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Not able to run R script in zeppeling


Dear HDP community,

I am trying to setup R interpreter. R is installed and running on host (means I can run R script in ssh session through command line) and Spark is installed through HDP/ambari platform.

This is my notebook:


1 + 1

which fails like below:

org.apache.zeppelin.interpreter.InterpreterException: sparkr is not responding 
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
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> args <- commandArgs(trailingOnly = TRUE)
> hashCode <- as.integer(args[1])
> port <- as.integer(args[2])
> libPath <- args[3]
> version <- as.integer(args[4])
> timeout <- as.integer(args[5])
> authSecret <- NULL
> if (length(args) >= 6) {
+   authSecret <- args[6]
+ }
> rm(args)
> print(paste("Port ", toString(port)))
[1] "Port  42291"
> print(paste("LibPath ", libPath))
[1] "LibPath  /usr/hdp/"
> .libPaths(c(file.path(libPath), .libPaths()))
> library(SparkR)

Attaching package: ‘SparkR’

The following objects are masked from ‘package:stats’:

    cov, fi> lter, lag, na.omit, predict, sd, var, window

The following objects are masked from ‘package:base’:

i    as.f (is.null(authSecret)) {dat
a+. frame, colnames, colname  SparkR:::connectBackend("localhost",s <p-o,r drop, endsWith, interste,ct, ti
 +r } else {
+   SparkR:::connectBackend("localhost", port, timeout, authSecret)a
+ }
nk, rbind, sample, startsWith, subset, summary, transform, union

    at org.apache.zeppelin.spark.ZeppelinR.waitForRScriptInitialized(
    at org.apache.zeppelin.spark.ZeppelinR.request(
    at org.apache.zeppelin.spark.ZeppelinR.eval(
    at org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(
    at org.apache.zeppelin.scheduler.FIFOScheduler$
    at java.util.concurrent.Executors$
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(
    at java.util.concurrent.ScheduledThreadPoolExecutor$
    at java.util.concurrent.ThreadPoolExecutor.runWorker(
    at java.util.concurrent.ThreadPoolExecutor$

Any thoughts?

thank you very much



@Manuel Sopena Ballesteros

Can you share your Zeppelin R configuration steps? To run Zeppelin with the R Interpreter, the SPARK_HOME environment variable must be set.

The best way to do this is by editing conf/ If it is not set, the R Interpreter will not be able to interface with Spark.



I installed R from sources and copied to /usr/bin

then I went to ambari and setup the zeppeling configuration below:

      export JAVA_HOME={{java64_home}}       export MASTER=yarn-client       export ZEPPELIN_LOG_DIR={{zeppelin_log_dir}}       export ZEPPELIN_PID_DIR={{zeppelin_pid_dir}}       export ZEPPELIN_INTP_CLASSPATH_OVERRIDES="{{external_dependency_conf}}"       export KINIT_FAIL_THRESHOLD=5       export KERBEROS_REFRESH_INTERVAL=1d       export HADOOP_CONF_DIR=/etc/hadoop/conf 
export SPARK_HOME=/usr/hdp/

Hope this helps, please let me know otherwise


Are you still having the issue? If so, can you share your spark interpreter config?