[jira] [Updated] (SPARK-21727) Operating on an ArrayType in a SparkR DataFrame throws error
[
https://issues.apache.org/jira/browse/SPARK-21727?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Neil Alexander McQuarrie updated SPARK-21727:
-
Description:
Previously
[posted|https://stackoverflow.com/questions/45056973/sparkr-dataframe-with-r-lists-as-elements]
this as a stack overflow question but it seems to be a bug.
If I have an R data.frame where one of the column data types is an integer
*list* – i.e., each of the elements in the column embeds an entire R list of
integers – then it seems I can convert this data.frame to a SparkR DataFrame
just fine... SparkR treats the column as ArrayType(Double).
However, any subsequent operation on this SparkR DataFrame appears to throw an
error.
Create an example R data.frame:
{code:java}
indices <- 1:4
myDf <- data.frame(indices)
myDf$data <- list(rep(0, 20))
{code}
Examine it to make sure it looks okay:
{code:java}
> str(myDf)
'data.frame': 4 obs. of 2 variables:
$ indices: int 1 2 3 4
$ data :List of 4
..$ : num 0 0 0 0 0 0 0 0 0 0 ...
..$ : num 0 0 0 0 0 0 0 0 0 0 ...
..$ : num 0 0 0 0 0 0 0 0 0 0 ...
..$ : num 0 0 0 0 0 0 0 0 0 0 ...
> head(myDf)
indices data
1 1 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
2 2 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
3 3 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
4 4 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
{code}
Convert it to a SparkR DataFrame:
{code:java}
library(SparkR, lib.loc=paste0(Sys.getenv("SPARK_HOME"),"/R/lib"))
sparkR.session(master = "local[*]")
mySparkDf <- as.DataFrame(myDf)
{code}
Examine the SparkR DataFrame schema; notice that the list column was
successfully converted to ArrayType:
{code:java}
> schema(mySparkDf)
StructType
|-name = "indices", type = "IntegerType", nullable = TRUE
|-name = "data", type = "ArrayType(DoubleType,true)", nullable = TRUE
{code}
However, operating on the SparkR DataFrame throws an error:
{code:java}
> collect(mySparkDf)
17/07/13 17:23:00 ERROR executor.Executor: Exception in task 0.0 in stage 1.0
(TID 1)
java.lang.RuntimeException: Error while encoding: java.lang.RuntimeException:
java.lang.Double is not a valid external type for schema of array
if (assertnotnull(input[0, org.apache.spark.sql.Row, true]).isNullAt) null
else validateexternaltype(getexternalrowfield(assertnotnull(input[0,
org.apache.spark.sql.Row, true]), 0, indices), IntegerType) AS indices#0
... long stack trace ...
{code}
Using Spark 2.2.0, R 3.4.0, Java 1.8.0_131, Windows 10.
was:
Previously
[posted|https://stackoverflow.com/questions/45056973/sparkr-dataframe-with-r-lists-as-elements]
this as a stack overflow question but it seems to be a bug.
If I have an R data.frame where one of the column data types is an integer
*list* -- i.e., each of the elements in the column embeds an entire R list of
integers -- then it seems I can convert this data.frame to a SparkR DataFrame
just fine... SparkR treats the column as ArrayType(Double).
However, any subsequent operation on this SparkR DataFrame appears to throw an
error.
Create an example R data.frame:
{code}
indices <- 1:4
myDf <- data.frame(indices)
myDf$data <- list(rep(0, 20))}}
{code}
Examine it to make sure it looks okay:
{code}
> str(myDf)
'data.frame': 4 obs. of 2 variables:
$ indices: int 1 2 3 4
$ data :List of 4
..$ : num 0 0 0 0 0 0 0 0 0 0 ...
..$ : num 0 0 0 0 0 0 0 0 0 0 ...
..$ : num 0 0 0 0 0 0 0 0 0 0 ...
..$ : num 0 0 0 0 0 0 0 0 0 0 ...
