnce.scala:313)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.to(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
at
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toBuffer(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
at
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toArray(BaseRRunner.scala:102)
at org.apache.spark.rdd.RDD.$anonfun$collect$2(RDD.scala:1030)
at
org.apache.spark.SparkContext.$anonfun$runJob$5(SparkContext.scala:2148)
at
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:127)
at
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:464)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:467)
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)
Caused by: java.io.EOFException
at java.io.DataInputStream.readInt(DataInputStream.java:392)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:98)
... 27 more
20/06/24 10:24:14 ERROR TaskSetManager: Task 0 in stage 70.0 failed 1
times; aborting job
20/06/24 10:24:14 ERROR RBackendHandler: collect on 358 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:164)
at
org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:105)
at
org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:39)
at
io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:99)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at
io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:286)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at
io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at
io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:321)
at
io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:295)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at
io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1410)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:919)
at
io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:163)
at
io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:714)
at
io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:650)
at
io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:576)
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:493)
at
io.netty.util.concurrent.SingleThreadEventExecutor$4.run(SingleThreadEventExecutor.java:989)
at
io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74)
at
io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.spark.SparkException: Job aborted due to stage
failure: Task 0 in stage 70.0 failed 1 times, most recent failure: Lost
task 0.0 in stage 70.0 (TID 1148, 192.168.0.38, executor driver):
org.apache.spark.SparkException: R unexpectedly exited.
R worker produced errors: Error in FUN(X[[i]], ...) :
requireNamespace("e1071", quietly = TRUE) is not TRUE
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:144)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:137)
at
scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:128)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.hasNext(BaseRRunner.scala:113)
at scala.collection.Iterator.foreach(Iterator.scala:941)
at scala.collection.Iterator.foreach$(Iterator.scala:941)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.foreach(BaseRRunner.scala:102)
at
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
at
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>(TraversableOnce.scala:315)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>$(TraversableOnce.scala:313)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.to(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
at
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toBuffer(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
at
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toArray(BaseRRunner.scala:102)
at org.apache.spark.rdd.RDD.$anonfun$collect$2(RDD.scala:1030)
at
org.apache.spark.SparkContext.$anonfun$runJob$5(SparkContext.scala:2148)
at
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:127)
at
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:464)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:467)
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)
Caused by: java.io.EOFException
at java.io.DataInputStream.readInt(DataInputStream.java:392)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:98)
... 27 more
Driver stacktrace:
at
org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2117)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2066)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2065)
at
scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at
scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at
scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at
org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2065)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1021)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1021)
at scala.Option.foreach(Option.scala:407)
at
org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1021)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2297)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2246)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2235)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
at
org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:823)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2108)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2129)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2148)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2173)
at org.apache.spark.rdd.RDD.$anonfun$collect$1(RDD.scala:1030)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:414)
at org.apache.spark.rdd.RDD.collect(RDD.scala:1029)
at
org.apache.spark.api.java.JavaRDDLike.collect(JavaRDDLike.scala:361)
at
org.apache.spark.api.java.JavaRDDLike.collect$(JavaRDDLike.scala:360)
at
org.apache.spark.api.java.AbstractJavaRDDLike.collect(JavaRDDLike.scala:45)
... 37 more
Caused by: org.apache.spark.SparkException: R unexpectedly exited.
