Hi All, I am attaching the full procedure I adopted to run R from Apache Zeppelin using Datalayer's zeppelin-R repo on the github but I am facing voidEval function error.It has been one full week that I have been stuck at this problem. Any help would be appreciated.
Please find Steps.txt as the file in which I have written the steps that I have followed. Here is the code I wrote: %r print(1:5) voidEval failed Here is the error log: ERROR StatusLogger No log4j2 configuration file found. Using default configuration: logging only errors to the console. StartRserve: first connect try failed with: Cannot connect: Connection refused StartRserve: waiting for Rserve to start ... (java.lang.UNIXProcess@1c9c5521 ) StartRserve: Rserve> StartRserve: Rserve>Attaching package: ‘SparkR’ StartRserve: Rserve> StartRserve: Rserve>The following objects are masked from ‘package:base’: StartRserve: Rserve> StartRserve: Rserve> intersect, rbind, sample, summary, table StartRserve: Rserve> StartRserve: Rserve>Launching java with spark-submit command /Users/ashish.dalal/downloads/spark/bin/spark-submit sparkr-shell /var/folders/62/5997pbmn0qjg8766pv4mjxwrr8n54y/T//RtmpDWgRDn/backend_portd74679a20ac StartRserve: Rserve>SLF4J: Class path contains multiple SLF4J bindings. StartRserve: Rserve>SLF4J: Found binding in [jar:file:/Users/ashish.dalal/Downloads/incubator-zeppelin/interpreter/R/log4j-slf4j-impl-2.3.jar!/org/slf4j/impl/StaticLoggerBinder.class] StartRserve: Rserve>SLF4J: Found binding in [jar:file:/Users/ashish.dalal/Downloads/incubator-zeppelin/interpreter/R/slf4j-log4j12-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class] StartRserve: Rserve>SLF4J: Found binding in [jar:file:/Users/ashish.dalal/Downloads/incubator-zeppelin/zeppelin-interpreter/target/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class] StartRserve: Rserve>SLF4J: Found binding in [jar:file:/Users/ashish.dalal/Downloads/incubator-zeppelin/zeppelin-server/target/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class] StartRserve: Rserve>SLF4J: Found binding in [jar:file:/Users/ashish.dalal/Downloads/incubator-zeppelin/zeppelin-zengine/target/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class] StartRserve: Rserve>SLF4J: Found binding in [jar:file:/Users/ashish.dalal/Downloads/spark/assembly/target/scala-2.10/spark-assembly-1.5.0-SNAPSHOT-hadoop2.2.0.jar!/org/slf4j/impl/StaticLoggerBinder.class] StartRserve: Rserve>SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. StartRserve: Rserve>SLF4J: Actual binding is of type [org.apache.logging.slf4j.Log4jLoggerFactory] StartRserve: Rserve>ERROR StatusLogger No log4j2 configuration file found. Using default configuration: logging only errors to the console. StartRserve: Rserve>log4j:ERROR setFile(null,true) call failed. StartRserve: Rserve>java.io.FileNotFoundException: (No such file or directory) StartRserve: Rserve> at java.io.FileOutputStream.open(Native Method) StartRserve: Rserve> at java.io.FileOutputStream.<init>(FileOutputStream.java:221) StartRserve: Rserve> at java.io.FileOutputStream.<init>(FileOutputStream.java:142) StartRserve: Rserve> at org.apache.log4j.FileAppender.setFile(FileAppender.java:294) StartRserve: Rserve> at org.apache.log4j.FileAppender.activateOptions(FileAppender.java:165) StartRserve: Rserve> at org.apache.log4j.DailyRollingFileAppender.activateOptions(DailyRollingFileAppender.java:223) StartRserve: Rserve> at org.apache.log4j.config.PropertySetter.activate(PropertySetter.java:307) StartRserve: Rserve> at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:172) StartRserve: Rserve> at org.apache.log4j.config.PropertySetter.setProperties(PropertySetter.java:104) StartRserve: Rserve> at org.apache.log4j.PropertyConfigurator.parseAppender(PropertyConfigurator.java:809) StartRserve: Rserve> at org.apache.log4j.PropertyConfigurator.parseCategory(PropertyConfigurator.java:735) StartRserve: Rserve> at org.apache.log4j.PropertyConfigurator.configureRootCategory(PropertyConfigurator.java:615) StartRserve: Rserve> at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:502) StartRserve: Rserve> at org.apache.log4j.PropertyConfigurator.doConfigure(PropertyConfigurator.java:547) StartRserve: Rserve> at org.apache.log4j.helpers.OptionConverter.selectAndConfigure(OptionConverter.java:483) StartRserve: Rserve> at org.apache.log4j.LogManager.<clinit>(LogManager.java:127) StartRserve: Rserve> at org.apache.log4j.Logger.getLogger(Logger.java:104) StartRserve: Rserve> at org.apache.spark.util.AkkaUtils$.org$apache$spark$util$AkkaUtils$$doCreateActorSystem(AkkaUtils.scala:75) StartRserve: Rserve> at org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:53) StartRserve: Rserve> at org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:52) StartRserve: Rserve> at org.apache.spark.util.Utils$$anonfun$startServiceOnPort$1.apply$mcVI$sp(Utils.scala:2034) StartRserve: Rserve> at scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:141) StartRserve: Rserve> at org.apache.spark.util.Utils$.startServiceOnPort(Utils.scala:2025) StartRserve: Rserve> at org.apache.spark.util.AkkaUtils$.createActorSystem(AkkaUtils.scala:55) StartRserve: Rserve> at org.apache.spark.rpc.akka.AkkaRpcEnvFactory.create(AkkaRpcEnv.scala:253) StartRserve: Rserve> at org.apache.spark.rpc.RpcEnv$.create(RpcEnv.scala:53) StartRserve: Rserve> at org.apache.spark.SparkEnv$.create(SparkEnv.scala:252) StartRserve: Rserve> at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:193) StartRserve: Rserve> at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:267) StartRserve: Rserve> at org.apache.spark.SparkContext.