Commit graph

358 commits

Author SHA1 Message Date
Hossein 2881a2d1d1 [SPARK-17919] Make timeout to RBackend configurable in SparkR
## What changes were proposed in this pull request?

This patch makes RBackend connection timeout configurable by user.

## How was this patch tested?
N/A

Author: Hossein <hossein@databricks.com>

Closes #15471 from falaki/SPARK-17919.
2016-10-30 16:17:23 -07:00
Felix Cheung 44c8bfda79 [SQL][DOC] updating doc for JSON source to link to jsonlines.org
## What changes were proposed in this pull request?

API and programming guide doc changes for Scala, Python and R.

## How was this patch tested?

manual test

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #15629 from felixcheung/jsondoc.
2016-10-26 23:06:11 -07:00
Felix Cheung 1dbe9896b7 [SPARK-17157][SPARKR][FOLLOW-UP] doc fixes
## What changes were proposed in this pull request?

a couple of small late finding fixes for doc

## How was this patch tested?

manually
wangmiao1981

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #15650 from felixcheung/logitfix.
2016-10-26 23:02:54 -07:00
wm624@hotmail.com 29cea8f332 [SPARK-17157][SPARKR] Add multiclass logistic regression SparkR Wrapper
## What changes were proposed in this pull request?

As we discussed in #14818, I added a separate R wrapper spark.logit for logistic regression.

This single interface supports both binary and multinomial logistic regression. It also has "predict" and "summary" for binary logistic regression.

## How was this patch tested?

New unit tests are added.

Author: wm624@hotmail.com <wm624@hotmail.com>

Closes #15365 from wangmiao1981/glm.
2016-10-26 16:12:55 -07:00
WeichenXu fb0a8a8dd7 [SPARK-17961][SPARKR][SQL] Add storageLevel to DataFrame for SparkR
## What changes were proposed in this pull request?

Add storageLevel to DataFrame for SparkR.
This is similar to this RP:  https://github.com/apache/spark/pull/13780

but in R I do not make a class for `StorageLevel`
but add a method `storageToString`

## How was this patch tested?

test added.

Author: WeichenXu <WeichenXu123@outlook.com>

Closes #15516 from WeichenXu123/storageLevel_df_r.
2016-10-26 13:26:43 -07:00
WeichenXu 12b3e8d2e0 [SPARK-18007][SPARKR][ML] update SparkR MLP - add initalWeights parameter
## What changes were proposed in this pull request?

update SparkR MLP, add initalWeights parameter.

## How was this patch tested?

test added.

Author: WeichenXu <WeichenXu123@outlook.com>

Closes #15552 from WeichenXu123/mlp_r_add_initialWeight_param.
2016-10-25 21:42:59 -07:00
Felix Cheung 3a423f5a03 [SPARKR][BRANCH-2.0] R merge API doc and example fix
## What changes were proposed in this pull request?

Fixes for R doc

## How was this patch tested?

N/A

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #15589 from felixcheung/rdocmergefix.

(cherry picked from commit 0e0d83a597)
Signed-off-by: Felix Cheung <felixcheung@apache.org>
2016-10-23 10:53:43 -07:00
Hossein e371040a01 [SPARK-17811] SparkR cannot parallelize data.frame with NA or NULL in Date columns
## What changes were proposed in this pull request?
NA date values are serialized as "NA" and NA time values are serialized as NaN from R. In the backend we did not have proper logic to deal with them. As a result we got an IllegalArgumentException for Date and wrong value for time. This PR adds support for deserializing NA as Date and Time.

## How was this patch tested?
* [x] TODO

Author: Hossein <hossein@databricks.com>

Closes #15421 from falaki/SPARK-17811.
2016-10-21 12:38:52 -07:00
Felix Cheung e21e1c946c [SPARK-18013][SPARKR] add crossJoin API
## What changes were proposed in this pull request?

Add crossJoin and do not default to cross join if joinExpr is left out

## How was this patch tested?

unit test

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #15559 from felixcheung/rcrossjoin.
2016-10-21 12:35:37 -07:00
Felix Cheung 3180272d2d [SPARKR] fix warnings
## What changes were proposed in this pull request?

