CODEWITHSUNDEEP
rapache-sparkapache-spark-sqlsparkr
sharp
sharp

Reputation: 2158

How to load csv file into SparkR on RStudio?

How do you load csv file into SparkR on RStudio? Below are the steps I had to perform to run SparkR on RStudio. I have used read.df to read .csv not sure how else to write this. Not sure if this step is considered to create RDDs. 

#Set sys environment variables
Sys.setenv(SPARK_HOME = "C:/Users/Desktop/spark/spark-1.4.1-bin-hadoop2.6")
.libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))

#Sys.setenv('SPARKR_SUBMIT_ARGS'='"--packages" "com.databricks:spark-csv_2.10:1.0.3" "sparkr-shell"')

#Load libraries
library(SparkR)
library(magrittr)

sc <- sparkR.init(master="local")
sc <- sparkR.init()
sc <- sparkR.init(sparkPackages="com.databricks:spark-csv_2.11:1.0.3")
sqlContext <- sparkRSQL.init(sc)

data <- read.df(sqlContext, "C:/Users/Desktop/DataSets/hello_world.csv", "com.databricks.spark.csv", header="true")

I am getting error: 

Error in writeJobj(con, object) : invalid jobj 1

Upvotes: 5

Views: 1995

Answers (3)

zero323
zero323

Reputation: 330413

Spark 2.0.0+:

You can use csv data source:

loadDF(sqlContext, path="some_path", source="csv", header="true")

without loading spark-csv.

Original answer:

As far as I can tell you're using a wrong version of spark-csv. Pre-built versions of Spark are using Scala 2.10, but you're using Spark CSV for Scala 2.11. Try this instead:

sc <- sparkR.init(sparkPackages="com.databricks:spark-csv_2.10:1.2.0")

Upvotes: 3

sharp
sharp

Reputation: 2158

I appreciate everyone's input and solutions!!! I figured out another way to load .csv file into SparkR RStudio. Here it is: 

#set sc
sc <- sparkR.init(master = "local")
sqlContext <- sparkRSQL.init(sc)

#load .csv 
patients <- read.csv("C:/...") #Insert your .csv file path

df <- createDataFrame(sqlContext, patients)
df
head(df)
str(df)

Upvotes: 1

loicmathieu
loicmathieu

Reputation: 5562

I successfully solve this issue by providing the commons-csv-1.2.jar together with the spark-csv package.

Apparently, spark-csv uses commons-csv but is not package with it.

Using the following SPARKR_SUBMIT_ARGS solved the issue (I use --jars rather than --packages).

Sys.setenv('SPARKR_SUBMIT_ARGS'='"--jars" "/usr/lib/spark-1.5.1-bin-hadoop2.6/lib/spark-csv_2.11-1.2.0.jar,/usr/lib/spark-1.5.1-bin-hadoop2.6/lib/commons-csv-1.2.jar" "sparkr-shell"')

In fact, the rather obscure error

Error in writeJobj(con, object) : invalid jobj 1

Is more clear using the R shell directly instead from R Studio and clearly state

java.lang.NoClassDefFoundError: org/apache/commons/csv/CSVFormat

The needed commons-csv jar can be found here : https://commons.apache.org/proper/commons-csv/download_csv.cgi

Upvotes: 1

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