<init>(SparkContext.scala:432) StartRserve: Rserve> at org.apache.spark.api.java.JavaSparkContext.<init>(JavaSparkContext.scala:61) StartRserve: Rserve> at org.apache.spark.api.r.RRDD$.createSparkContext(RRDD.scala:375) StartRserve: Rserve> at org.apache.spark.api.r.RRDD.createSparkContext(RRDD.scala) StartRserve: Rserve> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) StartRserve: Rserve> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) StartRserve: Rserve> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) StartRserve: Rserve> at java.lang.reflect.Method.invoke(Method.java:606) StartRserve: Rserve> at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:132) StartRserve: Rserve> at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:79) StartRserve: Rserve> at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:38) StartRserve: Rserve> at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105) StartRserve: Rserve> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308) StartRserve: Rserve> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294) StartRserve: Rserve> at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:103) StartRserve: Rserve> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308) StartRserve: Rserve> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294) StartRserve: Rserve> at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:244) StartRserve: Rserve> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:308) StartRserve: Rserve> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:294) StartRserve: Rserve> at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:846) 14:30:34.949 [pool-3-thread-2] ERROR io.datalayer.zeppelin.R.RInterpreter - Exception while connecting to Rserve org.rosuda.REngine.Rserve.RserveException: voidEval failed at org.rosuda.REngine.Rserve.RConnection.voidEval(RConnection.java:209) ~[Rserve-1.8.2-SNAPSHOT.jar:?] at io.datalayer.zeppelin.R.RInterpreter.interpret(RInterpreter.java:117) [zeppelin-R-1.0.0-SNAPSHOT.jar:?] at io.datalayer.zeppelin.R.RInterpreter.interpret(RInterpreter.java:98) [zeppelin-R-1.0.0-SNAPSHOT.jar:?] at org.apache.zeppelin.interpreter.ClassloaderInterpreter.interpret(ClassloaderInterpreter.java:57) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at org.apache.zeppelin.interpreter.LazyOpenInterpreter.interpret(LazyOpenInterpreter.java:93) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:276) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at org.apache.zeppelin.scheduler.Job.run(Job.java:170) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at org.apache.zeppelin.scheduler.FIFOScheduler$1.run(FIFOScheduler.java:118) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) [?:1.7.0_79] at java.util.concurrent.FutureTask.run(FutureTask.java:262) [?:1.7.0_79] at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:178) [?:1.7.0_79] at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:292) [?:1.7.0_79] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [?:1.7.0_79] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [?:1.7.0_79] at java.lang.Thread.run(Thread.java:745) [?:1.7.0_79] 14:30:34.995 [pool-3-thread-2] ERROR io.datalayer.zeppelin.R.RInterpreter - Exception while connecting to Rserve org.rosuda.REngine.Rserve.RserveException: voidEval failed at org.rosuda.REngine.Rserve.RConnection.voidEval(RConnection.java:209) ~[Rserve-1.8.2-SNAPSHOT.jar:?] at io.datalayer.zeppelin.R.RInterpreter.interpret(RInterpreter.java:117) [zeppelin-R-1.0.0-SNAPSHOT.jar:?] at org.apache.zeppelin.interpreter.ClassloaderInterpreter.interpret(ClassloaderInterpreter.java:57) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at org.apache.zeppelin.interpreter.LazyOpenInterpreter.interpret(LazyOpenInterpreter.java:93) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:276) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at org.apache.zeppelin.scheduler.Job.run(Job.java:170) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at org.apache.zeppelin.scheduler.FIFOScheduler$1.run(FIFOScheduler.java:118) [zeppelin-interpreter-0.6.0-incubating-SNAPSHOT.jar:0.6.0-incubating-SNAPSHOT] at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) [?:1.7.0_79] at java.util.concurrent.FutureTask.run(FutureTask.java:262) [?:1.7.0_79] at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:178) [?:1.7.0_79] at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:292) [?:1.7.0_79] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) [?:1.7.0_79] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) [?:1.7.0_79] at java.lang.Thread.run(Thread.java:745) [?:1.7.0_79] On Thu, Jul 30, 2015 at 9:25 PM, Ashish Dalal <dalalstree...