Fix for a bunch of test warnings that were added recently.
We need to investigate why warnings are not turning into errors.

```
Warnings -----------------------------------------------------------------------
1. createDataFrame uses files for large objects (test_sparkSQL.R#215) - Use Sepal_Length instead of Sepal.Length  as column name

2. createDataFrame uses files for large objects (test_sparkSQL.R#215) - Use Sepal_Width instead of Sepal.Width  as column name

3. createDataFrame uses files for large objects (test_sparkSQL.R#215) - Use Petal_Length instead of Petal.Length  as column name

4. createDataFrame uses files for large objects (test_sparkSQL.R#215) - Use Petal_Width instead of Petal.Width  as column name

Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
```

## How was this patch tested?

unit tests

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #15560 from felixcheung/rwarnings.
2016-10-20 21:12:55 -07:00
Hossein 5cc503f4fe [SPARK-17790][SPARKR] Support for parallelizing R data.frame larger than 2GB
## What changes were proposed in this pull request?
If the R data structure that is being parallelized is larger than `INT_MAX` we use files to transfer data to JVM. The serialization protocol mimics Python pickling. This allows us to simply call `PythonRDD.readRDDFromFile` to create the RDD.

I tested this on my MacBook. Following code works with this patch:
```R
intMax <- .Machine$integer.max
largeVec <- 1:intMax
rdd <- SparkR:::parallelize(sc, largeVec, 2)
```

## How was this patch tested?
* [x] Unit tests

Author: Hossein <hossein@databricks.com>

Closes #15375 from falaki/SPARK-17790.
2016-10-12 10:32:38 -07:00
Wenchen Fan b9a147181d [SPARK-17720][SQL] introduce static SQL conf
## What changes were proposed in this pull request?

SQLConf is session-scoped and mutable. However, we do have the requirement for a static SQL conf, which is global and immutable, e.g. the `schemaStringThreshold` in `HiveExternalCatalog`, the flag to enable/disable hive support, the global temp view database in https://github.com/apache/spark/pull/14897.

Actually we've already implemented static SQL conf implicitly via `SparkConf`, this PR just make it explicit and expose it to users, so that they can see the config value via SQL command or `SparkSession.conf`, and forbid users to set/unset static SQL conf.

## How was this patch tested?

new tests in SQLConfSuite

Author: Wenchen Fan <wenchen@databricks.com>

Closes #15295 from cloud-fan/global-conf.
2016-10-11 20:27:08 -07:00
Yanbo Liang 23405f324a [SPARK-15153][ML][SPARKR] Fix SparkR spark.naiveBayes error when label is numeric type
## What changes were proposed in this pull request?
Fix SparkR ```spark.naiveBayes``` error when response variable of dataset is numeric type.
See details and how to reproduce this bug at [SPARK-15153](https://issues.apache.org/jira/browse/SPARK-15153).

## How was this patch tested?
Add unit test.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #15431 from yanboliang/spark-15153-2.
2016-10-11 12:41:35 -07:00
hyukjinkwon 9d8ae853ec [SPARK-17665][SPARKR] Support options/mode all for read/write APIs and options in other types
## What changes were proposed in this pull request?

This PR includes the changes below:

  - Support `mode`/`options` in `read.parquet`, `write.parquet`, `read.orc`, `write.orc`, `read.text`, `write.text`, `read.json` and `write.json` APIs

  - Support other types (logical, numeric and string) as options for `write.df`, `read.df`, `read.parquet`, `write.parquet`, `read.orc`, `write.orc`, `read.text`, `write.text`, `read.json` and `write.json`

## How was this patch tested?

Unit tests in `test_sparkSQL.R`/ `utils.R`.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #15239 from HyukjinKwon/SPARK-17665.
2016-10-07 11:34:49 -07:00
hyukjinkwon c9fe10d4ed [SPARK-17658][SPARKR] read.df/write.df API taking path optionally in SparkR
## What changes were proposed in this pull request?

`write.df`/`read.df` API require path which is not actually always necessary in Spark. Currently, it only affects the datasources implementing `CreatableRelationProvider`. Currently, Spark currently does not have internal data sources implementing this but it'd affect other external datasources.

In addition we'd be able to use this way in Spark's JDBC datasource after https://github.com/apache/spark/pull/12601 is merged.

