MAINTENANCE: Automated closing of pull requests.

This commit exists to close the following pull requests on Github:

Closes #740 (close requested by 'rxin')
Closes #647 (close requested by 'rxin')
Closes #1383 (close requested by 'rxin')
Closes #1485 (close requested by 'pwendell')
Closes #693 (close requested by 'rxin')
Closes #478 (close requested by 'JoshRosen')
[SPARK-2716][SQL] Don't check resolved for having filters.

For queries like `... HAVING COUNT(*) > 9` the expression is always resolved since it contains no attributes.  This was causing us to avoid doing the Having clause aggregation rewrite.

Author: Michael Armbrust <michael@databricks.com>

Closes #1640 from marmbrus/havingNoRef and squashes the following commits:

92d3901 [Michael Armbrust] Don't check resolved for having filters.
[SPARK-2631][SQL] Use SQLConf to configure in-memory columnar caching

Author: Michael Armbrust <michael@databricks.com>

Closes #1638 from marmbrus/cachedConfig and squashes the following commits:

2362082 [Michael Armbrust] Use SQLConf to configure in-memory columnar caching
[SPARK-2305] [PySpark] Update Py4J to version 0.8.2.1

Author: Josh Rosen <joshrosen@apache.org>

Closes #1626 from JoshRosen/SPARK-2305 and squashes the following commits:

03fb283 [Josh Rosen] Update Py4J to version 0.8.2.1.
[SPARK-2054][SQL] Code Generation for Expression Evaluation

Adds a new method for evaluating expressions using code that is generated though Scala reflection.  This functionality is configured by the SQLConf option `spark.sql.codegen` and is currently turned off by default.

Evaluation can be done in several specialized ways:
 - *Projection* - Given an input row, produce a new row from a set of expressions that define each column in terms of the input row.  This can either produce a new Row object or perform the projection in-place on an existing Row (MutableProjection).
 - *Ordering* - Compares two rows based on a list of `SortOrder` expressions
 - *Condition* - Returns `true` or `false` given an input row.

For each of the above operations there is both a Generated and Interpreted version.  When generation for a given expression type is undefined, the code generator falls back on calling the `eval` function of the expression class.  Even without custom code, there is still a potential speed up, as loops are unrolled and code can still be inlined by JIT.

This PR also contains a new type of Aggregation operator, `GeneratedAggregate`, that performs aggregation by using generated `Projection` code.  Currently the required expression rewriting only works for simple aggregations like `SUM` and `COUNT`.  This functionality will be extended in a future PR.

This PR also performs several clean ups that simplified the implementation:
 - The notion of `Binding` all expressions in a tree automatically before query execution has been removed.  Instead it is the responsibly of an operator to provide the input schema when creating one of the specialized evaluators defined above.  In cases when the standard eval method is going to be called, binding can still be done manually using `BindReferences`.  There are a few reasons for this change:  First, there were many operators where it just didn't work before.  For example, operators with more than one child, and operators like aggregation that do significant rewriting of the expression. Second, the semantics of equality with `BoundReferences` are broken.  Specifically, we have had a few bugs where partitioning breaks because of the binding.
 - A copy of the current `SQLContext` is automatically propagated to all `SparkPlan` nodes by the query planner.  Before this was done ad-hoc for the nodes that needed this.  However, this required a lot of boilerplate as one had to always remember to make it `transient` and also had to modify the `otherCopyArgs`.

Author: Michael Armbrust <michael@databricks.com>

Closes #993 from marmbrus/newCodeGen and squashes the following commits:

96ef82c [Michael Armbrust] Merge remote-tracking branch 'apache/master' into newCodeGen
f34122d [Michael Armbrust] Merge remote-tracking branch 'apache/master' into newCodeGen
67b1c48 [Michael Armbrust] Use conf variable in SQLConf object
4bdc42c [Michael Armbrust] Merge remote-tracking branch 'origin/master' into newCodeGen
41a40c9 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into newCodeGen
de22aac [Michael Armbrust] Merge remote-tracking branch 'origin/master' into newCodeGen
fed3634 [Michael Armbrust] Inspectors are not serializable.
ef8d42b [Michael Armbrust] comments
533fdfd [Michael Armbrust] More logging of expression rewriting for GeneratedAggregate.
3cd773e [Michael Armbrust] Allow codegen for Generate.
64b2ee1 [Michael Armbrust] Implement copy
3587460 [Michael Armbrust] Drop unused string builder function.
9cce346 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into newCodeGen
1a61293 [Michael Armbrust] Address review comments.
0672e8a [Michael Armbrust] Address comments.
1ec2d6e [Michael Armbrust] Address comments
033abc6 [Michael Armbrust] off by default
4771fab [Michael Armbrust] Docs, more test coverage.
d30fee2 [Michael Armbrust] Merge remote-tracking branch 'origin/master' into newCodeGen
d2ad5c5 [Michael Armbrust] Refactor putting SQLContext into SparkPlan. Fix ordering, other test cases.
be2cd6b [Michael Armbrust] WIP: Remove old method for reference binding, more work on configuration.
bc88ecd [Michael Armbrust] Style
6cc97ca [Michael Armbrust] Merge remote-tracking branch 'origin/master' into newCodeGen
4220f1e [Michael Armbrust] Better config, docs, etc.
ca6cc6b [Michael Armbrust] WIP
9d67d85 [Michael Armbrust] Fix hive planner
fc522d5 [Michael Armbrust] Hook generated aggregation in to the planner.
e742640 [Michael Armbrust] Remove unneeded changes and code.
675e679 [Michael Armbrust] Upgrade paradise.
0093376 [Michael Armbrust] Comment / indenting cleanup.
d81f998 [Michael Armbrust] include schema for binding.
0e889e8 [Michael Armbrust] Use typeOf instead tq
f623ffd [Michael Armbrust] Quiet logging from test suite.
efad14f [Michael Armbrust] Remove some half finished functions.
92e74a4 [Michael Armbrust] add overrides
a2b5408 [Michael Armbrust] WIP: Code generation with scala reflection.
[SPARK-2568] RangePartitioner should run only one job if data is balanced

As of Spark 1.0, RangePartitioner goes through data twice: once to compute the count and once to do sampling. As a result, to do sortByKey, Spark goes through data 3 times (once to count, once to sample, and once to sort).

`RangePartitioner` should go through data only once, collecting samples from input partitions as well as counting. If the data is balanced, this should give us a good sketch. If we see big partitions, we re-sample from them in order to collect enough items.

The downside is that we need to collect more from each partition in the first pass. An alternative solution is caching the intermediate result and decide whether to fetch the data after.

Author: Xiangrui Meng <meng@databricks.com>
Author: Reynold Xin <rxin@apache.org>

Closes #1562 from mengxr/range-partitioner and squashes the following commits:

6cc2551 [Xiangrui Meng] change foreach to for
eb39b08 [Xiangrui Meng] Merge branch 'master' into range-partitioner
eb95dd8 [Xiangrui Meng] separate sketching and determining bounds impl
c436d30 [Xiangrui Meng] fix binary metrics unit tests
db58a55 [Xiangrui Meng] add unit tests
a6e35d6 [Xiangrui Meng] minor update
60be09e [Xiangrui Meng] remove importance sampler
9ee9992 [Xiangrui Meng] update range partitioner to run only one job on roughly balanced data
cc12f47 [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into range-part
06ac2ec [Xiangrui Meng] Merge remote-tracking branch 'apache/master' into range-part
17bcbf3 [Reynold Xin] Added seed.
badf20d [Reynold Xin] Renamed the method.
6940010 [Reynold Xin] Reservoir sampling implementation.
[SQL] Handle null values in debug()

Author: Michael Armbrust <michael@databricks.com>

Closes #1646 from marmbrus/nullDebug and squashes the following commits:

49050a8 [Michael Armbrust] Handle null values in debug()
[SPARK-2260] Fix standalone-cluster mode, which was broken

The main thing was that spark configs were not propagated to the driver, and so applications that do not specify `master` or `appName` automatically failed. This PR fixes that and a couple of miscellaneous things that are related.

