THANKS !
It appears that was the last dependency for the build. sudo apt-get install -y r-cran-e1071. Shout out to ZOOM https://zoomadmin.com/HowToInstall/UbuntuPackage/r-cran-e1071 again like they say it was "It’s Super Easy! " package knitr was the previous missing dependency which I was able to work out from build error message sudo apt install knitr 'e1071' doesn't appear to be a package name or namespace. package 'e1071' seems to be a formidable package for machine learning algorithms. *** 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) /opt/spark/R + popd + mkdir /opt/spark/dist/conf + cp /opt/spark/conf/fairscheduler.xml.template /opt/spark/conf/log4j.properties.template /opt/spark/conf/metrics.properties.template /opt/spark/conf/slaves.template /opt/spark/conf/spark-defaults.conf.template /opt/spark/conf/spark-env.sh.template /opt/spark/dist/conf + cp /opt/spark/README.md /opt/spark/dist + cp -r /opt/spark/bin /opt/spark/dist + cp -r /opt/spark/python /opt/spark/dist + '[' true == true ']' + rm -f /opt/spark/dist/python/dist/pyspark-3.1.0.dev0.tar.gz + cp -r /opt/spark/sbin /opt/spark/dist + '[' -d /opt/spark/R/lib/SparkR ']' + mkdir -p /opt/spark/dist/R/lib + cp -r /opt/spark/R/lib/SparkR /opt/spark/dist/R/lib + cp /opt/spark/R/lib/sparkr.zip /opt/spark/dist/R/lib + '[' true == true ']' + TARDIR_NAME=spark-3.1.0-SNAPSHOT-bin-custom-spark + TARDIR=/opt/spark/spark-3.1.0-SNAPSHOT-bin-custom-spark + rm -rf /opt/spark/spark-3.1.0-SNAPSHOT-bin-custom-spark + cp -r /opt/spark/dist /opt/spark/spark-3.1.0-SNAPSHOT-bin-custom-spark + tar czf spark-3.1.0-SNAPSHOT-bin-custom-spark.tgz -C /opt/spark spark-3.1.0-SNAPSHOT-bin-custom-spark + rm -rf /opt/spark/spark-3.1.0-SNAPSHOT-bin-custom-spark <http://www.backbutton.co.uk/> On Wed, 24 Jun 2020, 11:07 Hyukjin Kwon, <gurwls...@gmail.com> wrote: > Looks like you haven't installed the 'e1071' package. > > 2020년 6월 24일 (수) 오후 6:49, Anwar AliKhan <anwaralikhan...@gmail.com>님이 작성: > >> ./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) >> >> <http://www.backbutton.co.uk/> >> >>