**Before**

 - `read.df`

  ```r
> read.df(source = "json")
Error in dispatchFunc("read.df(path = NULL, source = NULL, schema = NULL, ...)",  :
  argument "x" is missing with no default
```

  ```r
> read.df(path = c(1, 2))
Error in dispatchFunc("read.df(path = NULL, source = NULL, schema = NULL, ...)",  :
  argument "x" is missing with no default
```

  ```r
> read.df(c(1, 2))
Error in invokeJava(isStatic = TRUE, className, methodName, ...) :
  java.lang.ClassCastException: java.lang.Double cannot be cast to java.lang.String
	at org.apache.spark.sql.execution.datasources.DataSource.hasMetadata(DataSource.scala:300)
	at
...
In if (is.na(object)) { :
...
```

 - `write.df`

  ```r
> write.df(df, source = "json")
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘write.df’ for signature ‘"function", "missing"’
```

  ```r
> write.df(df, source = c(1, 2))
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘write.df’ for signature ‘"SparkDataFrame", "missing"’
```

  ```r
> write.df(df, mode = TRUE)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘write.df’ for signature ‘"SparkDataFrame", "missing"’
```

**After**

- `read.df`

  ```r
> read.df(source = "json")
Error in loadDF : analysis error - Unable to infer schema for JSON at . It must be specified manually;
```

  ```r
> read.df(path = c(1, 2))
Error in f(x, ...) : path should be charactor, null or omitted.
```

  ```r
> read.df(c(1, 2))
Error in f(x, ...) : path should be charactor, null or omitted.
```

- `write.df`

  ```r
> write.df(df, source = "json")
Error in save : illegal argument - 'path' is not specified
```

  ```r
> write.df(df, source = c(1, 2))
Error in .local(df, path, ...) :
  source should be charactor, null or omitted. It is 'parquet' by default.
```

  ```r
> write.df(df, mode = TRUE)
Error in .local(df, path, ...) :
  mode should be charactor or omitted. It is 'error' by default.
```

## How was this patch tested?

Unit tests in `test_sparkSQL.R`

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #15231 from HyukjinKwon/write-default-r.
2016-10-04 22:58:43 -07:00
Felix Cheung 068c198e95 [SPARKR][DOC] minor formatting and output cleanup for R vignettes
## What changes were proposed in this pull request?

Clean up output, format table, truncate long example output, hide warnings

(new - Left; existing - Right)
![image](https://cloud.githubusercontent.com/assets/8969467/19064018/5dcde4d0-89bc-11e6-857b-052df3f52a4e.png)

![image](https://cloud.githubusercontent.com/assets/8969467/19064034/6db09956-89bc-11e6-8e43-232d5c3fe5e6.png)

![image](https://cloud.githubusercontent.com/assets/8969467/19064058/88f09590-89bc-11e6-9993-61639e29dfdd.png)

![image](https://cloud.githubusercontent.com/assets/8969467/19064066/95ccbf64-89bc-11e6-877f-45af03ddcadc.png)

![image](https://cloud.githubusercontent.com/assets/8969467/19064082/a8445404-89bc-11e6-8532-26d8bc9b206f.png)

## How was this patch tested?

Run create-doc.sh manually

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #15340 from felixcheung/vignettes.
2016-10-04 09:22:26 -07:00
hyukjinkwon 4a83395681 [SPARK-17499][SPARKR][FOLLOWUP] Check null first for layers in spark.mlp to avoid warnings in test results
## What changes were proposed in this pull request?

Some tests in `test_mllib.r` are as below:

```r
expect_error(spark.mlp(df, layers = NULL), "layers must be a integer vector with length > 1.")
expect_error(spark.mlp(df, layers = c()), "layers must be a integer vector with length > 1.")
```

The problem is, `is.na` is internally called via `na.omit` in `spark.mlp` which causes warnings as below:

```
Warnings -----------------------------------------------------------------------
1. spark.mlp (test_mllib.R#400) - is.na() applied to non-(list or vector) of type 'NULL'

2. spark.mlp (test_mllib.R#401) - is.na() applied to non-(list or vector) of type 'NULL'
```

## How was this patch tested?

Manually tested. Also, Jenkins tests and AppVeyor.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #15232 from HyukjinKwon/remove-warnnings.
2016-09-27 21:19:59 -07:00
Yanbo Liang 93c743f1ac [SPARK-17577][FOLLOW-UP][SPARKR] SparkR spark.addFile supports adding directory recursively
## What changes were proposed in this pull request?
#15140 exposed ```JavaSparkContext.addFile(path: String, recursive: Boolean)``` to Python/R, then we can update SparkR ```spark.addFile``` to support adding directory recursively.

## How was this patch tested?
Added unit test.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #15216 from yanboliang/spark-17577-2.
2016-09-26 16:47:57 -07:00
Jeff Zhang f62ddc5983 [SPARK-17210][SPARKR] sparkr.zip is not distributed to executors when running sparkr in RStudio
## What changes were proposed in this pull request?