> head(myDf)
indices data
1 1 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
2 2 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
3 3 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
4 4 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
{code}
Convert it to a SparkR DataFrame:
{code}
library(SparkR, lib.loc=paste0(Sys.getenv("SPARK_HOME"),"/R/lib"))
sparkR.session(master = "local[*]")
mySparkDf <- as.DataFrame(myDf)
{code}
Examine the SparkR DataFrame schema; notice that the list column was
successfully converted to ArrayType:
{code}
> schema(mySparkDf)
StructType
|-name = "indices", type = "IntegerType", nullable = TRUE
|-name = "data", type = "ArrayType(DoubleType,true)", nullable = TRUE
{code}
However, operating on the SparkR DataFrame throws an error:
{code}
> collect(mySparkDf)
17/07/13 17:23:00 ERROR executor.Executor: Exception in task 0.0 in stage 1.0
(TID 1)
java.lang.RuntimeException: Error while encoding: java.lang.RuntimeException:
java.lang.Double is not a valid external type for schema of array
if (assertnotnull(input[0, org.apache.spark.sql.Row, true]).isNullAt) null
else validateexternaltype(getexternalrowfield(assertnotnull(input[0,
[jira] [Commented] (SPARK-21727) Operating on an ArrayType in a SparkR DataFrame throws error
[
https://issues.apache.org/jira/browse/SPARK-21727?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16320439#comment-16320439
]
Neil Alexander McQuarrie commented on SPARK-21727:
--
Okay great. Implemented and tests are passing. I'll submit a PR shortly. Thanks
for the help.
> Operating on an ArrayType in a SparkR DataFrame throws error
>
>
> Key: SPARK-21727
> URL: https://issues.apache.org/jira/browse/SPARK-21727
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.2.0
>Reporter: Neil Alexander McQuarrie
>Assignee: Neil Alexander McQuarrie
>
> Previously
> [posted|https://stackoverflow.com/questions/45056973/sparkr-dataframe-with-r-lists-as-elements]
> this as a stack overflow question but it seems to be a bug.
> If I have an R data.frame where one of the column data types is an integer
> *list* -- i.e., each of the elements in the column embeds an entire R list of
> integers -- then it seems I can convert this data.frame to a SparkR DataFrame
> just fine... SparkR treats the column as ArrayType(Double).
> However, any subsequent operation on this SparkR DataFrame appears to throw
> an error.
> Create an example R data.frame:
> {code}
> indices <- 1:4
> myDf <- data.frame(indices)
> myDf$data <- list(rep(0, 20))}}
> {code}
> Examine it to make sure it looks okay:
> {code}
> > str(myDf)
> 'data.frame': 4 obs. of 2 variables:
> $ indices: int 1 2 3 4
> $ data :List of 4
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
> > head(myDf)
> indices data
> 1 1 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 2 2 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 3 3 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 4 4 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> {code}
> Convert it to a SparkR DataFrame:
> {code}
> library(SparkR, lib.loc=paste0(Sys.getenv("SPARK_HOME"),"/R/lib"))
> sparkR.session(master = "local[*]")
> mySparkDf <- as.DataFrame(myDf)
> {code}
> Examine the SparkR DataFrame schema; notice that the list column was
> successfully converted to ArrayType:
> {code}
> > schema(mySparkDf)
> StructType
> |-name = "indices", type = "IntegerType", nullable = TRUE
> |-name = "data", type = "ArrayType(DoubleType,true)", nullable = TRUE
> {code}
> However, operating on the SparkR DataFrame throws an error:
> {code}
> > collect(mySparkDf)
> 17/07/13 17:23:00 ERROR executor.Executor: Exception in task 0.0 in stage 1.0
> (TID 1)
> java.lang.RuntimeException: Error while encoding: java.lang.RuntimeException:
> java.lang.Double is not a valid external type for schema of array
> if (assertnotnull(input[0, org.apache.spark.sql.Row, true]).isNullAt) null
> else validateexternaltype(getexternalrowfield(assertnotnull(input[0,
> org.apache.spark.sql.Row, true]), 0, indices), IntegerType) AS indices#0
> ... long stack trace ...
> {code}
> Using Spark 2.2.0, R 3.4.0, Java 1.8.0_131, Windows 10.
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[jira] [Commented] (SPARK-21727) Operating on an ArrayType in a SparkR DataFrame throws error
[
https://issues.apache.org/jira/browse/SPARK-21727?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16319647#comment-16319647
]
Neil Alexander McQuarrie commented on SPARK-21727:
--
Oh -- interesting... thanks.
I think "raw" type is atomic though?
Is
{code}is.atomic(object) & !is.raw(object){code}
too clunky?
> Operating on an ArrayType in a SparkR DataFrame throws error
>
>
> Key: SPARK-21727
> URL: https://issues.apache.org/jira/browse/SPARK-21727
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.2.0
>Reporter: Neil Alexander McQuarrie
>Assignee: Neil Alexander McQuarrie
>
> Previously
> [posted|https://stackoverflow.com/questions/45056973/sparkr-dataframe-with-r-lists-as-elements]
> this as a stack overflow question but it seems to be a bug.
