[SPARK-11756][SPARKR] Fix use of aliases - SparkR can not output help information for SparkR:::summary correctly

Fix use of aliases and changes uses of rdname and seealso
`aliases` is the hint for `?` - it should not be linked to some other name - those should be seealso
https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html

Clean up usage on family, as multiple use of family with the same rdname is causing duplicated See Also html blocks (like http://spark.apache.org/docs/latest/api/R/count.html)
Also changing some rdname for dplyr-like variant for better R user visibility in R doc, eg. rbind, summary, mutate, summarize

shivaram yanboliang

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #9750 from felixcheung/rdocaliases.

[SPARK-11716][SQL] UDFRegistration just drops the input type when re-creating the UserDefinedFunction

https://issues.apache.org/jira/browse/SPARK-11716

This is one is #9739 and a regression test. When commit it, please make sure the author is jbonofre.

You can find the original PR at https://github.com/apache/spark/pull/9739

closes #9739

Author: Jean-Baptiste Onofré <jbonofre@apache.org>
Author: Yin Huai <yhuai@databricks.com>

Closes #9868 from yhuai/SPARK-11716.

In PersistenceEngineSuite, we do not call `close()` on the PersistenceEngine at the end of the test. For the ZooKeeperPersistenceEngine, this causes us to leak a ZooKeeper client, causing the logs of unrelated tests to be periodically spammed with connection error messages from that client:

```
15/11/20 05:13:35.789 pool-1-thread-1-ScalaTest-running-PersistenceEngineSuite-SendThread(localhost:15741) INFO ClientCnxn: Opening socket connection to server localhost/127.0.0.1:15741. Will not attempt to authenticate using SASL (unknown error)
15/11/20 05:13:35.790 pool-1-thread-1-ScalaTest-running-PersistenceEngineSuite-SendThread(localhost:15741) WARN ClientCnxn: Session 0x15124ff48dd0000 for server null, unexpected error, closing socket connection and attempting reconnect
java.net.ConnectException: Connection refused
	at sun.nio.ch.SocketChannelImpl.checkConnect(Native Method)
	at sun.nio.ch.SocketChannelImpl.finishConnect(SocketChannelImpl.java:739)
	at org.apache.zookeeper.ClientCnxnSocketNIO.doTransport(ClientCnxnSocketNIO.java:350)
	at org.apache.zookeeper.ClientCnxn$SendThread.run(ClientCnxn.java:1068)
```

This patch fixes this by using a `finally` block.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #9864 from JoshRosen/close-zookeeper-client-in-tests.

[SPARK-11870][STREAMING][PYSPARK] Rethrow the exceptions in TransformFunction and TransformFunctionSerializer

TransformFunction and TransformFunctionSerializer don't rethrow the exception, so when any exception happens, it just return None. This will cause some weird NPE and confuse people.

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #9847 from zsxwing/pyspark-streaming-exception.

Hive has since changed this behavior as well. https://issues.apache.org/jira/browse/HIVE-3454

Author: Nong Li <nong@databricks.com>
Author: Nong Li <nongli@gmail.com>
Author: Yin Huai <yhuai@databricks.com>

Closes #9685 from nongli/spark-11724.

This patch reduces some RPC timeouts in order to speed up the slow "AkkaUtilsSuite.remote fetch ssl on - untrusted server", which used to take two minutes to run.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #9869 from JoshRosen/SPARK-11650.

before this PR, when users try to get an encoder for an un-supported class, they will only get a very simple error message like `Encoder for type xxx is not supported`.

After this PR, the error message become more friendly, for example:
```
No Encoder found for abc.xyz.NonEncodable
- array element class: "abc.xyz.NonEncodable"
- field (class: "scala.Array", name: "arrayField")
- root class: "abc.xyz.AnotherClass"
```

Author: Wenchen Fan <wenchen@databricks.com>

Closes #9810 from cloud-fan/error-message.

JIRA: https://issues.apache.org/jira/browse/SPARK-11817

Instead of return None, we should truncate the fractional seconds to prevent inserting NULL.

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

Closes #9834 from viirya/truncate-fractional-sec.