Spark will add sparkr.zip to archive only when it is yarn mode (SparkSubmit.scala).
```
    if (args.isR && clusterManager == YARN) {
      val sparkRPackagePath = RUtils.localSparkRPackagePath
      if (sparkRPackagePath.isEmpty) {
        printErrorAndExit("SPARK_HOME does not exist for R application in YARN mode.")
      }
      val sparkRPackageFile = new File(sparkRPackagePath.get, SPARKR_PACKAGE_ARCHIVE)
      if (!sparkRPackageFile.exists()) {
        printErrorAndExit(s"$SPARKR_PACKAGE_ARCHIVE does not exist for R application in YARN mode.")
      }
      val sparkRPackageURI = Utils.resolveURI(sparkRPackageFile.getAbsolutePath).toString

      // Distribute the SparkR package.
      // Assigns a symbol link name "sparkr" to the shipped package.
      args.archives = mergeFileLists(args.archives, sparkRPackageURI + "#sparkr")

      // Distribute the R package archive containing all the built R packages.
      if (!RUtils.rPackages.isEmpty) {
        val rPackageFile =
          RPackageUtils.zipRLibraries(new File(RUtils.rPackages.get), R_PACKAGE_ARCHIVE)
        if (!rPackageFile.exists()) {
          printErrorAndExit("Failed to zip all the built R packages.")
        }

        val rPackageURI = Utils.resolveURI(rPackageFile.getAbsolutePath).toString
        // Assigns a symbol link name "rpkg" to the shipped package.
        args.archives = mergeFileLists(args.archives, rPackageURI + "#rpkg")
      }
    }
```
So it is necessary to pass spark.master from R process to JVM. Otherwise sparkr.zip won't be distributed to executor.  Besides that I also pass spark.yarn.keytab/spark.yarn.principal to spark side, because JVM process need them to access secured cluster.

## How was this patch tested?

Verify it manually in R Studio using the following code.
```
Sys.setenv(SPARK_HOME="/Users/jzhang/github/spark")
.libPaths(c(file.path(Sys.getenv(), "R", "lib"), .libPaths()))
library(SparkR)
sparkR.session(master="yarn-client", sparkConfig = list(spark.executor.instances="1"))
df <- as.DataFrame(mtcars)
head(df)

```

…

Author: Jeff Zhang <zjffdu@apache.org>

Closes #14784 from zjffdu/SPARK-17210.
2016-09-23 11:37:43 -07:00
WeichenXu f89808b0fd [SPARK-17499][SPARKR][ML][MLLIB] make the default params in sparkR spark.mlp consistent with MultilayerPerceptronClassifier
## What changes were proposed in this pull request?

update `MultilayerPerceptronClassifierWrapper.fit` paramter type:
`layers: Array[Int]`
`seed: String`

update several default params in sparkR `spark.mlp`:
`tol` --> 1e-6
`stepSize` --> 0.03
`seed` --> NULL ( when seed == NULL, the scala-side wrapper regard it as a `null` value and the seed will use the default one )
r-side `seed` only support 32bit integer.

remove `layers` default value, and move it in front of those parameters with default value.
add `layers` parameter validation check.

## How was this patch tested?

tests added.

Author: WeichenXu <WeichenXu123@outlook.com>

Closes #15051 from WeichenXu123/update_py_mlp_default.
2016-09-23 11:14:22 -07:00
Yanbo Liang 6902edab7e [SPARK-17315][FOLLOW-UP][SPARKR][ML] Fix print of Kolmogorov-Smirnov test summary
## What changes were proposed in this pull request?
#14881 added Kolmogorov-Smirnov Test wrapper to SparkR. I found that ```print.summary.KSTest``` was implemented inappropriately and result in no effect.
Running the following code for KSTest:
```Scala
data <- data.frame(test = c(0.1, 0.15, 0.2, 0.3, 0.25, -1, -0.5))
df <- createDataFrame(data)
testResult <- spark.kstest(df, "test", "norm")
summary(testResult)
```
Before this PR:
![image](https://cloud.githubusercontent.com/assets/1962026/18615016/b9a2823a-7d4f-11e6-934b-128beade355e.png)
After this PR:
![image](https://cloud.githubusercontent.com/assets/1962026/18615014/aafe2798-7d4f-11e6-8b99-c705bb9fe8f2.png)
The new implementation is similar with [```print.summary.GeneralizedLinearRegressionModel```](https://github.com/apache/spark/blob/master/R/pkg/R/mllib.R#L284) of SparkR and [```print.summary.glm```](https://svn.r-project.org/R/trunk/src/library/stats/R/glm.R) of native R.

