[SPARK-20307][ML][SPARKR][FOLLOW-UP] RFormula should handle invalid for both features and label column.

## What changes were proposed in this pull request?
```RFormula``` should handle invalid for both features and label column.
#18496 only handle invalid values in features column. This PR add handling invalid values for label column and test cases.

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

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #18613 from yanboliang/spark-20307.

## What changes were proposed in this pull request?

Update internal references from programming-guide to rdd-programming-guide

See https://github.com/apache/spark-website/commit/5ddf243fd84a0f0f98a5193a207737cea9cdc083 and https://github.com/apache/spark/pull/18485#issuecomment-314789751

Let's keep the redirector even if it's problematic to build, but not rely on it internally.

## How was this patch tested?

(Doc build)

Author: Sean Owen <sowen@cloudera.com>

Closes #18625 from srowen/SPARK-21267.2.

## What changes were proposed in this pull request?

- Remove Scala 2.10 build profiles and support
- Replace some 2.10 support in scripts with commented placeholders for 2.12 later
- Remove deprecated API calls from 2.10 support
- Remove usages of deprecated context bounds where possible
- Remove Scala 2.10 workarounds like ScalaReflectionLock
- Other minor Scala warning fixes

## How was this patch tested?

Existing tests

Author: Sean Owen <sowen@cloudera.com>

Closes #17150 from srowen/SPARK-19810.

## What changes were proposed in this pull request?

This PR supports schema in a DDL formatted string for `from_json` in R/Python and `dapply` and `gapply` in R, which are commonly used and/or consistent with Scala APIs.

Additionally, this PR exposes `structType` in R to allow working around in other possible corner cases.

**Python**

`from_json`

```python
from pyspark.sql.functions import from_json

data = [(1, '''{"a": 1}''')]
df = spark.createDataFrame(data, ("key", "value"))
df.select(from_json(df.value, "a INT").alias("json")).show()
```

**R**

`from_json`

```R
df <- sql("SELECT named_struct('name', 'Bob') as people")
df <- mutate(df, people_json = to_json(df$people))
head(select(df, from_json(df$people_json, "name STRING")))
```

`structType.character`

```R
structType("a STRING, b INT")
```

`dapply`

```R
dapply(createDataFrame(list(list(1.0)), "a"), function(x) {x}, "a DOUBLE")
```

`gapply`

```R
gapply(createDataFrame(list(list(1.0)), "a"), "a", function(key, x) { x }, "a DOUBLE")
```

## How was this patch tested?

Doc tests for `from_json` in Python and unit tests `test_sparkSQL.R` in R.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #18498 from HyukjinKwon/SPARK-21266.

## What changes were proposed in this pull request?

This is a retry for #18320. This PR was reverted due to unexpected test failures with -10 error code.

I was unable to reproduce in MacOS, CentOS and Ubuntu but only in Jenkins. So, the tests proceeded to verify this and revert the past try here - https://github.com/apache/spark/pull/18456

This new approach was tested in https://github.com/apache/spark/pull/18463.

**Test results**:

- With the part of suspicious change in the past try (https://github.com/apache/spark/pull/18463/commits/466325d3fd353668583f3bde38ae490d9db0b189)

  Tests ran 4 times and 2 times passed and 2 time failed.

- Without the part of suspicious change in the past try (https://github.com/apache/spark/pull/18463/commits/466325d3fd353668583f3bde38ae490d9db0b189)

  Tests ran 5 times and they all passed.

- With this new approach (https://github.com/apache/spark/pull/18463/commits/0a7589c09f53dfc2094497d8d3e59d6407569417)

  Tests ran 5 times and they all passed.

It looks the cause is as below (see https://github.com/apache/spark/pull/18463/commits/466325d3fd353668583f3bde38ae490d9db0b189):

```diff
+ exitCode <- 1
...
+   data <- parallel:::readChild(child)
+   if (is.raw(data)) {
+     if (unserialize(data) == exitCode) {
      ...
+     }
+   }

...