R worker produced errors: Error in FUN(X[[i]], ...) :
requireNamespace("e1071", quietly = TRUE) is not TRUE
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:144)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:137)
at
scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:128)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.hasNext(BaseRRunner.scala:113)
at scala.collection.Iterator.foreach(Iterator.scala:941)
at scala.collection.Iterator.foreach$(Iterator.scala:941)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.foreach(BaseRRunner.scala:102)
at
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
at
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>(TraversableOnce.scala:315)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>$(TraversableOnce.scala:313)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.to(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
at
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toBuffer(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
at
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toArray(BaseRRunner.scala:102)
at org.apache.spark.rdd.RDD.$anonfun$collect$2(RDD.scala:1030)
at
org.apache.spark.SparkContext.$anonfun$runJob$5(SparkContext.scala:2148)
at
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:127)
at
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:464)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:467)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
... 1 more
Caused by: java.io.EOFException
at java.io.DataInputStream.readInt(DataInputStream.java:392)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:98)
... 27 more
20/06/24 10:24:14 ERROR RRunner: R Writer thread got an exception
org.apache.spark.TaskKilledException
at
org.apache.spark.TaskContextImpl.killTaskIfInterrupted(TaskContextImpl.scala:156)
at
org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:36)
at
org.apache.spark.api.r.BaseRRunner$WriterThread.run(BaseRRunner.scala:197)
Quitting from lines 470-471 (sparkr-vignettes.Rmd)
Error: processing vignette 'sparkr-vignettes.Rmd' failed with diagnostics:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0
in stage 70.0 failed 1 times, most recent failure: Lost task 0.0 in stage
70.0 (TID 1148, 192.168.0.38, executor driver):
org.apache.spark.SparkException: R unexpectedly exited.
R worker produced errors: Error in FUN(X[[i]], ...) :
requireNamespace("e1071", quietly = TRUE) is not TRUE
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:144)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator$$anonfun$1.applyOrElse(BaseRRunner.scala:137)
at
scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:128)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.hasNext(BaseRRunner.scala:113)
at scala.collection.Iterator.foreach(Iterator.scala:941)
at scala.collection.Iterator.foreach$(Iterator.scala:941)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.foreach(BaseRRunner.scala:102)
at
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
at
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
at
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>(TraversableOnce.scala:315)
at scala.collection.TraversableOnce.to
<http://scala.collection.traversableonce.to/>$(TraversableOnce.scala:313)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.to(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
at
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toBuffer(BaseRRunner.scala:102)
at
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
at
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
at
org.apache.spark.api.r.BaseRRunner$ReaderIterator.toArray(BaseRRunner.scala:102)
at org.apache.spark.rdd.RDD.$anonfun$collect$2(RDD.scala:1030)
at
org.apache.spark.SparkContext.$anonfun$runJob$5(SparkContext.scala:2148)
at
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
at org.apache.spark.scheduler.Task.run(Task.scala:127)
at
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:464)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:467)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.io.EOFException
at java.io.DataInputStream.readInt(DataInputStream.java:392)
at org.apache.spark.api.r.RRunner$$anon$1.read(RRunner.scala:98)
... 27 more
Driver stacktrace:
at
org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2117)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2066)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2065)
at
scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at
scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at
scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at
org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2065)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1021)
at
org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1021)
at scala.Option.foreach(Option.scala:407)
at
org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1021)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2297)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2246)
at
org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2235)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
at
org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:823)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2108)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2129)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2148)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2173)
at org.apache.spark.rdd.RDD.$anonfun$collect$1(RDD.scala:1030)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at
org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:414)
at org.apache.spark.rdd.RDD.collect(RDD.scala:1029)
at
org.apache.spark.api.java.JavaRDDLike.collect(JavaRDDLike.scala:361)
at
org.apache.spark.api.java.JavaRDDLike.collect$(JavaRDDLike.scala:360)
at
org.apache.spark.api.java.AbstractJavaRDDLike.collect(JavaRDDLike.scala:45)
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:164)
at
org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:105)
at
org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:39)
at
io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:99)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at
io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:286)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at
io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at
io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:321)
at
io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:295)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:357)
at
io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1410)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:379)
at
io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:365)
at
io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:919)
at
io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:163)
at
io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:714)
at
io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:650)
at
io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:576)
at io.netty.channel.nio.NioEventLoop.run(NioEventLo
--- failed re-building ‘sparkr-vignettes.Rmd’
SUMMARY: processing the following file failed:
‘sparkr-vignettes.Rmd’
Error: Vignette re-building failed.
Execution halted
20/06/24 10:24:15 WARN TaskSetManager: Lost task 1.0 in stage 70.0 (TID
1149, 192.168.0.38, executor driver): TaskKilled (Stage cancelled)
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