BTW, I removed the comparison of ```print.summary.KSTest``` in unit test, since it's only wrappers of the summary output which has been checked. Another reason is that these comparison will output summary information to the test console, it will make the test output in a mess.

## How was this patch tested?
Existing test.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #15139 from yanboliang/spark-17315.
2016-09-21 20:14:18 -07:00
Yanbo Liang c133907c5d [SPARK-17577][SPARKR][CORE] SparkR support add files to Spark job and get by executors
## What changes were proposed in this pull request?
Scala/Python users can add files to Spark job by submit options ```--files``` or ```SparkContext.addFile()```. Meanwhile, users can get the added file by ```SparkFiles.get(filename)```.
We should also support this function for SparkR users, since they also have the requirements for some shared dependency files. For example, SparkR users can download third party R packages to driver firstly, add these files to the Spark job as dependency by this API and then each executor can install these packages by ```install.packages```.

## How was this patch tested?
Add unit test.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #15131 from yanboliang/spark-17577.
2016-09-21 20:08:28 -07:00
Sean Owen d720a40194
[SPARK-17297][DOCS] Clarify window/slide duration as absolute time, not relative to a calendar
## What changes were proposed in this pull request?

Clarify that slide and window duration are absolute, and not relative to a calendar.

## How was this patch tested?

Doc build (no functional change)

Author: Sean Owen <sowen@cloudera.com>

Closes #15142 from srowen/SPARK-17297.
2016-09-19 09:38:25 +01:00
Sean Owen dc0a4c9161 [SPARK-17445][DOCS] Reference an ASF page as the main place to find third-party packages
## What changes were proposed in this pull request?

Point references to spark-packages.org to https://cwiki.apache.org/confluence/display/SPARK/Third+Party+Projects

This will be accompanied by a parallel change to the spark-website repo, and additional changes to this wiki.

## How was this patch tested?

Jenkins tests.

Author: Sean Owen <sowen@cloudera.com>

Closes #15075 from srowen/SPARK-17445.
2016-09-14 10:10:16 +01:00
junyangq a454a4d86b [SPARK-17317][SPARKR] Add SparkR vignette
## What changes were proposed in this pull request?

This PR tries to add a SparkR vignette, which works as a friendly guidance going through the functionality provided by SparkR.

## How was this patch tested?

Manual test.

Author: junyangq <qianjunyang@gmail.com>
Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Author: Junyang Qian <junyangq@databricks.com>

Closes #14980 from junyangq/SPARKR-vignette.
2016-09-13 21:01:03 -07:00
Xin Ren 71b7d42f5f [SPARK-16445][MLLIB][SPARKR] Fix @return description for sparkR mlp summary() method
## What changes were proposed in this pull request?

Fix summary() method's `return` description for spark.mlp

## How was this patch tested?

Ran tests locally on my laptop.

Author: Xin Ren <iamshrek@126.com>

Closes #15015 from keypointt/SPARK-16445-2.
2016-09-10 09:52:53 -07:00
Yanbo Liang 2ed601217f [SPARK-17464][SPARKR][ML] SparkR spark.als argument reg should be 0.1 by default.
## What changes were proposed in this pull request?
SparkR ```spark.als``` arguments ```reg``` should be 0.1 by default, which need to be consistent with ML.

## How was this patch tested?
Existing tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #15021 from yanboliang/spark-17464.
2016-09-09 05:43:34 -07:00
Felix Cheung f0d21b7f90 [SPARK-17442][SPARKR] Additional arguments in write.df are not passed to data source
## What changes were proposed in this pull request?

additional options were not passed down in write.df.

## How was this patch tested?

unit tests
falaki shivaram

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #15010 from felixcheung/testreadoptions.
2016-09-08 08:22:58 -07:00
hyukjinkwon 6b41195bca [SPARK-17339][SPARKR][CORE] Fix some R tests and use Path.toUri in SparkContext for Windows paths in SparkR
## What changes were proposed in this pull request?

This PR fixes the Windows path issues in several APIs. Please refer https://issues.apache.org/jira/browse/SPARK-17339 for more details.

## How was this patch tested?

Tests via AppVeyor CI - https://ci.appveyor.com/project/HyukjinKwon/spark/build/82-SPARK-17339-fix-r

Also, manually,

![2016-09-06 3 14 38](https://cloud.githubusercontent.com/assets/6477701/18263406/b93a98be-7444-11e6-9521-b28ee65a4771.png)

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #14960 from HyukjinKwon/SPARK-17339.
2016-09-07 19:24:03 +09:00
Clark Fitzgerald 9fccde4ff8 [SPARK-16785] R dapply doesn't return array or raw columns
## What changes were proposed in this pull request?

