Tested locally with a Win7 VM. Connected to a Spark SQL Thrift server instance running on Mac OS X with the following command line:

```
bin\beeline.cmd -u jdbc:hive2://10.0.2.2:10000 -n lian
```

<!-- Reviewable:start -->
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Author: Cheng Lian <lian@databricks.com>

Closes #3599 from liancheng/beeline.cmd and squashes the following commits:

79092e7 [Cheng Lian] Windows script for BeeLine

and some minor changes in ScalaDoc.

Author: Xiangrui Meng <meng@databricks.com>

Closes #3601 from mengxr/SPARK-4575-fix and squashes the following commits:

c559768 [Xiangrui Meng] minor code update
ce94da8 [Xiangrui Meng] Java Bean -> JavaBean
0b5c182 [Xiangrui Meng] fix links in ml-guide

Documentation:
* Added ml-guide.md, linked from mllib-guide.md
* Updated mllib-guide.md with small section pointing to ml-guide.md

Examples:
* CrossValidatorExample
* SimpleParamsExample
* (I copied these + the SimpleTextClassificationPipeline example into the ml-guide.md)

Bug fixes:
* PipelineModel: did not use ParamMaps correctly
* UnaryTransformer: issues with TypeTag serialization (Thanks to mengxr for that fix!)

CC: mengxr shivaram  etrain  Documentation for Pipelines: I know the docs are not complete, but the goal is to have enough to let interested people get started using spark.ml and to add more docs once the package is more established/complete.

Author: Joseph K. Bradley <joseph@databricks.com>
Author: jkbradley <joseph.kurata.bradley@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #3588 from jkbradley/ml-package-docs and squashes the following commits:

d393b5c [Joseph K. Bradley] fixed bug in Pipeline (typo from last commit).  updated examples for CV and Params for spark.ml
c38469c [Joseph K. Bradley] Updated ml-guide with CV examples
99f88c2 [Joseph K. Bradley] Fixed bug in PipelineModel.transform* with usage of params.  Updated CrossValidatorExample to use more training examples so it is less likely to get a 0-size fold.
ea34dc6 [jkbradley] Merge pull request #4 from mengxr/ml-package-docs
3b83ec0 [Xiangrui Meng] replace TypeTag with explicit datatype
41ad9b1 [Joseph K. Bradley] Added examples for spark.ml: SimpleParamsExample + Java version, CrossValidatorExample + Java version.  CrossValidatorExample not working yet.  Added programming guide for spark.ml, but need to add CrossValidatorExample to it once CrossValidatorExample works.

When you use the SPARK_JAVA_OPTS env variable, Spark complains:

```
SPARK_JAVA_OPTS was detected (set to ' -verbose:gc -XX:+PrintGCDetails -XX:+PrintGCTimeStamps ').
This is deprecated in Spark 1.0+.

Please instead use:
 - ./spark-submit with conf/spark-defaults.conf to set defaults for an application
 - ./spark-submit with --driver-java-options to set -X options for a driver
 - spark.executor.extraJavaOptions to set -X options for executors
 - SPARK_DAEMON_JAVA_OPTS to set java options for standalone daemons (master or worker)
```

This updates the docs to redirect the user to the relevant part of the configuration docs.

CC: mengxr  but please CC someone else as needed

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

Closes #3592 from jkbradley/tuning-doc and squashes the following commits:

0760ce1 [Joseph K. Bradley] fixed outdated comment in tuning guide

Just found this instance while doing some jstack-based profiling of a Spark SQL job. It is very unlikely that this is causing much of a perf issue anywhere, but it is unnecessarily suboptimal.

Author: Aaron Davidson <aaron@databricks.com>

Closes #3593 from aarondav/seq-opt and squashes the following commits:

962cdfc [Aaron Davidson] [SQL] Minor: Avoid calling Seq#size in a loop

This is #3554 from Lewuathe except that I put both `spark.ml` and `spark.mllib` in the group 'MLlib`.