- parallel:::mcexit(0L)
+ parallel:::mcexit(0L, send = exitCode)
```

Two possibilities I think

 - `parallel:::mcexit(.. , send = exitCode)`

   https://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mcfork.html

   > It sends send to the master (unless NULL) and then shuts down the child process.

   However, it looks possible that the parent attemps to terminate the child right after getting our custom exit code. So, the child gets terminated between "send" and "shuts down", failing to exit properly.

 - A bug between `parallel:::mcexit(..., send = ...)` and `parallel:::readChild`.

**Proposal**:

To resolve this, I simply decided to avoid both possibilities with this new approach here (https://github.com/apache/spark/pull/18465/commits/9ff89a7859cb9f427fc774f33c3521c7d962b723). To support this idea, I explained with some quotation of the documentation as below:

https://stat.ethz.ch/R-manual/R-devel/library/parallel/html/mcfork.html

> `readChild` and `readChildren` return a raw vector with a "pid" attribute if data were available, an integer vector of length one with the process ID if a child terminated or `NULL` if the child no longer exists (no children at all for `readChildren`).

`readChild` returns "an integer vector of length one with the process ID if a child terminated" so we can check if it is `integer` and the same selected "process ID". I believe this makes sure that the children are exited.

In case that children happen to send any data manually to parent (which is why we introduced the suspicious part of the change (https://github.com/apache/spark/pull/18463/commits/466325d3fd353668583f3bde38ae490d9db0b189)), this should be raw bytes and will be discarded (and then will try to read the next and check if it is `integer` in the next loop).

## How was this patch tested?

Manual tests and Jenkins tests.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #18465 from HyukjinKwon/SPARK-21093-retry-1.

## What changes were proposed in this pull request?

This adds documentation to many functions in pyspark.sql.functions.py:
`upper`, `lower`, `reverse`, `unix_timestamp`, `from_unixtime`, `rand`, `randn`, `collect_list`, `collect_set`, `lit`
Add units to the trigonometry functions.
Renames columns in datetime examples to be more informative.
Adds links between some functions.

## How was this patch tested?

`./dev/lint-python`
`python python/pyspark/sql/functions.py`
`./python/run-tests.py --module pyspark-sql`

Author: Michael Patterson <map222@gmail.com>

Closes #17865 from map222/spark-20456.

[SPARK-20307][SPARKR] SparkR: pass on setHandleInvalid to spark.mllib functions that use StringIndexer

## What changes were proposed in this pull request?

For randomForest classifier, if test data contains unseen labels, it will throw an error. The StringIndexer already has the handleInvalid logic. The patch add a new method to set the underlying StringIndexer handleInvalid logic.

This patch should also apply to other classifiers. This PR focuses on the main logic and randomForest classifier. I will do follow-up PR for other classifiers.

## How was this patch tested?

Add a new unit test based on the error case in the JIRA.

Author: wangmiao1981 <wm624@hotmail.com>

Closes #18496 from wangmiao1981/handle.

## What changes were proposed in this pull request?
Add doc for methods that were left out, and fix various style and consistency issues.

Author: actuaryzhang <actuaryzhang10@gmail.com>

Closes #18493 from actuaryzhang/sparkRDocCleanup.

## What changes were proposed in this pull request?

Grouped documentation for column window methods.

Author: actuaryzhang <actuaryzhang10@gmail.com>

Closes #18481 from actuaryzhang/sparkRDocWindow.

## What changes were proposed in this pull request?

Grouped documentation for column collection methods.

Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>

Closes #18458 from actuaryzhang/sparkRDocCollection.

## What changes were proposed in this pull request?
Grouped documentation for column misc methods.

Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>

Closes #18448 from actuaryzhang/sparkRDocMisc.

## What changes were proposed in this pull request?

Grouped documentation for nonaggregate column methods.

Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>

Closes #18422 from actuaryzhang/sparkRDocNonAgg.

Revert "[SPARK-21094][R] Terminate R's worker processes in the parent of R's daemon to prevent a leak"

This reverts commit 6b3d0228.

## What changes were proposed in this pull request?

This PR proposes to support a DDL-formetted string as schema as below:

```r
mockLines <- c("{\"name\":\"Michael\"}",
               "{\"name\":\"Andy\", \"age\":30}",
               "{\"name\":\"Justin\", \"age\":19}")
jsonPath <- tempfile(pattern = "sparkr-test", fileext = ".tmp")
writeLines(mockLines, jsonPath)
df <- read.df(jsonPath, "json", "name STRING, age DOUBLE")
collect(df)
```

## How was this patch tested?

Tests added in `test_streaming.R` and `test_sparkSQL.R` and manual tests.

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #18431 from HyukjinKwon/r-ddl-schema.

## What changes were proposed in this pull request?

Grouped documentation for string column methods.

Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>

Closes #18366 from actuaryzhang/sparkRDocString.

## What changes were proposed in this pull request?

Grouped documentation for math column methods.

Author: actuaryzhang <actuaryzhang10@gmail.com>
Author: Wayne Zhang <actuaryzhang10@gmail.com>

Closes #18371 from actuaryzhang/sparkRDocMath.

## What changes were proposed in this pull request?

`mcfork` in R looks opening a pipe ahead but the existing logic does not properly close it when it is executed hot. This leads to the failure of more forking due to the limit for number of files open.

This hot execution looks particularly for `gapply`/`gapplyCollect`. For unknown reason, this happens more easily in CentOS and could be reproduced in Mac too.

All the details are described in https://issues.apache.org/jira/browse/SPARK-21093

This PR proposes simply to terminate R's worker processes in the parent of R's daemon to prevent a leak.

## How was this patch tested?

I ran the codes below on both CentOS and Mac with that configuration disabled/enabled.

```r
df <- createDataFrame(list(list(1L, 1, "1", 0.1)), c("a", "b", "c", "d"))
collect(gapply(df, "a", function(key, x) { x }, schema(df)))
collect(gapply(df, "a", function(key, x) { x }, schema(df)))
...  # 30 times
```

Also, now it passes R tests on CentOS as below:

```
SparkSQL functions: Spark package found in SPARK_HOME: .../spark
..............................................................................................................................................................
..............................................................................................................................................................
..............................................................................................................................................................
..............................................................................................................................................................
..............................................................................................................................................................
....................................................................................................................................
```

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #18320 from HyukjinKwon/SPARK-21093.

## What changes were proposed in this pull request?

Extend `setJobDescription` to SparkR API.

## How was this patch tested?

It looks difficult to add a test. Manually tested as below:

```r
df <- createDataFrame(iris)
count(df)
setJobDescription("This is an example job.")
count(df)
```

prints ...

![2017-06-22 12 05 49](https://user-images.githubusercontent.com/6477701/27415670-2a649936-5743-11e7-8e95-312f1cd103af.png)

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #18382 from HyukjinKwon/SPARK-21149.

## What changes were proposed in this pull request?
Grouped documentation for datetime column methods.

Author: actuaryzhang <actuaryzhang10@gmail.com>

Closes #18114 from actuaryzhang/sparkRDocDate.

## What changes were proposed in this pull request?

PR https://github.com/apache/spark/pull/17715 Added Constrained Logistic Regression for ML. We should add it to SparkR.

## How was this patch tested?

Add new unit tests.

Author: wangmiao1981 <wm624@hotmail.com>

Closes #18128 from wangmiao1981/test.

## What changes were proposed in this pull request?

Add `stringIndexerOrderType` to `spark.glm` and `spark.survreg` to support string encoding that is consistent with default R.

## How was this patch tested?
new tests

Author: actuaryzhang <actuaryzhang10@gmail.com>

Closes #18140 from actuaryzhang/sparkRFormula.

## What changes were proposed in this pull request?

LinearSVC should use its own threshold param, rather than the shared one, since it applies to rawPrediction instead of probability.  This PR changes the param in the Scala, Python and R APIs.

## How was this patch tested?

New unit test to make sure the threshold can be set to any Double value.

Author: Joseph K. Bradley <joseph@databricks.com>

Closes #18151 from jkbradley/ml-2.2-linearsvc-cleanup.

## What changes were proposed in this pull request?
Grouped documentation for the aggregate functions for Column.

Author: actuaryzhang <actuaryzhang10@gmail.com>

Closes #18025 from actuaryzhang/sparkRDoc4.

## What changes were proposed in this pull request?

#17753 bumps master branch version to 2.3.0-SNAPSHOT, but it seems SparkR and PySpark version were omitted.

ditto of https://github.com/apache/spark/pull/16488 / https://github.com/apache/spark/pull/17523

## How was this patch tested?

N/A

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #18341 from HyukjinKwon/r-version.

## What changes were proposed in this pull request?

Add SQL trunc function

## How was this patch tested?
standard test

Author: actuaryzhang <actuaryzhang10@gmail.com>

Closes #18291 from actuaryzhang/sparkRTrunc2.

## What changes were proposed in this pull request?

This PR proposes to list the files in test _after_ removing both "spark-warehouse" and "metastore_db" so that the next run of R tests pass fine. This is sometimes a bit annoying.

## How was this patch tested?

Manually running multiple times R tests via `./R/run-tests.sh`.

**Before**

Second run:

```
SparkSQL functions: Spark package found in SPARK_HOME: .../spark
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
....................................................................................................1234.......................

Failed -------------------------------------------------------------------------
1. Failure: No extra files are created in SPARK_HOME by starting session and making calls (test_sparkSQL.R#3384)
length(list1) not equal to length(list2).
1/1 mismatches
[1] 25 - 23 == 2

2. Failure: No extra files are created in SPARK_HOME by starting session and making calls (test_sparkSQL.R#3384)
sort(list1, na.last = TRUE) not equal to sort(list2, na.last = TRUE).
10/25 mismatches
x[16]: "metastore_db"
y[16]: "pkg"

x[17]: "pkg"
y[17]: "R"

x[18]: "R"
y[18]: "README.md"

x[19]: "README.md"
y[19]: "run-tests.sh"

x[20]: "run-tests.sh"
y[20]: "SparkR_2.2.0.tar.gz"

x[21]: "metastore_db"
y[21]: "pkg"

x[22]: "pkg"
y[22]: "R"

x[23]: "R"
y[23]: "README.md"

x[24]: "README.md"
y[24]: "run-tests.sh"

x[25]: "run-tests.sh"
y[25]: "SparkR_2.2.0.tar.gz"

3. Failure: No extra files are created in SPARK_HOME by starting session and making calls (test_sparkSQL.R#3388)
length(list1) not equal to length(list2).
1/1 mismatches
[1] 25 - 23 == 2

4. Failure: No extra files are created in SPARK_HOME by starting session and making calls (test_sparkSQL.R#3388)
sort(list1, na.last = TRUE) not equal to sort(list2, na.last = TRUE).
10/25 mismatches
x[16]: "metastore_db"
y[16]: "pkg"

x[17]: "pkg"
y[17]: "R"

x[18]: "R"
y[18]: "README.md"

x[19]: "README.md"
y[19]: "run-tests.sh"

x[20]: "run-tests.sh"
y[20]: "SparkR_2.2.0.tar.gz"

x[21]: "metastore_db"
y[21]: "pkg"

x[22]: "pkg"
y[22]: "R"

x[23]: "R"
y[23]: "README.md"

x[24]: "README.md"
y[24]: "run-tests.sh"

x[25]: "run-tests.sh"
y[25]: "SparkR_2.2.0.tar.gz"

DONE ===========================================================================
```

**After**

Second run:

```
SparkSQL functions: Spark package found in SPARK_HOME: .../spark
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................................................
...............................................................................................................................
```

Author: hyukjinkwon <gurwls223@gmail.com>

Closes #18335 from HyukjinKwon/SPARK-21128.

## What changes were proposed in this pull request?

Update Running R Tests dependence packages to:
```bash
R -e "install.packages(c('knitr', 'rmarkdown', 'testthat', 'e1071', 'survival'), repos='http://cran.us.r-project.org')"
```

## How was this patch tested?
manual tests

Author: Yuming Wang <wgyumg@gmail.com>

Closes #18271 from wangyum/building-spark.

### What changes were proposed in this pull request?
The current option name `wholeFile` is misleading for CSV users. Currently, it is not representing a record per file. Actually, one file could have multiple records. Thus, we should rename it. Now, the proposal is `multiLine`.

### How was this patch tested?
N/A

Author: Xiao Li <gatorsmile@gmail.com>

Closes #18202 from gatorsmile/renameCVSOption.

## What changes were proposed in this pull request?

clean up after big test move

## How was this patch tested?

unit tests, jenkins

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #18267 from felixcheung/rtestset2.

## What changes were proposed in this pull request?

Move all existing tests to non-installed directory so that it will never run by installing SparkR package

For a follow-up PR:
- remove all skip_on_cran() calls in tests
- clean up test timer
- improve or change basic tests that do run on CRAN (if anyone has suggestion)

It looks like `R CMD build pkg` will still put pkg\tests (ie. the full tests) into the source package but `R CMD INSTALL` on such source package does not install these tests (and so `R CMD check` does not run them)

## How was this patch tested?

- [x] unit tests, Jenkins
- [x] AppVeyor
- [x] make a source package, install it, `R CMD check` it - verify the full tests are not installed or run

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #18264 from felixcheung/rtestset.

## What changes were proposed in this pull request?
Document Dataset.union is resolution by position, not by name, since this has been a confusing point for a lot of users.

## How was this patch tested?
N/A - doc only change.

Author: Reynold Xin <rxin@databricks.com>

Closes #18256 from rxin/SPARK-21042.

## What changes were proposed in this pull request?

to investigate how long they run

## How was this patch tested?

Jenkins, AppVeyor

Author: Felix Cheung <felixcheung_m@hotmail.com>

Closes #18104 from felixcheung/rtimetest.

## What changes were proposed in this pull request?
1, add an example for sparkr `decisionTree`
2, document it in user guide

## How was this patch tested?
local submit

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #18067 from zhengruifeng/dt_example.

## What changes were proposed in this pull request?
Joint coefficients with intercept for SparkR linear SVM summary.

## How was this patch tested?
Existing tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #18035 from yanboliang/svm-r.

## What changes were proposed in this pull request?

This change skips tests that use the Hadoop libraries while running
on CRAN check with Windows as the operating system. This is to handle
cases where the Hadoop winutils binaries are missing on the target
system. The skipped tests consist of
1. Tests that save, load a model in MLlib
2. Tests that save, load CSV, JSON and Parquet files in SQL
3. Hive tests

## How was this patch tested?

Tested by running on a local windows VM with HADOOP_HOME unset. Also testing with https://win-builder.r-project.org

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

Closes #17966 from shivaram/sparkr-windows-cran.

## What changes were proposed in this pull request?
support decision tree in R

## How was this patch tested?
added tests

Author: Zheng RuiFeng <ruifengz@foxmail.com>

Closes #17981 from zhengruifeng/dt_r.

## What changes were proposed in this pull request?
Some examples in the DataFrame methods are syntactically wrong, even though they are pseudo code. Fix these and some style issues.

Author: Wayne Zhang <actuaryzhang@uber.com>

Closes #18003 from actuaryzhang/sparkRDoc3.

## What changes were proposed in this pull request?

Rename `carsDF` to `df` in SparkR `rollup` and `cube` examples.

## How was this patch tested?

Manual tests.

Author: zero323 <zero323@users.noreply.github.com>

Closes #17988 from zero323/cube-docs.

## What changes were proposed in this pull request?

- Adds R wrapper for `o.a.s.sql.functions.broadcast`.
- Renames `broadcast` to `broadcast_`.

## How was this patch tested?

Unit tests, check `check-cran.sh`.

Author: zero323 <zero323@users.noreply.github.com>

Closes #17965 from zero323/SPARK-20726.

## What changes were proposed in this pull request?

- Change current short annotations (same as Scala `group`) to verbose names (same as Scala `groupname`).

    Before:

    ![image](https://cloud.githubusercontent.com/assets/1554276/26033909/9a98b596-38b4-11e7-961e-15fd9ea7440d.png)

    After:
    ![image](https://cloud.githubusercontent.com/assets/1554276/26033903/727a9944-38b4-11e7-8873-b09c553f4ec3.png)

- Add missing `family` annotations.

## How was this patch tested?

`check-cran.R` (skipping tests), manual inspection.

Author: zero323 <zero323@users.noreply.github.com>

Closes #17976 from zero323/SPARKR-FUNCTIONS-DOCSTRINGS.