Fixed bug in `dapplyCollect` by changing the `compute` function of `worker.R` to explicitly handle raw (binary) vectors.

cc shivaram

## How was this patch tested?

Unit tests

Author: Clark Fitzgerald <clarkfitzg@gmail.com>

Closes #14783 from clarkfitzg/SPARK-16785.
2016-09-06 23:40:37 -07:00
Junyang Qian abb2f92103 [SPARK-17315][SPARKR] Kolmogorov-Smirnov test SparkR wrapper
## What changes were proposed in this pull request?

This PR tries to add Kolmogorov-Smirnov Test wrapper to SparkR. This wrapper implementation only supports one sample test against normal distribution.

## How was this patch tested?

R unit test.

Author: Junyang Qian <junyangq@databricks.com>

Closes #14881 from junyangq/SPARK-17315.
2016-09-03 12:26:30 -07:00
Junyang Qian d2fde6b72c [SPARKR][MINOR] Fix docs for sparkR.session and count
## What changes were proposed in this pull request?

This PR tries to add some more explanation to `sparkR.session`. It also modifies doc for `count` so when grouped in one doc, the description doesn't confuse users.

## How was this patch tested?

Manual test.

![screen shot 2016-09-02 at 1 21 36 pm](https://cloud.githubusercontent.com/assets/15318264/18217198/409613ac-7110-11e6-8dae-cb0c8df557bf.png)

Author: Junyang Qian <junyangq@databricks.com>

Closes #14942 from junyangq/fixSparkRSessionDoc.
2016-09-02 21:11:57 -07:00
Srinath Shankar e6132a6cf1 [SPARK-17298][SQL] Require explicit CROSS join for cartesian products
## What changes were proposed in this pull request?

Require the use of CROSS join syntax in SQL (and a new crossJoin
DataFrame API) to specify explicit cartesian products between relations.
By cartesian product we mean a join between relations R and S where
there is no join condition involving columns from both R and S.

If a cartesian product is detected in the absence of an explicit CROSS
join, an error must be thrown. Turning on the
"spark.sql.crossJoin.enabled" configuration flag will disable this check
and allow cartesian products without an explicit CROSS join.

The new crossJoin DataFrame API must be used to specify explicit cross
joins. The existing join(DataFrame) method will produce a INNER join
that will require a subsequent join condition.
That is df1.join(df2) is equivalent to select * from df1, df2.

## How was this patch tested?

Added cross-join.sql to the SQLQueryTestSuite to test the check for cartesian products. Added a couple of tests to the DataFrameJoinSuite to test the crossJoin API. Modified various other test suites to explicitly specify a cross join where an INNER join or a comma-separated list was previously used.

Author: Srinath Shankar <srinath@databricks.com>

Closes #14866 from srinathshankar/crossjoin.
2016-09-03 00:20:43 +02:00
Felix Cheung eac1d0e921 [SPARK-17376][SPARKR] followup - change since version
## What changes were proposed in this pull request?

change since version in doc

## How was this patch tested?

manual

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #14939 from felixcheung/rsparkversion2.
2016-09-02 11:08:25 -07:00
Felix Cheung 419eefd811 [SPARKR][DOC] regexp_extract should doc that it returns empty string when match fails
## What changes were proposed in this pull request?

Doc change - see https://issues.apache.org/jira/browse/SPARK-16324

## How was this patch tested?

manual check

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #14934 from felixcheung/regexpextractdoc.
2016-09-02 10:28:37 -07:00
Felix Cheung 812333e433 [SPARK-17376][SPARKR] Spark version should be available in R
## What changes were proposed in this pull request?

Add sparkR.version() API.

```
> sparkR.version()
[1] "2.1.0-SNAPSHOT"
```

## How was this patch tested?

manual, unit tests

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #14935 from felixcheung/rsparksessionversion.
2016-09-02 10:12:10 -07:00
wm624@hotmail.com 0f30cdedbd [SPARK-16883][SPARKR] SQL decimal type is not properly cast to number when collecting SparkDataFrame
## What changes were proposed in this pull request?