One thing that may or may not be an issue is that the jars must be available on the driver node. In `standalone-cluster` mode, this effectively means these jars must be available on all the worker machines, since the driver is launched on one of them. The semantics here are not the same as `yarn-cluster` mode,  where all the relevant jars are uploaded to a distributed cache automatically and shipped to the containers. This is probably not a concern, but still worth a mention.

Author: Andrew Or <andrewor14@gmail.com>

Closes #1538 from andrewor14/standalone-cluster and squashes the following commits:

8c11a0d [Andrew Or] Clean up imports / comments (minor)
2678d13 [Andrew Or] Handle extraJavaOpts properly
7660547 [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-cluster
6f64a9b [Andrew Or] Revert changes in YARN
2f2908b [Andrew Or] Fix tests
ed01491 [Andrew Or] Don't go overboard with escaping
8e105e1 [Andrew Or] Merge branch 'master' of github.com:apache/spark into standalone-cluster
b890949 [Andrew Or] Abstract usages of converting spark opts to java opts
79f63a3 [Andrew Or] Move sparkProps into javaOpts
78752f8 [Andrew Or] Fix tests
5a9c6c7 [Andrew Or] Fix line too long
c141a00 [Andrew Or] Don't display "unknown app" on driver log pages
d7e2728 [Andrew Or] Avoid deprecation warning in standalone Client
6ceb14f [Andrew Or] Allow relevant configs to propagate to standalone Driver
7f854bc [Andrew Or] Fix test
855256e [Andrew Or] Fix standalone-cluster mode
fd9da51 [Andrew Or] Formatting changes (minor)
[SPARK-2179][SQL] Public API for DataTypes and Schema

The current PR contains the following changes:
* Expose `DataType`s in the sql package (internal details are private to sql).
* Users can create Rows.
* Introduce `applySchema` to create a `SchemaRDD` by applying a `schema: StructType` to an `RDD[Row]`.
* Add a function `simpleString` to every `DataType`. Also, the schema represented by a `StructType` can be visualized by `printSchema`.
* `ScalaReflection.typeOfObject` provides a way to infer the Catalyst data type based on an object. Also, we can compose `typeOfObject` with some custom logics to form a new function to infer the data type (for different use cases).
* `JsonRDD` has been refactored to use changes introduced by this PR.
* Add a field `containsNull` to `ArrayType`. So, we can explicitly mark if an `ArrayType` can contain null values. The default value of `containsNull` is `false`.

New APIs are introduced in the sql package object and SQLContext. You can find the scaladoc at
[sql package object](http://yhuai.github.io/site/api/scala/index.html#org.apache.spark.sql.package) and [SQLContext](http://yhuai.github.io/site/api/scala/index.html#org.apache.spark.sql.SQLContext).

An example of using `applySchema` is shown below.
```scala
import org.apache.spark.sql._
val sqlContext = new org.apache.spark.sql.SQLContext(sc)

val schema =
  StructType(
    StructField("name", StringType, false) ::
    StructField("age", IntegerType, true) :: Nil)

val people = sc.textFile("examples/src/main/resources/people.txt").map(_.split(",")).map(p => Row(p(0), p(1).trim.toInt))
val peopleSchemaRDD = sqlContext. applySchema(people, schema)
peopleSchemaRDD.printSchema
// root
// |-- name: string (nullable = false)
// |-- age: integer (nullable = true)

peopleSchemaRDD.registerAsTable("people")
sqlContext.sql("select name from people").collect.foreach(println)
```

I will add new contents to the SQL programming guide later.

JIRA: https://issues.apache.org/jira/browse/SPARK-2179

Author: Yin Huai <huai@cse.ohio-state.edu>

Closes #1346 from yhuai/dataTypeAndSchema and squashes the following commits:

1d45977 [Yin Huai] Clean up.
a6e08b4 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
c712fbf [Yin Huai] Converts types of values based on defined schema.
4ceeb66 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
e5f8df5 [Yin Huai] Scaladoc.
122d1e7 [Yin Huai] Address comments.
03bfd95 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
2476ed0 [Yin Huai] Minor updates.
ab71f21 [Yin Huai] Format.
fc2bed1 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
bd40a33 [Yin Huai] Address comments.
991f860 [Yin Huai] Move "asJavaDataType" and "asScalaDataType" to DataTypeConversions.scala.
1cb35fe [Yin Huai] Add "valueContainsNull" to MapType.
3edb3ae [Yin Huai] Python doc.
692c0b9 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
1d93395 [Yin Huai] Python APIs.
246da96 [Yin Huai] Add java data type APIs to javadoc index.
1db9531 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
d48fc7b [Yin Huai] Minor updates.
33c4fec [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
b9f3071 [Yin Huai] Java API for applySchema.
1c9f33c [Yin Huai] Java APIs for DataTypes and Row.
624765c [Yin Huai] Tests for applySchema.
aa92e84 [Yin Huai] Update data type tests.
8da1a17 [Yin Huai] Add Row.fromSeq.
9c99bc0 [Yin Huai] Several minor updates.
1d9c13a [Yin Huai] Update applySchema API.
85e9b51 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
e495e4e [Yin Huai] More comments.
42d47a3 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
c3f4a02 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
2e58dbd [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
b8b7db4 [Yin Huai] 1. Move sql package object and package-info to sql-core. 2. Minor updates on APIs. 3. Update scala doc.
68525a2 [Yin Huai] Update JSON unit test.
3209108 [Yin Huai] Add unit tests.
dcaf22f [Yin Huai] Add a field containsNull to ArrayType to indicate if an array can contain null values or not. If an ArrayType is constructed by "ArrayType(elementType)" (the existing constructor), the value of containsNull is false.
9168b83 [Yin Huai] Update comments.
fc649d7 [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
eca7d04 [Yin Huai] Add two apply methods which will be used to extract StructField(s) from a StructType.
949d6bb [Yin Huai] When creating a SchemaRDD for a JSON dataset, users can apply an existing schema.
7a6a7e5 [Yin Huai] Fix bug introduced by the change made on SQLContext.inferSchema.
43a45e1 [Yin Huai] Remove sql.util.package introduced in a previous commit.
0266761 [Yin Huai] Format
03eec4c [Yin Huai] Merge remote-tracking branch 'upstream/master' into dataTypeAndSchema
90460ac [Yin Huai] Infer the Catalyst data type from an object and cast a data value to the expected type.
3fa0df5 [Yin Huai] Provide easier ways to construct a StructType.
16be3e5 [Yin Huai] This commit contains three changes: * Expose `DataType`s in the sql package (internal details are private to sql). * Introduce `createSchemaRDD` to create a `SchemaRDD` from an `RDD` with a provided schema (represented by a `StructType`) and a provided function to construct `Row`, * Add a function `simpleString` to every `DataType`. Also, the schema represented by a `StructType` can be visualized by `printSchema`.
SPARK-2543: Allow user to set maximum Kryo buffer size

Author: Koert Kuipers <koert@tresata.com>

Closes #735 from koertkuipers/feat-kryo-max-buffersize and squashes the following commits:

15f6d81 [Koert Kuipers] change default for spark.kryoserializer.buffer.max.mb to 64mb and add some documentation
1bcc22c [Koert Kuipers] Merge branch 'master' into feat-kryo-max-buffersize
0c9f8eb [Koert Kuipers] make default for kryo max buffer size 16MB
143ec4d [Koert Kuipers] test resizable buffer in kryo Output
0732445 [Koert Kuipers] support setting maxCapacity to something different than capacity in kryo Output
SPARK-2748 [MLLIB] [GRAPHX] Loss of precision for small arguments to Math.exp, Math.log

In a few places in MLlib, an expression of the form `log(1.0 + p)` is evaluated. When p is so small that `1.0 + p == 1.0`, the result is 0.0. However the correct answer is very near `p`. This is why `Math.log1p` exists.

Similarly for one instance of `exp(m) - 1` in GraphX; there's a special `Math.expm1` method.

While the errors occur only for very small arguments, given their use in machine learning algorithms, this is entirely possible.

Also note the related PR for Python: https://github.com/apache/spark/pull/1652

Author: Sean Owen <srowen@gmail.com>

Closes #1659 from srowen/SPARK-2748 and squashes the following commits:

c5926d4 [Sean Owen] Use log1p, expm1 for better precision for tiny arguments
[SPARK-2521] Broadcast RDD object (instead of sending it along with every task)

This is a resubmission of #1452. It was reverted because it broke the build.

