Why don't you simply use sparklyr for a more R native integration of spark?
Simone Pallotta <simone.pallo...@mail.polimi.it> schrieb am So. 27. Aug.
2017 um 09:47:
> In my R code, I am using rscala package to bridge to a scala method. in
> scala method I have initialized a spark context to be used later.
>
>
> R code:
>
> s <- scala(classpath = "<path to jar>", heap.maximum = "4g")
>
> assign("WrappeR",s$.it.wrapper.r.Wrapper)
>
> WrappeR$init()
>
> where init is a scala function and Wrapper is scala class name (see below).
>
> I created a scala object (Wrapper) with init function
>
>
> scala code:
>
> package it.wrapper.r
>
> object Wrapper {
>
> var Spark_context: SparkContext = _
>
> def init(): Unit = {
>
> val spark_conf = new SparkConf()
>
> .setMaster("local[*]")
>
> .setAppName("GMQL-R")
>
> .set("spark.serializer",
> "org.apache.spark.serializer.KryoSerializer")
>
> .set("spark.executor.memory", "6g")
>
> .set("spark.driver.memory", "2g")
>
> Spark_context = SparkContext.getOrCreate(spark_conf)
>
> }
>
> }
>
> I removed the following code after Spark_context because is not useful.
>
> this code works without flaws under OS X and Linux. Of course window is
> not gentle as other OSes. I checked out my project under windows (I have
> installed scala 2.11.8, java 1.8 and create environment variable JAVA_HOME
> and SCALA_HOME that are mandatory for running rscala package in R, I did
> the same in OS X/Linux)
>
> when I run the jar file as standalone application it works fine under
> windows, but when I invoke the same function from R it fails giving this
> error:
>
> Caused by: java.lang.RuntimeException: java.lang.RuntimeException: class
> org.apache.hadoop.security.JniBasedUnixGroupsMappingWithFallback not
> org.apache.hadoop.security.GroupMappingServiceProvider
>
> at
> org.apache.hadoop.conf.Configuration.getClass(Configuration.java:1752)
>
> at org.apache.hadoop.security.Groups.<init>(Groups.java:55)
>
> at
> org.apache.hadoop.security.Groups.getUserToGroupsMappingService(Groups.java:182)
>
> at
> org.apache.hadoop.security.UserGroupInformation.initialize(UserGroupInformation.java:235)
>
> at
> org.apache.hadoop.security.UserGroupInformation.ensureInitialized(UserGroupInformation.java:214)
>
> at
> org.apache.hadoop.security.UserGroupInformation.getLoginUser(UserGroupInformation.java:669)
>
> at `enter code
> here`org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:571)
>
> at
> org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2391)
>
> at
> org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2391)
>
> at scala.Option.getOrElse(Option.scala:121)
>
> at
> org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2391)
>
> at org.apache.spark.SparkContext.<init>(SparkContext.scala:295)
>
> at org.apache.spark.SparkContext.<init>(SparkContext.scala:145)
>
> at it.polimi.genomics.r.Wrapper$.initGMQL(Wrapper.scala:98)
>
> at $line4.$read$$iw$$iw$$anonfun$1.apply$mcV$sp(<console>:19)
>
> at $line4.$read$$iw$$iw$$anonfun$1.apply(<console>:16)
>
> at $line4.$read$$iw$$iw$$anonfun$1.apply(<console>:16)
>
> ... 46 more
>
> Caused by: java.lang.RuntimeException: class
> org.apache.hadoop.security.JniBasedUnixGroupsMappingWithFallback not
> org.apache.hadoop.security.GroupMappingServiceProvider
>
> at
> org.apache.hadoop.conf.Configuration.getClass(Configuration.java:1746)
>
> ... 62 more
>
> java.lang.reflect.InvocationTargetException
>
> java.lang.RuntimeException: java.lang.RuntimeException: class
> org.apache.hadoop.security.JniBasedUnixGroupsMappingWithFallback not
> org.apache.hadoop.security.GroupMappingServiceProvider
>
>
> Does anyone has already seen this kind of behavior?
>