Closes #3554

jkbradley

Author: lewuathe <lewuathe@me.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #3598 from mengxr/Lewuathe-modify-javadoc-setting and squashes the following commits:

184609a [Xiangrui Meng] merge spark.ml and spark.mllib into the same group in javadoc
f7535e6 [lewuathe] [SPARK-4685] Update JavaDoc settings to include spark.ml and all spark.mllib subpackages in the right sections

MappedRDD, MappedValuesRDD, FlatMappedValuesRDD, FilteredRDD, GlommedRDD, FlatMappedRDD are not necessary. They can be implemented trivially using MapPartitionsRDD.

Author: Reynold Xin <rxin@databricks.com>

Closes #3578 from rxin/SPARK-4719 and squashes the following commits:

eed9853 [Reynold Xin] Preserve partitioning for filter.
eb1a89b [Reynold Xin] [SPARK-4719][API] Consolidate various narrow dep RDD classes with MapPartitionsRDD.

Author: Jacky Li <jacky.likun@huawei.com>

Closes #3585 from jackylk/remove and squashes the following commits:

045423d [Jacky Li] remove unnecessary import

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

Closes #1875 (close requested by 'marmbrus')
Closes #3566 (close requested by 'andrewor14')
Closes #3487 (close requested by 'pwendell')

This commit involves three main changes:

(1) It separates the translation of contributor names from the
generation of the contributors list. This is largely motivated
by the Github API limit; even if we exceed this limit, we should
at least be able to proceed manually as before. This is why the
translation logic is abstracted into its own script
translate-contributors.py.

(2) When we look for candidate replacements for invalid author
names, we should look for the assignees of the associated JIRAs
too. As a result, the intermediate file must keep track of these.

(3) This provides an interactive mode with which the user can
sit at the terminal and manually pick the candidate replacement
that he/she thinks makes the most sense. As before, there is a
non-interactive mode that picks the first candidate that the
script considers "valid."

TODO: We should have a known_contributors file that stores
known mappings so we don't have to go through all of this
translation every time. This is also valuable because some
contributors simply cannot be automatically translated.

Major changes:
* Added programming guide sections for tree ensembles
* Added examples for tree ensembles
* Updated DecisionTree programming guide with more info on parameters
* **API change**: Standardized the tree parameter for the number of classes (for classification)

Minor changes:
* Updated decision tree documentation
* Updated existing tree and tree ensemble examples
 * Use train/test split, and compute test error instead of training error.
 * Fixed decision_tree_runner.py to actually use the number of classes it computes from data. (small bug fix)

Note: I know this is a lot of lines, but most is covered by:
* Programming guide sections for gradient boosting and random forests.  (The changes are probably best viewed by generating the docs locally.)
* New examples (which were copied from the programming guide)
* The "numClasses" renaming

I have run all examples and relevant unit tests.

CC: mengxr manishamde codedeft

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

Closes #3461 from jkbradley/ensemble-docs and squashes the following commits:

70a75f3 [Joseph K. Bradley] updated forest vs boosting comparison
d1de753 [Joseph K. Bradley] Added note about toString and toDebugString for DecisionTree to migration guide
8e87f8f [Joseph K. Bradley] Combined GBT and RandomForest guides into one ensembles guide
6fab846 [Joseph K. Bradley] small fixes based on review
b9f8576 [Joseph K. Bradley] updated decision tree doc
375204c [Joseph K. Bradley] fixed python style
2b60b6e [Joseph K. Bradley] merged Java RandomForest examples into 1 file.  added header.  Fixed small bug in same example in the programming guide.
706d332 [Joseph K. Bradley] updated python DT runner to print full model if it is small
c76c823 [Joseph K. Bradley] added migration guide for mllib
abe5ed7 [Joseph K. Bradley] added examples for random forest in Java and Python to examples folder
07fc11d [Joseph K. Bradley] Renamed numClassesForClassification to numClasses everywhere in trees and ensembles. This is a breaking API change, but it was necessary to correct an API inconsistency in Spark 1.1 (where Python DecisionTree used numClasses but Scala used numClassesForClassification).
cdfdfbc [Joseph K. Bradley] added examples for GBT
6372a2b [Joseph K. Bradley] updated decision tree examples to use random split.  tested all of them.
ad3e695 [Joseph K. Bradley] added gbt and random forest to programming guide.  still need to update their examples

I have heard requests for the docs to include advice about choosing an optimization method. The programming guide could include a brief statement about this (so the user does not have to read the whole optimization section).