> If I have an R data.frame where one of the column data types is an integer
> *list* -- i.e., each of the elements in the column embeds an entire R list of
> integers -- then it seems I can convert this data.frame to a SparkR DataFrame
> just fine... SparkR treats the column as ArrayType(Double).
> However, any subsequent operation on this SparkR DataFrame appears to throw
> an error.
> Create an example R data.frame:
> {code}
> indices <- 1:4
> myDf <- data.frame(indices)
> myDf$data <- list(rep(0, 20))}}
> {code}
> Examine it to make sure it looks okay:
> {code}
> > str(myDf)
> 'data.frame': 4 obs. of 2 variables:
> $ indices: int 1 2 3 4
> $ data :List of 4
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
> > head(myDf)
> indices data
> 1 1 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 2 2 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 3 3 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 4 4 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> {code}
> Convert it to a SparkR DataFrame:
> {code}
> library(SparkR, lib.loc=paste0(Sys.getenv("SPARK_HOME"),"/R/lib"))
> sparkR.session(master = "local[*]")
> mySparkDf <- as.DataFrame(myDf)
> {code}
> Examine the SparkR DataFrame schema; notice that the list column was
> successfully converted to ArrayType:
> {code}
> > schema(mySparkDf)
> StructType
> |-name = "indices", type = "IntegerType", nullable = TRUE
> |-name = "data", type = "ArrayType(DoubleType,true)", nullable = TRUE
> {code}
> However, operating on the SparkR DataFrame throws an error:
> {code}
> > collect(mySparkDf)
> 17/07/13 17:23:00 ERROR executor.Executor: Exception in task 0.0 in stage 1.0
> (TID 1)
> java.lang.RuntimeException: Error while encoding: java.lang.RuntimeException:
> java.lang.Double is not a valid external type for schema of array
> if (assertnotnull(input[0, org.apache.spark.sql.Row, true]).isNullAt) null
> else validateexternaltype(getexternalrowfield(assertnotnull(input[0,
> org.apache.spark.sql.Row, true]), 0, indices), IntegerType) AS indices#0
> ... long stack trace ...
> {code}
> Using Spark 2.2.0, R 3.4.0, Java 1.8.0_131, Windows 10.
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[jira] [Commented] (SPARK-21727) Operating on an ArrayType in a SparkR DataFrame throws error
[
https://issues.apache.org/jira/browse/SPARK-21727?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16312466#comment-16312466
]
Neil Alexander McQuarrie commented on SPARK-21727:
--
I was able to get a version working by checking for length > 1, as well as
whether the type is integer, character, logical, double, numeric, Date,
POSIXlt, or POSIXct.
[https://github.com/neilalex/spark/blob/neilalex-sparkr-arraytype/R/pkg/R/serialize.R#L39]
The reason I'm checking the specific type is that it seems quite a few objects
flow through getSerdeType() besides just the object we're converting -- for
example, after calling 'as.DataFrame(myDf)' per above, I saw a jobj "Java ref
type org.apache.spark.sql.SparkSession id 1" of length 2, as well as a raw
object of length ~700, both pass through getSerdeType(). So, it seems we can't
just check length?
Also, in general this makes me a little nervous -- will there be scenarios when
a 2+ length vector of one of the above types should also not be converted to
array? I'll familiarize myself further with how getSerdeType() is called, to
see if I can think this through.
> Operating on an ArrayType in a SparkR DataFrame throws error
>
>
> Key: SPARK-21727
> URL: https://issues.apache.org/jira/browse/SPARK-21727
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.2.0
>Reporter: Neil Alexander McQuarrie
>Assignee: Neil Alexander McQuarrie
>
> Previously
> [posted|https://stackoverflow.com/questions/45056973/sparkr-dataframe-with-r-lists-as-elements]
> this as a stack overflow question but it seems to be a bug.
> If I have an R data.frame where one of the column data types is an integer
> *list* -- i.e., each of the elements in the column embeds an entire R list of
> integers -- then it seems I can convert this data.frame to a SparkR DataFrame
> just fine... SparkR treats the column as ArrayType(Double).
> However, any subsequent operation on this SparkR DataFrame appears to throw
> an error.