@gmail.com> wrote: > I am able to see that R interpreter is registered in the Interpreter Group > but when I write R code and evaluate it, it throws an error saying > "voidEval failed". > > Thanks > > On Thu, Jul 30, 2015 at 8:00 PM, <felixcheun...@hotmail.com> wrote: > >> *There* is another effort (that is not GPLv3 licensed) I am part of for >> a SparkR interpreter. >> >> What is the issue you are seeing? >> >> From: Ashish Dalal >> Sent: Wednesday, July 29, 2:02 PM >> Subject: Adding R interpreter to Zeppelin >> To: users@zeppelin.incubator.apache.org >> >> Hi all, >> >> I am working on adding R interpreter to Zeppelin. >> >> There is a github repo by datalayer.io ( >> https://github.com/datalayer/zeppelin-R) and I have added it's >> RInterpreter.java & RInterpreterTest.java along with modifying pom.xml but >> I am still not able to run R code in Apache Zeppelin. >> >> I am able to see the R interpreter registered in the list of interpreters >> when I start running the Zeppelin, but the evaluations for the R code I >> write is not getting done. >> >> Please help if you can. >> >> Thanks! >> >> Regards, >> >> Ashish Dalal >> >> >
1. Go to the github repo at https://github.com/apache/spark and git clone this repo in your downloads directory. 2. Go to your home directory, and make a .Rprofile file by using the vi command. 3. Write in it the following text to set your SparkR home directory. Sys.setenv(SPARK_HOME="/Users/ashish.dalal/downloads/spark") .libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths())) library(SparkR) sc <- sparkR.init(master="local") 4. Make a .profile file in the home directory and set the following maven option inside it: export MAVEN_OPTS="-Xmx512m -XX:MaxPermSize=512m” 5. The place where I have specified the SPARK_HOME = " ", in between " ", write down full path of the directory where spark is installed. Save the file and get back to the terminal. 6. Again go the spark directory via terminal and run the following command to build spark from source enabling SparkR from shell. Command-> build/mvn -DskipTests -Psparkr package 7. Wait for sometime till the spark builds from source. 8. Once the spark is successfully built from source, go to the apache zeppelin repo on github at https://github.com/apache/incubator-zeppelin/ and clone this repo on your local machine in the downloads directory. 9. Build Zeppelin from source by running the following command. mvn clean install -DskipTests -Pspark-1.4 10. Once Zeppelin is successfully built from source, go to the zeppelin-R repo on github at https://github.com/datalayer/zeppelin-R and clone this repo on your local machine in the incubator-zeppelin directory. 11. Change your directory to Zeppelin-R and run the following command mvn install 12. Once Zeppelin-R is successfully built from source, you will see a target folder in your zeppelin-R directory which earlier was not present. 13. create conf/zeppelin-site.xml by copying conf/zeppelin-site.xml.template to conf/zeppelin-site.xml 14. Add your interpreter class name to the zeppelin.interpreters property in conf/zeppelin-site.xml Property value is comma separated [INTERPRETERCLASSNAME] for example, <property> <name>zeppelin.interpreters</name> <value>org.apache.zeppelin.spark.SparkInterpreter,org.apache.zeppelin.spark.PySparkInterpreter,org.apache.zeppelin.spark.SparkSqlInterpreter,org.apache.zeppelin.spark.DepInterpreter,org.apache.zeppelin.markdown.Markdown,org.apache.zeppelin.shell.ShellInterpreter,org.apache.zeppelin.hive.HiveInterpreter,io.datalayer.zeppelin.R.RInterpreter</value> </property> 13. Go to the incubator-zeppelin directory and then go to the interpreter subdirectory, and make a directory named “R”. 14. Copy all the dependency jars in the R folder. For copying the dependencies, first copy the jar files from target folder inside zeppelin-R directory to the R folder inside the incubator-zeppelin/interpreter/ directory. 15. Once the jars from the target folder are copied, go to the zeppelin-R directory and run the following command: mvn dependency:copy-dependencies 16. Once the dependencies are copied to the target folder, you will see a target/dependency folder filled with all the dependencies, including transitive. 17.Now copy all the jar files from the dependency folder to the r folder inside the interpreter directory. 18.Once the files are copied, go to the zeppelin-zengine directory inside the incubator-zeppelin directory and add the RInterpreter class in the zeppelinconfiguration.java file inside the /src/main/java/org/apache/zeppelin/conf/. 19. Now go to the incubator-zeppelin and run mvm install -DskipTests -Pspark-1.4 20. Install Rserve package and load Rserve package in R 21. Install Rserve package and load Rserve package in Rstudio 22. Now run go to the incubator-zeppelin directory and run ./bin/zeppelin-dameon.sh start 23. open localhost:8080 in the web browser and create a new notebook 24. type %r and then write any R code for e.g. print(1:5). 25. Getting a voidEval function error