CC: mengxr

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

Closes #3569 from jkbradley/lr-doc and squashes the following commits:

654aeb5 [Joseph K. Bradley] updated section header for mllib-optimization
5035ad0 [Joseph K. Bradley] updated based on review
94f6dec [Joseph K. Bradley] Updated linear methods and optimization docs with quick advice on choosing an optimization method

cc aarondav kayousterhout pwendell

This should go into 1.2?

Author: Reynold Xin <rxin@databricks.com>

Closes #3579 from rxin/SPARK-4085 and squashes the following commits:

255b4fd [Reynold Xin] Updated test.
f9814d9 [Reynold Xin] Code review feedback.
2afaf35 [Reynold Xin] [SPARK-4085] Propagate FetchFailedException when Spark fails to read local shuffle file.

The ExecutorInfo only reaches the RUNNING state if the Driver is alive to send the ExecutorStateChanged message to master.  Else, appInfo.resetRetryCount() is never called and failing Executors will eventually exceed ApplicationState.MAX_NUM_RETRY, resulting in the application being removed from the master's accounting.

JoshRosen

Author: Mark Hamstra <markhamstra@gmail.com>

Closes #3550 from markhamstra/SPARK-4498 and squashes the following commits:

8f543b1 [Mark Hamstra] Don't transition ExecutorInfo to RUNNING until Executor is added by Driver

This is a very small fix that catches one specific exception and returns an empty table.  #3441 will address this in a more principled way.

Author: Michael Armbrust <michael@databricks.com>

Closes #3586 from marmbrus/fixEmptyParquet and squashes the following commits:

2781d9f [Michael Armbrust] Handle empty lists for newParquet
04dd376 [Michael Armbrust] Avoid exception when reading empty parquet data through Hive

This is caused by a975dc32

Author: Andrew Or <andrew@databricks.com>

Closes #3589 from andrewor14/yarn-hot-fix and squashes the following commits:

a4fad5f [Andrew Or] Check whether lib directory exists before listing its files

Added descriptions about these parameters.
- spark.yarn.queue

Modified description about the defalut value of this parameter.
- spark.yarn.submit.file.replication

Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp>

Closes #3500 from tsudukim/feature/SPARK-4642 and squashes the following commits:

ce99655 [Masayoshi TSUZUKI] better gramatically.
21cf624 [Masayoshi TSUZUKI] Removed intentionally undocumented properties.
88cac9b [Masayoshi TSUZUKI] [SPARK-4642] Documents about running-on-YARN needs update

ShuffleMemoryManager.tryToAcquire may return a negative value. The unit test demonstrates this bug. It will output `0 did not equal -200 granted is negative`.

Author: zsxwing <zsxwing@gmail.com>

Closes #3575 from zsxwing/SPARK-4715 and squashes the following commits:

a193ae6 [zsxwing] Make sure tryToAcquire won't return a negative value

Modified typo.

Author: Masayoshi TSUZUKI <tsudukim@oss.nttdata.co.jp>

Closes #3560 from tsudukim/feature/SPARK-4701 and squashes the following commits:

ed2a3f1 [Masayoshi TSUZUKI] Another whitespace position error.
1af3a35 [Masayoshi TSUZUKI] [SPARK-4701] Typo in sbt/sbt

If `spark-submit` finds the datanucleus jars, it adds them to the driver's classpath, but does not add it to the container.