(Please fill in changes proposed in this fix)

registerTempTable(createDataFrame(iris), "iris")
str(collect(sql("select cast('1' as double) as x, cast('2' as decimal) as y  from iris limit 5")))

'data.frame':	5 obs. of  2 variables:
 $ x: num  1 1 1 1 1
 $ y:List of 5
  ..$ : num 2
  ..$ : num 2
  ..$ : num 2
  ..$ : num 2
  ..$ : num 2

The problem is that spark returns `decimal(10, 0)` col type, instead of `decimal`. Thus, `decimal(10, 0)` is not handled correctly. It should be handled as "double".

As discussed in JIRA thread, we can have two potential fixes:
1). Scala side fix to add a new case when writing the object back; However, I can't use spark.sql.types._ in Spark core due to dependency issues. I don't find a way of doing type case match;

2). SparkR side fix: Add a helper function to check special type like `"decimal(10, 0)"` and replace it with `double`, which is PRIMITIVE type. This special helper is generic for adding new types handling in the future.

I open this PR to discuss pros and cons of both approaches. If we want to do Scala side fix, we need to find a way to match the case of DecimalType and StructType in Spark Core.

## How was this patch tested?

(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)

Manual test:
> str(collect(sql("select cast('1' as double) as x, cast('2' as decimal) as y  from iris limit 5")))
'data.frame':	5 obs. of  2 variables:
 $ x: num  1 1 1 1 1
 $ y: num  2 2 2 2 2
R Unit tests

Author: wm624@hotmail.com <wm624@hotmail.com>

Closes #14613 from wangmiao1981/type.
2016-09-02 01:47:17 -07:00
Xin Ren 7a5000f39e [SPARK-17241][SPARKR][MLLIB] SparkR spark.glm should have configurable regularization parameter
https://issues.apache.org/jira/browse/SPARK-17241

## What changes were proposed in this pull request?

Spark has configurable L2 regularization parameter for generalized linear regression. It is very important to have them in SparkR so that users can run ridge regression.

## How was this patch tested?

Test manually on local laptop.

Author: Xin Ren <iamshrek@126.com>

Closes #14856 from keypointt/SPARK-17241.
2016-08-31 21:39:31 -07:00
Junyang Qian d008638fbe [SPARKR][MINOR] Fix windowPartitionBy example
## What changes were proposed in this pull request?

The usage in the original example is incorrect. This PR fixes it.

## How was this patch tested?

Manual test.

Author: Junyang Qian <junyangq@databricks.com>

Closes #14903 from junyangq/SPARKR-FixWindowPartitionByDoc.
2016-08-31 21:28:53 -07:00
Shivaram Venkataraman 2f9c27364e [SPARK-16581][SPARKR] Fix JVM API tests in SparkR
## What changes were proposed in this pull request?

Remove cleanup.jobj test. Use JVM wrapper API for other test cases.

## How was this patch tested?

Run R unit tests with testthat 1.0

Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>

Closes #14904 from shivaram/sparkr-jvm-tests-fix.
2016-08-31 16:56:41 -07:00
hyukjinkwon 50bb142332 [SPARK-17326][SPARKR] Fix tests with HiveContext in SparkR not to be skipped always
## What changes were proposed in this pull request?

Currently, `HiveContext` in SparkR is not being tested and always skipped.
This is because the initiation of `TestHiveContext` is being failed due to trying to load non-existing data paths (test tables).

This is introduced from https://github.com/apache/spark/pull/14005

This enables the tests with SparkR.

## How was this patch tested?

Manually,

**Before** (on Mac OS)

```
...
Skipped ------------------------------------------------------------------------
1. create DataFrame from RDD (test_sparkSQL.R#200) - Hive is not build with SparkSQL, skipped
2. test HiveContext (test_sparkSQL.R#1041) - Hive is not build with SparkSQL, skipped
3. read/write ORC files (test_sparkSQL.R#1748) - Hive is not build with SparkSQL, skipped
4. enableHiveSupport on SparkSession (test_sparkSQL.R#2480) - Hive is not build with SparkSQL, skipped
5. sparkJars tag in SparkContext (test_Windows.R#21) - This test is only for Windows, skipped
...
```

**After** (on Mac OS)

```
...
Skipped ------------------------------------------------------------------------
1. sparkJars tag in SparkContext (test_Windows.R#21) - This test is only for Windows, skipped
...
```

Please refer the tests below (on Windows)
 - Before: https://ci.appveyor.com/project/HyukjinKwon/spark/build/45-test123
 - After: https://ci.appveyor.com/project/HyukjinKwon/spark/build/46-test123

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #14889 from HyukjinKwon/SPARK-17326.
2016-08-31 14:02:21 -07:00
Shivaram Venkataraman 736a7911cb [SPARK-16581][SPARKR] Make JVM backend calling functions public
## What changes were proposed in this pull request?