> Create an example R data.frame:
> {code}
> indices <- 1:4
> myDf <- data.frame(indices)
> myDf$data <- list(rep(0, 20))}}
> {code}
> Examine it to make sure it looks okay:
> {code}
> > str(myDf)
> 'data.frame': 4 obs. of 2 variables:
> $ indices: int 1 2 3 4
> $ data :List of 4
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
> > head(myDf)
> indices data
> 1 1 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 2 2 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 3 3 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 4 4 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> {code}
> Convert it to a SparkR DataFrame:
> {code}
> library(SparkR, lib.loc=paste0(Sys.getenv("SPARK_HOME"),"/R/lib"))
> sparkR.session(master = "local[*]")
> mySparkDf <- as.DataFrame(myDf)
> {code}
> Examine the SparkR DataFrame schema; notice that the list column was
> successfully converted to ArrayType:
> {code}
> > schema(mySparkDf)
> StructType
> |-name = "indices", type = "IntegerType", nullable = TRUE
> |-name = "data", type = "ArrayType(DoubleType,true)", nullable = TRUE
> {code}
> However, operating on the SparkR DataFrame throws an error:
> {code}
> > collect(mySparkDf)
> 17/07/13 17:23:00 ERROR executor.Executor: Exception in task 0.0 in stage 1.0
> (TID 1)
> java.lang.RuntimeException: Error while encoding: java.lang.RuntimeException:
> java.lang.Double is not a valid external type for schema of array
> if (assertnotnull(input[0, org.apache.spark.sql.Row, true]).isNullAt) null
> else validateexternaltype(getexternalrowfield(assertnotnull(input[0,
> org.apache.spark.sql.Row, true]), 0, indices), IntegerType) AS indices#0
> ... long stack trace ...
> {code}
> Using Spark 2.2.0, R 3.4.0, Java 1.8.0_131, Windows 10.
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[jira] [Commented] (SPARK-21727) Operating on an ArrayType in a SparkR DataFrame throws error
[
https://issues.apache.org/jira/browse/SPARK-21727?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16307277#comment-16307277
]
Neil Alexander McQuarrie commented on SPARK-21727:
--
[~felixcheung] Okay thanks -- sorry, need a few more days
> Operating on an ArrayType in a SparkR DataFrame throws error
>
>
> Key: SPARK-21727
> URL: https://issues.apache.org/jira/browse/SPARK-21727
> Project: Spark
> Issue Type: Bug
> Components: SparkR
>Affects Versions: 2.2.0
>Reporter: Neil Alexander McQuarrie
>Assignee: Neil Alexander McQuarrie
>
> Previously
> [posted|https://stackoverflow.com/questions/45056973/sparkr-dataframe-with-r-lists-as-elements]
> this as a stack overflow question but it seems to be a bug.
> If I have an R data.frame where one of the column data types is an integer
> *list* -- i.e., each of the elements in the column embeds an entire R list of
> integers -- then it seems I can convert this data.frame to a SparkR DataFrame
> just fine... SparkR treats the column as ArrayType(Double).
> However, any subsequent operation on this SparkR DataFrame appears to throw
> an error.
> Create an example R data.frame:
> {code}
> indices <- 1:4
> myDf <- data.frame(indices)
> myDf$data <- list(rep(0, 20))}}
> {code}
> Examine it to make sure it looks okay:
> {code}
> > str(myDf)
> 'data.frame': 4 obs. of 2 variables:
> $ indices: int 1 2 3 4
> $ data :List of 4
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
>..$ : num 0 0 0 0 0 0 0 0 0 0 ...
> > head(myDf)
> indices data
> 1 1 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 2 2 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 3 3 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> 4 4 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
> {code}
> Convert it to a SparkR DataFrame:
> {code}
> library(SparkR, lib.loc=paste0(Sys.getenv("SPARK_HOME"),"/R/lib"))
> sparkR.session(master = "local[*]")
> mySparkDf <- as.DataFrame(myDf)
> {code}
> Examine the SparkR DataFrame schema; notice that the list column was
> successfully converted to ArrayType:
> {code}
> > schema(mySparkDf)
> StructType
> |-name = "indices", type = "IntegerType", nullable = TRUE
> |-name = "data", type = "ArrayType(DoubleType,true)", nullable = TRUE
> {code}
> However, operating on the SparkR DataFrame throws an error:
> {code}
> > collect(mySparkDf)
> 17/07/13 17:23:00 ERROR executor.Executor: Exception in task 0.0 in stage 1.0
> (TID 1)
> java.lang.RuntimeException: Error while encoding: java.lang.RuntimeException:
> java.lang.Double is not a valid external type for schema of array
> if (assertnotnull(input[0, org.apache.spark.sql.Row, true]).isNullAt) null
> else validateexternaltype(getexternalrowfield(assertnotnull(input[0,
> org.apache.spark.sql.Row, true]), 0, indices), IntegerType) AS indices#0
> ... long stack trace ...
> {code}
> Using Spark 2.2.0, R 3.4.0, Java 1.8.0_131, Windows 10.
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