[SPARK-4537][Streaming] Expand StreamingSource to add more metrics

Add `processingDelay`, `schedulingDelay` and `totalDelay` for the last completed batch. Add `lastReceivedBatchRecords` and `totalReceivedBatchRecords` to the received records counting.

Author: jerryshao <saisai.shao@intel.com>

Closes #3466 from jerryshao/SPARK-4537 and squashes the following commits:

00f5f7f [jerryshao] Change the code style and add totalProcessedRecords
44721a6 [jerryshao] Further address the comments
c097ddc [jerryshao] Address the comments
02dd44f [jerryshao] Fix the addressed comments
c7a9376 [jerryshao] Expand StreamingSource to add more metrics
[SPARK-4608][Streaming] Reorganize StreamingContext implicit to improve API convenience

There is only one implicit function `toPairDStreamFunctions` in `StreamingContext`. This PR did similar reorganization like [SPARK-4397](https://issues.apache.org/jira/browse/SPARK-4397).

Compiled the following codes with Spark Streaming 1.1.0 and ran it with this PR. Everything is fine.
```Scala
import org.apache.spark._
import org.apache.spark.streaming._
import org.apache.spark.streaming.StreamingContext._

object StreamingApp {

  def main(args: Array[String]) {
    val conf = new SparkConf().setMaster("local[2]").setAppName("FileWordCount")
    val ssc = new StreamingContext(conf, Seconds(10))
    val lines = ssc.textFileStream("/some/path")
    val words = lines.flatMap(_.split(" "))
    val pairs = words.map(word => (word, 1))
    val wordCounts = pairs.reduceByKey(_ + _)
    wordCounts.print()

    ssc.start()
    ssc.awaitTermination()
  }
}
```

Author: zsxwing <zsxwing@gmail.com>

Closes #3464 from zsxwing/SPARK-4608 and squashes the following commits:

aa6d44a [zsxwing] Fix a copy-paste error
f74c190 [zsxwing] Merge branch 'master' into SPARK-4608
e6f9cc9 [zsxwing] Update the docs
27833bb [zsxwing] Remove `import StreamingContext._`
c15162c [zsxwing] Reorganize StreamingContext implicit to improve API convenience
SPARK-4971: Fix typo in BlockGenerator comment

Author: CodingCat <zhunansjtu@gmail.com>

Closes #3807 from CodingCat/new_branch and squashes the following commits:

5167f01 [CodingCat] fix typo in the comment
MAINTENANCE: Automated closing of pull requests.

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

Closes #3456 (close requested by 'pwendell')
Closes #1602 (close requested by 'tdas')
Closes #2633 (close requested by 'tdas')
Closes #2059 (close requested by 'JoshRosen')
Closes #2348 (close requested by 'tdas')
Closes #3662 (close requested by 'tdas')
Closes #2031 (close requested by 'andrewor14')
Closes #265 (close requested by 'JoshRosen')
[SPARK-3787][BUILD] Assembly jar name is wrong when we build with sbt omitting -Dhadoop.version

This PR is another solution for When we build with sbt with profile for hadoop and without property for hadoop version like:

    sbt/sbt -Phadoop-2.2 assembly

jar name is always used default version (1.0.4).

When we build with maven with same condition for sbt, default version for each profile is used.
For instance, if we  build like:

    mvn -Phadoop-2.2 package

jar name is used hadoop2.2.0 as a default version of hadoop-2.2.

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

Closes #3046 from sarutak/fix-assembly-jarname-2 and squashes the following commits:

41ef90e [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname-2
50c8676 [Kousuke Saruta] Merge branch 'fix-assembly-jarname-2' of github.com:sarutak/spark into fix-assembly-jarname-2
52a1cd2 [Kousuke Saruta] Fixed comflicts
dd30768 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname2
f1c90bb [Kousuke Saruta] Fixed SparkBuild.scala in order to read `hadoop.version` property from pom.xml
af6b100 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname
c81806b [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname
ad1f96e [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname
b2318eb [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-assembly-jarname
5fc1259 [Kousuke Saruta] Fixed typo.
eebbb7d [Kousuke Saruta] Fixed wrong jar name
HOTFIX: Slight tweak on previous commit.

Meant to merge this in when committing SPARK-3787.
[SPARK-3955] Different versions between jackson-mapper-asl and jackson-c...

...ore-asl

- set the same version to jackson-mapper-asl and jackson-core-asl
- It's related with #2818
- coded a same patch from a latest master

Author: Jongyoul Lee <jongyoul@gmail.com>

Closes #3716 from jongyoul/SPARK-3955 and squashes the following commits:

efa29aa [Jongyoul Lee] [SPARK-3955] Different versions between jackson-mapper-asl and jackson-core-asl - set the same version to jackson-mapper-asl and jackson-core-asl
[SPARK-4954][Core] add spark version infomation in log for standalone mode

The master and worker spark version may be not the same with Driver spark version. That is because spark Jar file might be replaced for new application without restarting the spark cluster. So there shall log out the spark-version in both Mater and Worker log.