This patch modifies the yarn deployment class to copy all `datanucleus-*` jars found in `[spark-home]/libs` to the container.

Author: Jim Lim <jim@quixey.com>

Closes #3238 from jimjh/SPARK-2624 and squashes the following commits:

3633071 [Jim Lim] SPARK-2624 update documentation and comments
fe95125 [Jim Lim] SPARK-2624 keep java imports together
6c31fe0 [Jim Lim] SPARK-2624 update documentation
6690fbf [Jim Lim] SPARK-2624 add tests
d28d8e9 [Jim Lim] SPARK-2624 add spark.yarn.datanucleus.dir option
84e6cba [Jim Lim] SPARK-2624 add datanucleus jars to the container in yarn-cluster

Have a local reference to `values` and `indices` array in the `Vector` object
so JVM can locate the value with one operation call. See `SPARK-4581`
for similar optimization, and the bytecode analysis.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #3577 from dbtsai/blasopt and squashes the following commits:

62d38c4 [DB Tsai] formating
0316cef [DB Tsai] first commit

Note that the usage of `breezeSquaredDistance` in
`org.apache.spark.mllib.util.MLUtils.fastSquaredDistance`
is in the critical path, and `breezeSquaredDistance` is slow.
We should replace it with our own implementation.

Here is the benchmark against mnist8m dataset.

Before
DenseVector: 70.04secs
SparseVector: 59.05secs

With this PR
DenseVector: 30.58secs
SparseVector: 21.14secs

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #3565 from dbtsai/kmean and squashes the following commits:

08bc068 [DB Tsai] restyle
de24662 [DB Tsai] address feedback
b185a77 [DB Tsai] cleanup
4554ddd [DB Tsai] first commit

Renamed StreamingKMeans to StreamingKMeansExample to avoid warning about name conflict with StreamingKMeans class.

Added import to DecisionTreeRunner to eliminate warning.

CC: mengxr

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

Closes #3568 from jkbradley/ml-compilation-warnings and squashes the following commits:

64d6bc4 [Joseph K. Bradley] Updated DecisionTreeRunner.scala and StreamingKMeans.scala to eliminate compilation warnings, including renaming StreamingKMeans to StreamingKMeansExample.

As #3262 wasn't merged to branch 1.2, the `since` value of `deprecated` should be '1.3.0'.

Author: zsxwing <zsxwing@gmail.com>

Closes #3573 from zsxwing/SPARK-4397-version and squashes the following commits:

1daa03c [zsxwing] Change the 'since' value to '1.3.0'

The related JIRA is https://issues.apache.org/jira/browse/SPARK-4672

The f closure of `PartitionsRDD(ZippedPartitionsRDD2)` contains a `$outer` that references EdgeRDD/VertexRDD, which causes task's serialization chain become very long in iterative GraphX applications. As a result, StackOverflow error will occur. If we set "f = null" in `clearDependencies()`, checkpoint() can cut off the long serialization chain. More details and explanation can be found in the JIRA.

Author: JerryLead <JerryLead@163.com>
Author: Lijie Xu <csxulijie@gmail.com>

Closes #3545 from JerryLead/my_core and squashes the following commits:

f7faea5 [JerryLead] checkpoint() should clear the f to avoid StackOverflow error
c0169da [JerryLead] Merge branch 'master' of https://github.com/apache/spark
52799e3 [Lijie Xu] Merge pull request #1 from apache/master

The related JIRA is https://issues.apache.org/jira/browse/SPARK-4672

In a nutshell, if `val partitionsRDD` in EdgeRDDImpl and VertexRDDImpl are non-transient, the serialization chain can become very long in iterative algorithms and finally lead to the StackOverflow error. More details and explanation can be found in the JIRA.

