## What changes were proposed in this pull request?
Define and use ```KMeansWrapper``` for ```SparkR::kmeans```. It's only the code refactor for the original ```KMeans``` wrapper.

## How was this patch tested?
Existing tests.

cc mengxr

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #12039 from yanboliang/spark-14059.

## What changes were proposed in this pull request?

Refactor RRDD by separating the common logic interacting with the R worker to a new class RRunner, which can be used to evaluate R UDFs.

Now RRDD relies on RRuner for RDD computation and RRDD could be reomved if we want to remove RDD API in SparkR later.

## How was this patch tested?
dev/lint-r
SparkR unit tests

Author: Sun Rui <rui.sun@intel.com>

Closes #12024 from sun-rui/SPARK-12792_new.

This reverts commit 40984f67.

Refactor RRDD by separating the common logic interacting with the R worker to a new class RRunner, which can be used to evaluate R UDFs.

Now RRDD relies on RRuner for RDD computation and RRDD could be reomved if we want to remove RDD API in SparkR later.

Author: Sun Rui <rui.sun@intel.com>

Closes #10947 from sun-rui/SPARK-12792.

## What changes were proposed in this pull request?

This reopens #11836, which was merged but promptly reverted because it introduced flaky Hive tests.

## How was this patch tested?

See `CatalogTestCases`, `SessionCatalogSuite` and `HiveContextSuite`.

Author: Andrew Or <andrew@databricks.com>

Closes #11938 from andrewor14/session-catalog-again.

## What changes were proposed in this pull request?
This PR continues the work in #11447, we implemented the wrapper of ```AFTSurvivalRegression``` named ```survreg``` in SparkR.

## How was this patch tested?
Test against output from R package survival's survreg.

cc mengxr felixcheung

Close #11447

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #11932 from yanboliang/spark-13010-new.

This reverts commit 5dfc0197.

## What changes were proposed in this pull request?

`SessionCatalog`, introduced in #11750, is a catalog that keeps track of temporary functions and tables, and delegates metastore operations to `ExternalCatalog`. This functionality overlaps a lot with the existing `analysis.Catalog`.

As of this commit, `SessionCatalog` and `ExternalCatalog` will no longer be dead code. There are still things that need to be done after this patch, namely:
- SPARK-14013: Properly implement temporary functions in `SessionCatalog`
- SPARK-13879: Decide which DDL/DML commands to support natively in Spark
- SPARK-?????: Implement the ones we do want to support through `SessionCatalog`.
- SPARK-?????: Merge SQL/HiveContext

## How was this patch tested?

This is largely a refactoring task so there are no new tests introduced. The particularly relevant tests are `SessionCatalogSuite` and `ExternalCatalogSuite`.

Author: Andrew Or <andrew@databricks.com>
Author: Yin Huai <yhuai@databricks.com>

Closes #11836 from andrewor14/use-session-catalog.

## What changes were proposed in this pull request?

This PR continues the work in #11486 from yinxusen with some code refactoring. In R package e1071, `naiveBayes` supports both categorical (Bernoulli) and continuous features (Gaussian), while in MLlib we support Bernoulli and multinomial. This PR implements the common subset: Bernoulli.

I moved the implementation out from SparkRWrappers to NaiveBayesWrapper to make it easier to read. Argument names, default values, and summary now match e1071's naiveBayes.

I removed the preprocess part that omit NA values because we don't know which columns to process.

## How was this patch tested?

Test against output from R package e1071's naiveBayes.

cc: yanboliang yinxusen

Closes #11486

Author: Xusen Yin <yinxusen@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #11890 from mengxr/SPARK-13449.

## What changes were proposed in this pull request?

Since `sparkR` is not used for submitting R Scripts from Spark 2.0, a user faces the following error message if he follows the instruction on `R/README.md`. This PR updates `R/README.md`.
```bash
$ ./bin/sparkR examples/src/main/r/dataframe.R
Running R applications through 'sparkR' is not supported as of Spark 2.0.
Use ./bin/spark-submit <R file>
```

## How was this patch tested?

Manual.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #11842 from dongjoon-hyun/update_r_readme.