Author: Zhang, Liye <liye.zhang@intel.com>

Closes #3790 from liyezhang556520/version4Standalone and squashes the following commits:

e05e1e3 [Zhang, Liye] add spark version infomation in log for standalone mode
[SPARK-4952][Core]Handle ConcurrentModificationExceptions in SparkEnv.environmentDetails

Author: GuoQiang Li <witgo@qq.com>

Closes #3788 from witgo/SPARK-4952 and squashes the following commits:

d903529 [GuoQiang Li] Handle ConcurrentModificationExceptions in SparkEnv.environmentDetails
[SPARK-4501][Core] - Create build/mvn to automatically download maven/zinc/scalac

Creates a top level directory script (as `build/mvn`) to automatically download zinc and the specific version of scala used to easily build spark. This will also download and install maven if the user doesn't already have it and all packages are hosted under the `build/` directory. Tested on both Linux and OSX OS's and both work. All commands pass through to the maven binary so it acts exactly as a traditional maven call would.

Author: Brennon York <brennon.york@capitalone.com>

Closes #3707 from brennonyork/SPARK-4501 and squashes the following commits:

0e5a0e4 [Brennon York] minor incorrect doc verbage (with -> this)
9b79e38 [Brennon York] fixed merge conflicts with dev/run-tests, properly quoted args in sbt/sbt, fixed bug where relative paths would fail if passed in from build/mvn
d2d41b6 [Brennon York] added blurb about leverging zinc with build/mvn
b979c58 [Brennon York] updated the merge conflict
c5634de [Brennon York] updated documentation to overview build/mvn, updated all points where sbt/sbt was referenced with build/sbt
b8437ba [Brennon York] set progress bars for curl and wget when not run on jenkins, no progress bar when run on jenkins, moved sbt script to build/sbt, wrote stub and warning under sbt/sbt which calls build/sbt, modified build/sbt to use the correct directory, fixed bug in build/sbt-launch-lib.bash to correctly pull the sbt version
be11317 [Brennon York] added switch to silence download progress only if AMPLAB_JENKINS is set
28d0a99 [Brennon York] updated to remove the python dependency, uses grep instead
7e785a6 [Brennon York] added silent and quiet flags to curl and wget respectively, added single echo output to denote start of a download if download is needed
14a5da0 [Brennon York] removed unnecessary zinc output on startup
1af4a94 [Brennon York] fixed bug with uppercase vs lowercase variable
3e8b9b3 [Brennon York] updated to properly only restart zinc if it was freshly installed
a680d12 [Brennon York] Added comments to functions and tested various mvn calls
bb8cc9d [Brennon York] removed package files
ef017e6 [Brennon York] removed OS complexities, setup generic install_app call, removed extra file complexities, removed help, removed forced install (defaults now), removed double-dash from cli
07bf018 [Brennon York] Updated to specifically handle pulling down the correct scala version
f914dea [Brennon York] Beginning final portions of localized scala home
69c4e44 [Brennon York] working linux and osx installers for purely local mvn build
4a1609c [Brennon York] finalizing working linux install for maven to local ./build/apache-maven folder
cbfcc68 [Brennon York] Changed the default sbt/sbt to build/sbt and added a build/mvn which will automatically download, install, and execute maven with zinc for easier build capability
[SPARK-4966][YARN]The MemoryOverhead value is setted not correctly

Author: meiyoula <1039320815@qq.com>

Closes #3797 from XuTingjun/MemoryOverhead and squashes the following commits:

5a780fc [meiyoula] Update ClientArguments.scala
[SPARK-4982][DOC] `spark.ui.retainedJobs` description is wrong in Spark UI configuration guide

Author: wangxiaojing <u9jing@gmail.com>

Closes #3818 from wangxiaojing/SPARK-4982 and squashes the following commits:

fe2ad5f [wangxiaojing] change stages to jobs
Adde LICENSE Header to build/mvn, build/sbt and sbt/sbt

Recently, build/mvn and build/sbt are added, and sbt/sbt is changed but there are no license headers. Should we add license headers to the scripts right?
If it's not right, please let me correct.

This PR doesn't affect behavior of Spark, I don't file in JIRA.