Author: JerryLead <JerryLead@163.com>
Author: Lijie Xu <csxulijie@gmail.com>

Closes #3544 from JerryLead/my_graphX and squashes the following commits:

628f33c [JerryLead] set PartitionsRDD to be transient in EdgeRDDImpl and VertexRDDImpl
c0169da [JerryLead] Merge branch 'master' of https://github.com/apache/spark
52799e3 [Lijie Xu] Merge pull request #1 from apache/master

The related JIRA is https://issues.apache.org/jira/browse/SPARK-4672

Iterative GraphX applications always have long lineage, while checkpoint() on EdgeRDD and VertexRDD themselves cannot shorten the lineage. In contrast, if we perform checkpoint() on their ParitionsRDD, the long lineage can be cut off. Moreover, the existing operations such as cache() in this code is performed on the PartitionsRDD, so checkpoint() should do the same way. More details and explanation can be found in the JIRA.

Author: JerryLead <JerryLead@163.com>
Author: Lijie Xu <csxulijie@gmail.com>

Closes #3549 from JerryLead/my_graphX_checkpoint and squashes the following commits:

d1aa8d8 [JerryLead] Perform checkpoint() on PartitionsRDD not VertexRDD and EdgeRDD themselves
ff08ed4 [JerryLead] Merge branch 'master' of https://github.com/apache/spark
c0169da [JerryLead] Merge branch 'master' of https://github.com/apache/spark
52799e3 [Lijie Xu] Merge pull request #1 from apache/master

Using ```executeCollect``` to collect the result, because executeCollect is a custom implementation of collect in spark sql which better than rdd's collect

Author: wangfei <wangfei1@huawei.com>

Closes #3547 from scwf/executeCollect and squashes the following commits:

a5ab68e [wangfei] Revert "adding debug info"
a60d680 [wangfei] fix test failure
0db7ce8 [wangfei] adding debug info
184c594 [wangfei] using executeCollect instead collect

We should use `~` instead of `-` for bitwise NOT.

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #3528 from adrian-wang/symbol and squashes the following commits:

affd4ad [Daoyuan Wang] fix code gen test case
56efb79 [Daoyuan Wang] ensure bitwise NOT over byte and short persist data type
f55fbae [Daoyuan Wang] wrong symbol for bitwise not

SELECT max(1/0) FROM src
would return a very large number, which is obviously not right.
For hive-0.12, hive would return `Infinity` for 1/0, while for hive-0.13.1, it is `NULL` for 1/0.
I think it is better to keep our behavior with newer Hive version.
This PR ensures that when the divider is 0, the result of expression should be NULL, same with hive-0.13.1

Author: Daoyuan Wang <daoyuan.wang@intel.com>

Closes #3443 from adrian-wang/div and squashes the following commits:

2e98677 [Daoyuan Wang] fix code gen for divide 0
85c28ba [Daoyuan Wang] temp
36236a5 [Daoyuan Wang] add test cases
6f5716f [Daoyuan Wang] fix comments
cee92bd [Daoyuan Wang] avoid evaluation 2 times
22ecd9a [Daoyuan Wang] fix style
cf28c58 [Daoyuan Wang] divide fix
2dfe50f [Daoyuan Wang] return null when divider is 0 of Double type

val jsc = new org.apache.spark.api.java.JavaSparkContext(sc)
val jhc = new org.apache.spark.sql.hive.api.java.JavaHiveContext(jsc)
val nrdd = jhc.hql("select null from spark_test.for_test")
println(nrdd.schema)
Then the error is thrown as follows:
scala.MatchError: NullType (of class org.apache.spark.sql.catalyst.types.NullType$)
at org.apache.spark.sql.types.util.DataTypeConversions$.asJavaDataType(DataTypeConversions.scala:43)

Author: YanTangZhai <hakeemzhai@tencent.com>
Author: yantangzhai <tyz0303@163.com>
Author: Michael Armbrust <michael@databricks.com>