## What changes were proposed in this pull request?

This PR fixes all newly captured SparkR lint-r errors after the lintr package is updated from github.

## How was this patch tested?

dev/lint-r
SparkR unit tests

Author: Sun Rui <rui.sun@intel.com>

Closes #11652 from sun-rui/SPARK-13812.

## What changes were proposed in this pull request?

SparkR support first/last with ignore NAs

cc sun-rui felixcheung shivaram

## How was the this patch tested?

unit tests

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #11267 from yanboliang/spark-13389.

Author: Oscar D. Lara Yejas <odlaraye@oscars-mbp.attlocal.net>
Author: Oscar D. Lara Yejas <odlaraye@oscars-mbp.usca.ibm.com>

Closes #11220 from olarayej/SPARK-13312-3.

## What changes were proposed in this pull request?
Add ```approxQuantile``` for SparkR.
## How was this patch tested?
unit tests

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #11383 from yanboliang/spark-13504 and squashes the following commits:

4f17adb [Yanbo Liang] Add approxQuantile for SparkR

JIRA: https://issues.apache.org/jira/browse/SPARK-13472

## What changes were proposed in this pull request?

One Kmeans test in R is unstable and sometimes fails. We should fix it.

## How was this patch tested?

Unit test is modified in this PR.

Author: Liang-Chi Hsieh <viirya@gmail.com>

Closes #11345 from viirya/fix-kmeans-r-test and squashes the following commits:

f959f61 [Liang-Chi Hsieh] Sort resulted clusters.

https://issues.apache.org/jira/browse/SPARK-13011

Author: Xusen Yin <yinxusen@gmail.com>

Closes #11124 from yinxusen/SPARK-13011.

## What changes were proposed in this pull request?

This PR tries to fix all typos in all markdown files under `docs` module,
and fixes similar typos in other comments, too.

## How was the this patch tested?

manual tests.

Author: Dongjoon Hyun <dongjoon@apache.org>

Closes #11300 from dongjoon-hyun/minor_fix_typos.

This PR introduces several major changes:

1. Replacing `Expression.prettyString` with `Expression.sql`

   The `prettyString` method is mostly an internal, developer faced facility for debugging purposes, and shouldn't be exposed to users.

1. Using SQL-like representation as column names for selected fields that are not named expression (back-ticks and double quotes should be removed)

   Before, we were using `prettyString` as column names when possible, and sometimes the result column names can be weird.  Here are several examples:

   Expression         | `prettyString` | `sql`      | Note
   ------------------ | -------------- | ---------- | ---------------
   `a && b`           | `a && b`       | `a AND b`  |
   `a.getField("f")`  | `a[f]`         | `a.f`      | `a` is a struct

1. Adding trait `NonSQLExpression` extending from `Expression` for expressions that don't have a SQL representation (e.g. Scala UDF/UDAF and Java/Scala object expressions used for encoders)

   `NonSQLExpression.sql` may return an arbitrary user facing string representation of the expression.

Author: Cheng Lian <lian@databricks.com>

Closes #10757 from liancheng/spark-12799.simplify-expression-string-methods.

Clarify that reduce functions need to be commutative, and fold functions do not

See https://github.com/apache/spark/pull/11091

Author: Sean Owen <sowen@cloudera.com>

Closes #11217 from srowen/SPARK-13339.

In spark-env.sh.template, there are multi-byte characters, this PR will remove it.

Author: Sasaki Toru <sasakitoa@nttdata.co.jp>

Closes #11149 from sasakitoa/remove_multibyte_in_sparkenv.

Add ```covar_samp``` and ```covar_pop``` for SparkR.
Should we also provide ```cov``` alias for ```covar_samp```? There is ```cov``` implementation at stats.R which masks ```stats::cov``` already, but may bring to breaking API change.

cc sun-rui felixcheung shivaram

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #10829 from yanboliang/spark-12903.