DataSet APIs look great! However, I am lost when doing multiple level joins.  For example,
```
val ds1 = Seq(("a", 1), ("b", 2)).toDS().as("a")
val ds2 = Seq(("a", 1), ("b", 2)).toDS().as("b")
val ds3 = Seq(("a", 1), ("b", 2)).toDS().as("c")

ds1.joinWith(ds2, $"a._2" === $"b._2").as("ab").joinWith(ds3, $"ab._1._2" === $"c._2").printSchema()
```

The printed schema is like
```
root
 |-- _1: struct (nullable = true)
 |    |-- _1: struct (nullable = true)
 |    |    |-- _1: string (nullable = true)
 |    |    |-- _2: integer (nullable = true)
 |    |-- _2: struct (nullable = true)
 |    |    |-- _1: string (nullable = true)
 |    |    |-- _2: integer (nullable = true)
 |-- _2: struct (nullable = true)
 |    |-- _1: string (nullable = true)
 |    |-- _2: integer (nullable = true)
```

Personally, I think we need the printSchema function. Sometimes, I do not know how to specify the column, especially when their data types are mixed. For example, if I want to write the following select for the above multi-level join, I have to know the schema:
```
newDS.select(expr("_1._2._2 + 1").as[Int]).collect()
```

marmbrus rxin cloud-fan  Do you have the same feeling?

Author: gatorsmile <gatorsmile@gmail.com>

Closes #9855 from gatorsmile/printSchemaDataSet.

jira: https://issues.apache.org/jira/browse/SPARK-11689

Add simple user guide for LDA under spark.ml and example code under examples/. Use include_example to include example code in the user guide markdown. Check SPARK-11606 for instructions.

