I'm a new user of SparkR. I'm trying to load a csv file into R using SparkR.
Sys.setenv(SPARK_HOME="/usr/local/bin/spark-1.5.1-bin-hadoop2.6")
.libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))
library(SparkR)
sc <- sparkR.init(master="local", sparkPackages="com.databricks:spark-csv_2.11:1.0.3")
sqlContext <- sparkRSQL.init(sc)
I used a subset of nyc flights dataset just for testing. It only has 4 rows and 4 columns: gyear month day dep_time 2013 1 1 517 2013 1 1 533 2013 1 1 542 2013 1 1 544
n5 <- read.df(sqlContext, "/users/zhiyi.zhang/Downloads/n5.csv", "com.databricks.spark.csv", header="true")
head(n5)
Then I saw these errors when I wanted to look at the data:
`15/11/03 13:45:53 ERROR CsvRelation$: Exception while parsing line: 2013,1,1,517.
java.lang.ClassCastException: java.lang.String cannot be cast to org.apache.spark.unsafe.types.UTF8String
at org.apache.spark.sql.catalyst.expressions.BaseGenericInternalRow$class.getUTF8String(rows.scala:45)
at org.apache.spark.sql.catalyst.expressions.GenericMutableRow.getUTF8String(rows.scala:247)
at org.apache.spark.sql.catalyst.expressions.BoundReference.eval(BoundAttribute.scala:49)
at org.apache.spark.sql.catalyst.expressions.UnaryExpression.eval(Expression.scala:247)
at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:82)
at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:61)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:150)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:130)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:308)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
at scala.collection.AbstractIterator.to(Iterator.scala:1157)
at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$5.apply(SparkPlan.scala:215)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$5.apply(SparkPlan.scala:215)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1848)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1848)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
15/11/03 13:45:53 ERROR CsvRelation$: Exception while parsing line: 2013,1,1,533.
java.lang.ClassCastException: java.lang.String cannot be cast to org.apache.spark.unsafe.types.UTF8String
at org.apache.spark.sql.catalyst.expressions.BaseGenericInternalRow$class.getUTF8String(rows.scala:45)
at org.apache.spark.sql.catalyst.expressions.GenericMutableRow.getUTF8String(rows.scala:247)
at org.apache.spark.sql.catalyst.expressions.BoundReference.eval(BoundAttribute.scala:49)
at org.apache.spark.sql.catalyst.expressions.UnaryExpression.eval(Expression.scala:247)
at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:82)
at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:61)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:150)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:130)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:308)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
at scala.collection.AbstractIterator.to(Iterator.scala:1157)
at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$5.apply(SparkPlan.scala:215)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$5.apply(SparkPlan.scala:215)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1848)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1848)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
15/11/03 13:45:53 ERROR CsvRelation$: Exception while parsing line: 2013,1,1,542.
java.lang.ClassCastException: java.lang.String cannot be cast to org.apache.spark.unsafe.types.UTF8String
at org.apache.spark.sql.catalyst.expressions.BaseGenericInternalRow$class.getUTF8String(rows.scala:45)
at org.apache.spark.sql.catalyst.expressions.GenericMutableRow.getUTF8String(rows.scala:247)
at org.apache.spark.sql.catalyst.expressions.BoundReference.eval(BoundAttribute.scala:49)
at org.apache.spark.sql.catalyst.expressions.UnaryExpression.eval(Expression.scala:247)
at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:82)
at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:61)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:150)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:130)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:308)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
at scala.collection.AbstractIterator.to(Iterator.scala:1157)
at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$5.apply(SparkPlan.scala:215)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$5.apply(SparkPlan.scala:215)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1848)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1848)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
15/11/03 13:45:53 ERROR CsvRelation$: Exception while parsing line: 2013,1,1,544.
java.lang.ClassCastException: java.lang.String cannot be cast to org.apache.spark.unsafe.types.UTF8String
at org.apache.spark.sql.catalyst.expressions.BaseGenericInternalRow$class.getUTF8String(rows.scala:45)
at org.apache.spark.sql.catalyst.expressions.GenericMutableRow.getUTF8String(rows.scala:247)
at org.apache.spark.sql.catalyst.expressions.BoundReference.eval(BoundAttribute.scala:49)
at org.apache.spark.sql.catalyst.expressions.UnaryExpression.eval(Expression.scala:247)
at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:82)
at org.apache.spark.sql.catalyst.expressions.InterpretedMutableProjection.apply(Projection.scala:61)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:150)
at com.databricks.spark.csv.CsvRelation$$anonfun$com$databricks$spark$csv$CsvRelation$$parseCSV$1.apply(CsvRelation.scala:130)
at scala.collection.Iterator$$anon$13.hasNext(Iterator.scala:371)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:308)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
at scala.collection.AbstractIterator.to(Iterator.scala:1157)
at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$5.apply(SparkPlan.scala:215)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$5.apply(SparkPlan.scala:215)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1848)
at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1848)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
15/11/03 13:45:53 INFO Executor: Finished task 0.0 in stage 3.0 (TID 3). 2069 bytes result sent to driver
15/11/03 13:45:53 INFO TaskSetManager: Finished task 0.0 in stage 3.0 (TID 3) in 20 ms on localhost (1/1)
15/11/03 13:45:53 INFO DAGScheduler: ResultStage 3 (dfToCols at NativeMethodAccessorImpl.java:-2) finished in 0.021 s
15/11/03 13:45:53 INFO TaskSchedulerImpl: Removed TaskSet 3.0, whose tasks have all completed, from pool
15/11/03 13:45:53 INFO DAGScheduler: Job 3 finished: dfToCols at NativeMethodAccessorImpl.java:-2, took 0.030738 s`
Then it comes with an empty output:
`[1] gyear month day dep_time
<0 rows> (or 0-length row.names)`
Can anyone help me with this? Many thanks!
Pre-built Spark distributions are still built with Scala 2.10, not 2.11. So, if you use such a distribution (which I think you do), you need also a spark-csv build that is for Scala 2.10, not for Scala 2.11 (as the one you use in your code). The following code should then work fine:
library(rJava)
library(SparkR)
library(nycflights13)
df <- flights[1:4, 1:4]
df
year month day dep_time
1 2013 1 1 517
2 2013 1 1 533
3 2013 1 1 542
4 2013 1 1 544
write.csv(df, file="~/scripts/temp.csv", quote=FALSE, row.names=FALSE)
sc <- sparkR.init(sparkHome= "/usr/local/bin/spark-1.5.1-bin-hadoop2.6/",
master="local",
sparkPackages="com.databricks:spark-csv_2.10:1.2.0") # 2.10 here
sqlContext <- sparkRSQL.init(sc)
df_spark <- read.df(sqlContext, "/home/vagrant/scripts/temp.csv", "com.databricks.spark.csv", header="true")
head(df_spark)
year month day dep_time
1 2013 1 1 517
2 2013 1 1 533
3 2013 1 1 542
4 2013 1 1 544
来源：https://stackoverflow.com/questions/33510075/empty-output-when-reading-a-csv-file-into-rstudio-using-sparkr