Closes #3538 from YanTangZhai/MatchNullType and squashes the following commits:

e052dff [yantangzhai] [SPARK-4676] [SQL] JavaSchemaRDD.schema may throw NullType MatchError if sql has null
4b4bb34 [yantangzhai] [SPARK-4676] [SQL] JavaSchemaRDD.schema may throw NullType MatchError if sql has null
896c7b7 [yantangzhai] fix NullType MatchError in JavaSchemaRDD when sql has null
6e643f8 [YanTangZhai] Merge pull request #11 from apache/master
e249846 [YanTangZhai] Merge pull request #10 from apache/master
d26d982 [YanTangZhai] Merge pull request #9 from apache/master
76d4027 [YanTangZhai] Merge pull request #8 from apache/master
03b62b0 [YanTangZhai] Merge pull request #7 from apache/master
8a00106 [YanTangZhai] Merge pull request #6 from apache/master
cbcba66 [YanTangZhai] Merge pull request #3 from apache/master
cdef539 [YanTangZhai] Merge pull request #1 from apache/master

Author: baishuo <vc_java@hotmail.com>

Closes #3526 from baishuo/master-trycatch and squashes the following commits:

d446e14 [baishuo] correct the code style
b36bf96 [baishuo] correct the code style
ae0e447 [baishuo] add finally to avoid resource leak

Spark SQL has embeded sqrt and abs but DSL doesn't support those functions.

Author: Kousuke Saruta <sarutak@oss.nttdata.co.jp>

Closes #3401 from sarutak/dsl-missing-operator and squashes the following commits:

07700cf [Kousuke Saruta] Modified Literal(null, NullType) to Literal(null) in DslQuerySuite
8f366f8 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into dsl-missing-operator
1b88e2e [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into dsl-missing-operator
0396f89 [Kousuke Saruta] Added sqrt and abs to Spark SQL DSL

A very small nit update.

Author: Reynold Xin <rxin@databricks.com>

Closes #3552 from rxin/license-header and squashes the following commits:

df8d1a4 [Reynold Xin] Indent license header properly for interfaces.scala.

The link points to the old scala programming guide; it should point to the submitting applications page.

This should be backported to 1.1.2 (it's been broken as of 1.0).

Author: Kay Ousterhout <kayousterhout@gmail.com>

Closes #3542 from kayousterhout/SPARK-4686 and squashes the following commits:

a8fc43b [Kay Ousterhout] [SPARK-4686] Link to allowed master URLs is broken

This PR cleans up `import SparkContext._` in core for SPARK-4397(#3262) to prove it really works well.

Author: zsxwing <zsxwing@gmail.com>

Closes #3530 from zsxwing/SPARK-4397-cleanup and squashes the following commits:

04e2273 [zsxwing] Cleanup 'import SparkContext._' in core

The vector norm in breeze is implemented by `activeIterator` which is known to be very slow.
In this PR, an efficient vector norm is implemented, and with this API, `Normalizer` and
`k-means` have big performance improvement.

Here is the benchmark against mnist8m dataset.

a) `Normalizer`
Before
DenseVector: 68.25secs
SparseVector: 17.01secs

With this PR
DenseVector: 12.71secs
SparseVector: 2.73secs

b) `k-means`
Before
DenseVector: 83.46secs
SparseVector: 61.60secs

With this PR
DenseVector: 70.04secs
SparseVector: 59.05secs

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #3462 from dbtsai/norm and squashes the following commits:

63c7165 [DB Tsai] typo
0c3637f [DB Tsai] add import org.apache.spark.SparkContext._ back
6fa616c [DB Tsai] address feedback
9b7cb56 [DB Tsai] move norm to static method
0b632e6 [DB Tsai] kmeans
dbed124 [DB Tsai] style
c1a877c [DB Tsai] first commit

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

Closes #1612 (close requested by 'marmbrus')
Closes #2723 (close requested by 'marmbrus')
Closes #1737 (close requested by 'marmbrus')
Closes #2252 (close requested by 'marmbrus')
Closes #2029 (close requested by 'marmbrus')
Closes #2386 (close requested by 'marmbrus')
Closes #2997 (close requested by 'marmbrus')