This change exposes a public API in SparkR to create objects, call methods on the Spark driver JVM

## How was this patch tested?

(Please explain how this patch was tested. E.g. unit tests, integration tests, manual tests)

Unit tests, CRAN checks

Author: Shivaram Venkataraman <shivaram@cs.berkeley.edu>

Closes #14775 from shivaram/sparkr-java-api.
2016-08-29 12:55:32 -07:00
Junyang Qian 6a0fda2c05 [SPARKR][MINOR] Fix LDA doc
## What changes were proposed in this pull request?

This PR tries to fix the name of the `SparkDataFrame` used in the example. Also, it gives a reference url of an example data file so that users can play with.

## How was this patch tested?

Manual test.

Author: Junyang Qian <junyangq@databricks.com>

Closes #14853 from junyangq/SPARKR-FixLDADoc.
2016-08-29 10:23:10 -07:00
Junyang Qian 1883216235 [SPARKR][MINOR] Fix example of spark.naiveBayes
## What changes were proposed in this pull request?

The original example doesn't work because the features are not categorical. This PR fixes this by changing to another dataset.

## How was this patch tested?

Manual test.

Author: Junyang Qian <junyangq@databricks.com>

Closes #14820 from junyangq/SPARK-FixNaiveBayes.
2016-08-26 11:01:48 -07:00
Junyang Qian 3a60be4b15 [SPARKR][MINOR] Add installation message for remote master mode and improve other messages
## What changes were proposed in this pull request?

This PR gives informative message to users when they try to connect to a remote master but don't have Spark package in their local machine.

As a clarification, for now, automatic installation will only happen if they start SparkR in R console (rather than from sparkr-shell) and connect to local master. In the remote master mode, local Spark package is still needed, but we will not trigger the install.spark function because the versions have to match those on the cluster, which involves more user input. Instead, we here try to provide detailed message that may help the users.

Some of the other messages have also been slightly changed.

## How was this patch tested?

Manual test.

Author: Junyang Qian <junyangq@databricks.com>

Closes #14761 from junyangq/SPARK-16579-V1.
2016-08-24 16:04:14 -07:00
Junyang Qian 18708f76c3 [SPARKR][MINOR] Add more examples to window function docs
## What changes were proposed in this pull request?

This PR adds more examples to window function docs to make them more accessible to the users.

It also fixes default value issues for `lag` and `lead`.

## How was this patch tested?

Manual test, R unit test.

Author: Junyang Qian <junyangq@databricks.com>

Closes #14779 from junyangq/SPARKR-FixWindowFunctionDocs.
2016-08-24 16:00:04 -07:00
Felix Cheung 945c04bcd4 [MINOR][SPARKR] fix R MLlib parameter documentation
## What changes were proposed in this pull request?

Fixed several misplaced param tag - they should be on the spark.* method generics

## How was this patch tested?

run knitr
junyangq

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #14792 from felixcheung/rdocmllib.
2016-08-24 15:59:09 -07:00
Xin Ren 2fbdb60639 [SPARK-16445][MLLIB][SPARKR] Multilayer Perceptron Classifier wrapper in SparkR
https://issues.apache.org/jira/browse/SPARK-16445

## What changes were proposed in this pull request?

Create Multilayer Perceptron Classifier wrapper in SparkR

## How was this patch tested?

Tested manually on local machine

Author: Xin Ren <iamshrek@126.com>

Closes #14447 from keypointt/SPARK-16445.
2016-08-24 11:18:10 -07:00
Junyang Qian d2932a0e98 [SPARKR][MINOR] Fix doc for show method
## What changes were proposed in this pull request?

The original doc of `show` put methods for multiple classes together but the text only talks about `SparkDataFrame`. This PR tries to fix this problem.

## How was this patch tested?

Manual test.

Author: Junyang Qian <junyangq@databricks.com>

Closes #14776 from junyangq/SPARK-FixShowDoc.
2016-08-24 10:40:09 -07:00
Junyang Qian 8fd63e808e [SPARKR][MINOR] Remove reference link for common Windows environment variables
## What changes were proposed in this pull request?

The PR removes reference link in the doc for environment variables for common Windows folders. The cran check gave code 503: service unavailable on the original link.

## How was this patch tested?

Manual check.

Author: Junyang Qian <junyangq@databricks.com>

Closes #14767 from junyangq/SPARKR-RemoveLink.
2016-08-23 11:22:32 -07:00