Currently (as of Spark 1.0.1), Spark sends RDD object (which contains closures) using Akka along with the task itself to the executors. This is inefficient because all tasks in the same stage use the same RDD object, but we have to send RDD object multiple times to the executors. This is especially bad when a closure references some variable that is very large. The current design led to users having to explicitly broadcast large variables.

The patch uses broadcast to send RDD objects and the closures to executors, and use Akka to only send a reference to the broadcast RDD/closure along with the partition specific information for the task. For those of you who know more about the internals, Spark already relies on broadcast to send the Hadoop JobConf every time it uses the Hadoop input, because the JobConf is large.

The user-facing impact of the change include:

1. Users won't need to decide what to broadcast anymore, unless they would want to use a large object multiple times in different operations
2. Task size will get smaller, resulting in faster scheduling and higher task dispatch throughput.

In addition, the change will simplify some internals of Spark, eliminating the need to maintain task caches and the complex logic to broadcast JobConf (which also led to a deadlock recently).

A simple way to test this:
```scala
val a = new Array[Byte](1000*1000); scala.util.Random.nextBytes(a);
sc.parallelize(1 to 1000, 1000).map { x => a; x }.groupBy { x => a; x }.count
```

Numbers on 3 r3.8xlarge instances on EC2
```
master branch: 5.648436068 s, 4.715361895 s, 5.360161877 s
with this change: 3.416348793 s, 1.477846558 s, 1.553432156 s
```

Author: Reynold Xin <rxin@apache.org>

Closes #1498 from rxin/broadcast-task and squashes the following commits:

f7364db [Reynold Xin] Code review feedback.
f8535dc [Reynold Xin] Fixed the style violation.
252238d [Reynold Xin] Serialize the final task closure as well as ShuffleDependency in taskBinary.
111007d [Reynold Xin] Fix broadcast tests.
797c247 [Reynold Xin] Properly send SparkListenerStageSubmitted and SparkListenerStageCompleted.
bab1d8b [Reynold Xin] Check for NotSerializableException in submitMissingTasks.
cf38450 [Reynold Xin] Use TorrentBroadcastFactory.
991c002 [Reynold Xin] Use HttpBroadcast.
de779f8 [Reynold Xin] Fix TaskContextSuite.
cc152fc [Reynold Xin] Don't cache the RDD broadcast variable.
d256b45 [Reynold Xin] Fixed unit test failures. One more to go.
cae0af3 [Reynold Xin] [SPARK-2521] Broadcast RDD object (instead of sending it along with every task).
[SPARK-2747] git diff --dirstat can miss sql changes and not run Hive tests

dev/run-tests use "git diff --dirstat master" to check whether sql is changed. However, --dirstat won't show sql if sql's change is negligible (e.g. 1k loc change in core, and only 1 loc change in hive).

We should use "git diff --name-only master" instead.

Author: Reynold Xin <rxin@apache.org>

Closes #1656 from rxin/hiveTest and squashes the following commits:

f5eab9f [Reynold Xin] [SPARK-2747] git diff --dirstat can miss sql changes and not run Hive tests.
Avoid numerical instability

This avoids basically doing 1 - 1, for example:

```python
>>> from math import exp
>>> margin = -40
>>> 1 - 1 / (1 + exp(margin))
0.0
>>> exp(margin) / (1 + exp(margin))
4.248354255291589e-18
>>>
```

Author: Naftali Harris <naftaliharris@gmail.com>

Closes #1652 from naftaliharris/patch-2 and squashes the following commits:

0d55a9f [Naftali Harris] Avoid numerical instability
[SPARK-2544][MLLIB] Improve ALS algorithm resource usage

Author: GuoQiang Li <witgo@qq.com>
Author: witgo <witgo@qq.com>

Closes #929 from witgo/improve_als and squashes the following commits:

ea25033 [GuoQiang Li] checkpoint products 3,6,9 ...
154dccf [GuoQiang Li] checkpoint products only
c5779ff [witgo] Improve ALS algorithm resource usage
SPARK-2664. Deal with `--conf` options in spark-submit that relate to flags