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #9722 from hhbyyh/ldaMLExample.

```withStd``` and ```withMean``` should be params of ```StandardScaler``` and ```StandardScalerModel```.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9839 from yanboliang/standardScaler-refactor.

This patch fixes an issue where the `spark.sql.TungstenAggregate.testFallbackStartsAt` SQLConf setting was not properly reset / cleared at the end of `TungstenAggregationQueryWithControlledFallbackSuite`. This ended up causing test failures in HiveCompatibilitySuite in Maven builds by causing spilling to occur way too frequently.

This configuration leak was inadvertently introduced during test cleanup in #9618.

Author: Josh Rosen <joshrosen@databricks.com>

Closes #9857 from JoshRosen/clear-fallback-prop-in-test-teardown.

https://issues.apache.org/jira/browse/SPARK-11867

Author: Xusen Yin <yinxusen@gmail.com>

Closes #9849 from yinxusen/SPARK-11867.

Need to remove parent directory (```className```) rather than just tempDir (```className/random_name```)

I tested this with IDFSuite, which has 2 read/write tests, and it fixes the problem.

CC: mengxr  Can you confirm this is fine?  I believe it is since the same ```random_name``` is used for all tests in a suite; we basically have an extra unneeded level of nesting.

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

Closes #9851 from jkbradley/tempdir-cleanup.

* Update doc for PySpark ```HasCheckpointInterval``` that users can understand how to disable checkpoint.
* Update doc for PySpark ```cacheNodeIds``` of ```DecisionTreeParams``` to notify the relationship between ```cacheNodeIds``` and ```checkpointInterval```.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9856 from yanboliang/spark-11875.

Add read/write support to the following estimators under spark.ml:
* ChiSqSelector
* PCA
* VectorIndexer
* Word2Vec

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #9838 from yanboliang/spark-11829.

https://issues.apache.org/jira/browse/SPARK-11846

mengxr

Author: Xusen Yin <yinxusen@gmail.com>

Closes #9836 from yinxusen/SPARK-11846.

Apply the user supplied pathfilter while retrieving the files from fs.

Author: Dilip Biswal <dbiswal@us.ibm.com>

Closes #9830 from dilipbiswal/spark-11544.

This PR has the following optimization:

1) The greatest/least already does the null-check, so the `If` and `IsNull` are not necessary.

2) In greatest/least, it should initialize the result using the first child (removing one block).

3) For primitive types, the generated greater expression is too complicated (`a > b ? 1 : (a < b) ? -1 : 0) > 0`), should be as simple as `a > b`

Combine these optimization, this could improve the performance of `ss_max` query by 30%.

Author: Davies Liu <davies@databricks.com>

Closes #9846 from davies/improve_max.

To make sure that all lineage is correctly truncated for TrackStateRDD when checkpointed.

Author: Tathagata Das <tathagata.das1565@gmail.com>

Closes #9831 from tdas/SPARK-11845.

Don't log ERROR messages when executors are explicitly killed or when
the exit reason is not yet known.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #9780 from vanzin/SPARK-11789.

Fixes bug with grouping sets (including cube/rollup) where aggregates that included grouping expressions would return the wrong (null) result.

Also simplifies the analyzer rule a bit and leaves column pruning to the optimizer.

Added multiple unit tests to DataFrameAggregateSuite and verified it passes hive compatibility suite:
```
build/sbt -Phive -Dspark.hive.whitelist='groupby.*_grouping.*' 'test-only org.apache.spark.sql.hive.execution.HiveCompatibilitySuite'
```

This is an alternative to pr https://github.com/apache/spark/pull/9419 but I think its better as it simplifies the analyzer rule instead of adding another special case to it.

Author: Andrew Ray <ray.andrew@gmail.com>

Closes #9815 from aray/groupingset-agg-fix.

a small change

Author: hushan <hushan@xiaomi.com>

Closes #9691 from suyanNone/unify-getDependency.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #9820 from vanzin/SPARK-11828.

…xceptions are thrown during executor shutdown

This commit will make sure that when uncaught exceptions are prepended with [Container in shutdown] when JVM is shutting down.

Author: Srinivasa Reddy Vundela <vsr@cloudera.com>

Closes #9809 from vundela/master_11799.

Use port 0 to fix port-contention-related flakiness

Author: Shixiong Zhu <shixiong@databricks.com>

Closes #9841 from zsxwing/SPARK-11831.

In addition, tightened visibility of a lot of classes in the columnar package from private[sql] to private[columnar].

Author: Reynold Xin <rxin@databricks.com>

Closes #9842 from rxin/SPARK-11858.

invFunc is optional and can be None. Instead of invFunc (the parameter) invReduceFunc (a local function) was checked for trueness (that is, not None, in this context). A local function is never None,
thus the case of invFunc=None (a common one when inverse reduction is not defined) was treated incorrectly, resulting in loss of data.

In addition, the docstring used wrong parameter names, also fixed.

Author: David Tolpin <david.tolpin@gmail.com>

Closes #9775 from dtolpin/master.

Fix a bug in DataFrameReader.table (table with schema name such as "db_name.table" doesn't work)
Use SqlParser.parseTableIdentifier to parse the table name before lookupRelation.

Author: Huaxin Gao <huaxing@oc0558782468.ibm.com>