I've tried to solve some of the issues mentioned in: https://issues.apache.org/jira/browse/SPARK-12629
Please, let me know what do you think.
Thanks!

Author: Narine Kokhlikyan <narine.kokhlikyan@gmail.com>

Closes #10580 from NarineK/sparkrSavaAsRable.

Author: Sun Rui <rui.sun@intel.com>

Closes #10201 from sun-rui/SPARK-12204.

Testing code:
```
$ ./install-dev.sh
USING R_HOME = /usr/bin
ERROR: this R is version 2.15.1, package 'SparkR' requires R >= 3.0
```

Using the new argument:
```
$ ./install-dev.sh /content/username/SOFTWARE/R-3.2.3
USING R_HOME = /content/username/SOFTWARE/R-3.2.3/bin
* installing *source* package ‘SparkR’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘colnames’ in package ‘SparkR’
Creating a new generic function for ‘colnames<-’ in package ‘SparkR’
Creating a new generic function for ‘cov’ in package ‘SparkR’
Creating a new generic function for ‘na.omit’ in package ‘SparkR’
Creating a new generic function for ‘filter’ in package ‘SparkR’
Creating a new generic function for ‘intersect’ in package ‘SparkR’
Creating a new generic function for ‘sample’ in package ‘SparkR’
Creating a new generic function for ‘transform’ in package ‘SparkR’
Creating a new generic function for ‘subset’ in package ‘SparkR’
Creating a new generic function for ‘summary’ in package ‘SparkR’
Creating a new generic function for ‘lag’ in package ‘SparkR’
Creating a new generic function for ‘rank’ in package ‘SparkR’
Creating a new generic function for ‘sd’ in package ‘SparkR’
Creating a new generic function for ‘var’ in package ‘SparkR’
Creating a new generic function for ‘predict’ in package ‘SparkR’
Creating a new generic function for ‘rbind’ in package ‘SparkR’
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘Filter’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘alias’ from package ‘stats’ in package ‘SparkR’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘%in%’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘mean’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘unique’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘head’ from package ‘utils’ in package ‘SparkR’
Creating a generic function for ‘factorial’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘atan2’ from package ‘base’ in package ‘SparkR’
Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘SparkR’
** help
No man pages found in package  ‘SparkR’
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (SparkR)

```

Author: Shubhanshu Mishra <smishra8@illinois.edu>

Closes #10836 from napsternxg/master.

The current parser turns a decimal literal, for example ```12.1```, into a Double. The problem with this approach is that we convert an exact literal into a non-exact ```Double```. The PR changes this behavior, a Decimal literal is now converted into an extact ```BigDecimal```.

The behavior for scientific decimals, for example ```12.1e01```, is unchanged. This will be converted into a Double.

This PR replaces the ```BigDecimal``` literal by a ```Double``` literal, because the ```BigDecimal``` is the default now. You can use the double literal by appending a 'D' to the value, for instance: ```3.141527D```

cc davies rxin

Author: Herman van Hovell <hvanhovell@questtec.nl>

Closes #10796 from hvanhovell/SPARK-12848.

shivaram sorry it took longer to fix some conflicts, this is the change to add an alias for `table`

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #10406 from felixcheung/readtable.

Author: Sun Rui <rui.sun@intel.com>

Closes #10309 from sun-rui/SPARK-12337.

Currently this is reported when loading the SparkR package in R (probably would add is.nan)
```
Loading required package: methods

Attaching package: ‘SparkR’

The following objects are masked from ‘package:stats’:

    cov, filter, lag, na.omit, predict, sd, var

The following objects are masked from ‘package:base’:

    colnames, colnames<-, intersect, rank, rbind, sample, subset,
    summary, table, transform
```

Adding this test adds an automated way to track changes to masked method.
Also, the second part of this test check for those functions that would not be accessible without namespace/package prefix.

Incidentally, this might point to how we would fix those inaccessible functions in base or stats.
Looking for feedback for adding this test.

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #10171 from felixcheung/rmaskedtest.

Slight correction: I'm leaving sparkR as-is (ie. R file not supported) and fixed only run-tests.sh as shivaram described.

I also assume we are going to cover all doc changes in https://issues.apache.org/jira/browse/SPARK-12846 instead of here.

rxin shivaram zjffdu

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #10792 from felixcheung/sparkRcmd.

Author: Oscar D. Lara Yejas <odlaraye@oscars-mbp.usca.ibm.com>
Author: Oscar D. Lara Yejas <olarayej@mail.usf.edu>
Author: Oscar D. Lara Yejas <oscar.lara.yejas@us.ibm.com>
Author: Oscar D. Lara Yejas <odlaraye@oscars-mbp.attlocal.net>

Closes #9613 from olarayej/SPARK-11031.

This PR makes bucketing and exchange share one common hash algorithm, so that we can guarantee the data distribution is same between shuffle and bucketed data source, which enables us to only shuffle one side when join a bucketed table and a normal one.

This PR also fixes the tests that are broken by the new hash behaviour in shuffle.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #10703 from cloud-fan/use-hash-expr-in-shuffle.

Add ```hash``` function for SparkR ```DataFrame```.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #10597 from yanboliang/spark-12645.

Add ```read.text``` and ```write.text``` for SparkR.
cc sun-rui felixcheung shivaram

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #10348 from yanboliang/spark-12393.

rxin davies shivaram
Took save mode from my PR #10480, and move everything to writer methods. This is related to PR #10559

- [x] it seems jsonRDD() is broken, need to investigate - this is not a public API though; will look into some more tonight. (fixed)

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #10584 from felixcheung/rremovedeprecated.

shivaram

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #10408 from felixcheung/rcodecomment.

* Changes api.r.SQLUtils to use ```SQLContext.getOrCreate``` instead of creating a new context.
* Adds a simple test

[SPARK-11199] #comment link with JIRA

Author: Hossein <hossein@databricks.com>

Closes #9185 from falaki/SPARK-11199.

`ifelse`, `when`, `otherwise` is unable to take `Column` typed S4 object as values.

For example:
```r
ifelse(lit(1) == lit(1), lit(2), lit(3))
ifelse(df$mpg > 0, df$mpg, 0)
```
will both fail with
```r
attempt to replicate an object of type 'environment'
```

The PR replaces `ifelse` calls with `if ... else ...` inside the function implementations to avoid attempt to vectorize(i.e. `rep()`). It remains to be discussed whether we should instead support vectorization in these functions for consistency because `ifelse` in base R is vectorized but I cannot foresee any scenarios these functions will want to be vectorized in SparkR.

For reference, added test cases which trigger failures:
```r
. Error: when(), otherwise() and ifelse() with column on a DataFrame ----------
error in evaluating the argument 'x' in selecting a method for function 'collect':
  error in evaluating the argument 'col' in selecting a method for function 'select':
  attempt to replicate an object of type 'environment'
Calls: when -> when -> ifelse -> ifelse

1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_equal(collect(select(df, when(df$a > 1 & df$b > 2, lit(1))))[, 1], c(NA, 1)) at test_sparkSQL.R:1126
5: expect_that(object, equals(expected, label = expected.label, ...), info = info, label = label)
6: condition(object)
7: compare(actual, expected, ...)
8: collect(select(df, when(df$a > 1 & df$b > 2, lit(1))))
Error: Test failures
Execution halted
```

Author: Forest Fang <forest.fang@outlook.com>

Closes #10481 from saurfang/spark-12526.

Author: Reynold Xin <rxin@databricks.com>

Closes #10387 from rxin/version-bump.

Add ```write.json``` and ```write.parquet``` for SparkR, and deprecated ```saveAsParquetFile```.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #10281 from yanboliang/spark-12310.

shivaram  Please help review.

Author: Jeff Zhang <zjffdu@apache.org>

Closes #10290 from zjffdu/SPARK-12318.