Closes #9773 from huaxingao/spark-11778.

After some experiment, I found it's not convenient to have separate encoder builders: `FlatEncoder` and `ProductEncoder`. For example, when create encoders for `ScalaUDF`, we have no idea if the type `T` is flat or not. So I revert the splitting change in https://github.com/apache/spark/pull/9693, while still keeping the bug fixes and tests.

Author: Wenchen Fan <wenchen@databricks.com>

Closes #9726 from cloud-fan/follow.

When debugging DataSet API, I always need to print the logical and physical plans.

I am wondering if we should provide a simple API for EXPLAIN?

Author: gatorsmile <gatorsmile@gmail.com>

Closes #9832 from gatorsmile/explainDS.

When handling self joins, the implementation did not consider the case insensitivity of HiveContext. It could cause an exception as shown in the JIRA:
```
TreeNodeException: Failed to copy node.
```

The fix is low risk. It avoids unnecessary attribute replacement. It should not affect the existing behavior of self joins. Also added the test case to cover this case.

Author: gatorsmile <gatorsmile@gmail.com>

Closes #9762 from gatorsmile/joinMakeCopy.

This PR includes the following change:

1. Bind NettyRpcEnv to the specified host
2. Fix the port information in the log for NettyRpcEnv.
3. Fix the service name of NettyRpcEnv.

Author: zsxwing <zsxwing@gmail.com>
Author: Shixiong Zhu <shixiong@databricks.com>

Closes #9821 from zsxwing/SPARK-11830.

The impact of this change is for a query that has a single distinct column and does not have any grouping expression like
`SELECT COUNT(DISTINCT a) FROM table`
The plan will be changed from
```
AGG-2 (count distinct)
  Shuffle to a single reducer
    Partial-AGG-2 (count distinct)
      AGG-1 (grouping on a)
        Shuffle by a
          Partial-AGG-1 (grouping on 1)
```
to the following one (1.5 uses this)
```
AGG-2
  AGG-1 (grouping on a)
    Shuffle to a single reducer
      Partial-AGG-1(grouping on a)
```
The first plan is more robust. However, to better benchmark the impact of this change, we should use 1.5's plan and use the conf of `spark.sql.specializeSingleDistinctAggPlanning` to control the plan.

Author: Yin Huai <yhuai@databricks.com>

Closes #9828 from yhuai/distinctRewriter.

We currently rely on the optimizer's constant folding to replace current_timestamp and current_date. However, this can still result in different values for different instances of current_timestamp/current_date if the optimizer is not running fast enough.

A better solution is to replace these functions in the analyzer in one shot.

Author: Reynold Xin <rxin@databricks.com>

Closes #9833 from rxin/SPARK-11849.

[SPARK-11339][SPARKR] Document the list of functions in R base package that are masked by functions with same name in SparkR

Added tests for function that are reported as masked, to make sure the base:: or stats:: function can be called.

For those we can't call, added them to SparkR programming guide.

It would seem to me `table, sample, subset, filter, cov` not working are not actually expected - I investigated/experimented with them but couldn't get them to work. It looks like as they are defined in base or stats they are missing the S3 generic, eg.
```
> methods("transform")
[1] transform,ANY-method       transform.data.frame
[3] transform,DataFrame-method transform.default
see '?methods' for accessing help and source code
> methods("subset")
[1] subset.data.frame       subset,DataFrame-method subset.default
[4] subset.matrix
see '?methods' for accessing help and source code
Warning message:
In .S3methods(generic.function, class, parent.frame()) :
  function 'subset' appears not to be S3 generic; found functions that look like S3 methods
```
Any idea?

More information on masking:
http://www.ats.ucla.edu/stat/r/faq/referencing_objects.htm
http://www.sfu.ca/~sweldon/howTo/guide4.pdf

This is what the output doc looks like (minus css):
![image](https://cloud.githubusercontent.com/assets/8969467/11229714/2946e5de-8d4d-11e5-94b0-dda9696b6fdd.png)

Author: felixcheung <felixcheung_m@hotmail.com>

Closes #9785 from felixcheung/rmasked.

Updates:
* Add repartition(1) to save() methods' saving of data for LogisticRegressionModel, LinearRegressionModel.
* Strengthen privacy to class and companion object for Writers and Readers
* Change LogisticRegressionSuite read/write test to fit intercept
* Add Since versions for read/write methods in Pipeline, LogisticRegression
* Switch from hand-written class names in Readers to using getClass

CC: mengxr

CC: yanboliang Would you mind taking a look at this PR?  mengxr might not be able to soon.  Thank you!

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

Closes #9829 from jkbradley/ml-io-cleanups.

see HIVE-7975 and HIVE-12373

With changed semantic of setters in thrift objects in hive, setter should be called only after all parameters are set. It's not problem of current state but will be a problem in some day.

Author: navis.ryu <navis@apache.org>

Closes #9580 from navis/SPARK-11614.

jira: https://issues.apache.org/jira/browse/SPARK-11816
Currently I only fixed some obvious comments issue like
// scalastyle:off println
on the bottom.

Yet the style in examples is not quite consistent, like only half of the examples  are with
// Example usage: ./bin/run-example mllib.FPGrowthExample \,

Author: Yuhao Yang <hhbyyh@gmail.com>

Closes #9808 from hhbyyh/exampleStyle.

This reverts commit 54db7970.