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

Closes #3817 from sarutak/add-license-header and squashes the following commits:

1abc972 [Kousuke Saruta] Added LICENSE Header
[SPARK-4946] [CORE] Using AkkaUtils.askWithReply in MapOutputTracker.askTracker to reduce the chance of the communicating problem

Using AkkaUtils.askWithReply in MapOutputTracker.askTracker to reduce the chance of the communicating problem

Author: YanTangZhai <hakeemzhai@tencent.com>
Author: yantangzhai <tyz0303@163.com>

Closes #3785 from YanTangZhai/SPARK-4946 and squashes the following commits:

9ca6541 [yantangzhai] [SPARK-4946] [CORE] Using AkkaUtils.askWithReply in MapOutputTracker.askTracker to reduce the chance of the communicating problem
e4c2c0a [YanTangZhai] Merge pull request #15 from apache/master
718afeb [YanTangZhai] Merge pull request #12 from apache/master
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
[Minor] Fix a typo of type parameter in JavaUtils.scala

In JavaUtils.scala, thare is a typo of type parameter. In addition, the type information is removed at the time of compile by erasure.

This issue is really minor so I don't  file in JIRA.

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

Closes #3789 from sarutak/fix-typo-in-javautils and squashes the following commits:

e20193d [Kousuke Saruta] Fixed a typo of type parameter
82bc5d9 [Kousuke Saruta] Merge branch 'master' of git://git.apache.org/spark into fix-typo-in-javautils
99f6f63 [Kousuke Saruta] Fixed a typo of type parameter in JavaUtils.scala
[SPARK-4409][MLlib] Additional Linear Algebra Utils

Addition of a very limited number of local matrix manipulation and generation methods that would be helpful in the further development for algorithms on top of BlockMatrix (SPARK-3974), such as Randomized SVD, and Multi Model Training (SPARK-1486).
The proposed methods for addition are:

For `Matrix`
 - map: maps the values in the matrix with a given function. Produces a new matrix.
 - update: the values in the matrix are updated with a given function. Occurs in place.

Factory methods for `DenseMatrix`:
 - *zeros: Generate a matrix consisting of zeros
 - *ones: Generate a matrix consisting of ones
 - *eye: Generate an identity matrix
 - *rand: Generate a matrix consisting of i.i.d. uniform random numbers
 - *randn: Generate a matrix consisting of i.i.d. gaussian random numbers
 - *diag: Generate a diagonal matrix from a supplied vector
*These methods already exist in the factory methods for `Matrices`, however for cases where we require a `DenseMatrix`, you constantly have to add `.asInstanceOf[DenseMatrix]` everywhere, which makes the code "dirtier". I propose moving these functions to factory methods for `DenseMatrix` where the putput will be a `DenseMatrix` and the factory methods for `Matrices` will call these functions directly and output a generic `Matrix`.

Factory methods for `SparseMatrix`:
 - speye: Identity matrix in sparse format. Saves a ton of memory when dimensions are large, especially in Multi Model Training, where each row requires being multiplied by a scalar.
 - sprand: Generate a sparse matrix with a given density consisting of i.i.d. uniform random numbers.
 - sprandn: Generate a sparse matrix with a given density consisting of i.i.d. gaussian random numbers.
 - diag: Generate a diagonal matrix from a supplied vector, but is memory efficient, because it just stores the diagonal. Again, very helpful in Multi Model Training.

Factory methods for `Matrices`:
 - Include all the factory methods given above, but return a generic `Matrix` rather than `SparseMatrix` or `DenseMatrix`.
 - horzCat: Horizontally concatenate matrices to form one larger matrix. Very useful in both Multi Model Training, and for the repartitioning of BlockMatrix.
 - vertCat: Vertically concatenate matrices to form one larger matrix. Very useful for the repartitioning of BlockMatrix.

The names for these methods were selected from MATLAB

Author: Burak Yavuz <brkyvz@gmail.com>
Author: Xiangrui Meng <meng@databricks.com>

Closes #3319 from brkyvz/SPARK-4409 and squashes the following commits:

b0354f6 [Burak Yavuz] [SPARK-4409] Incorporated mengxr's code
04c4829 [Burak Yavuz] Merge pull request #1 from mengxr/SPARK-4409
80cfa29 [Xiangrui Meng] minor changes
ecc937a [Xiangrui Meng] update sprand
4e95e24 [Xiangrui Meng] simplify fromCOO implementation
10a63a6 [Burak Yavuz] [SPARK-4409] Fourth pass of code review
f62d6c7 [Burak Yavuz] [SPARK-4409] Modified genRandMatrix
3971c93 [Burak Yavuz] [SPARK-4409] Third pass of code review
75239f8 [Burak Yavuz] [SPARK-4409] Second pass of code review
e4bd0c0 [Burak Yavuz] [SPARK-4409] Modified horzcat and vertcat
65c562e [Burak Yavuz] [SPARK-4409] Hopefully fixed Java Test
d8be7bc [Burak Yavuz] [SPARK-4409] Organized imports
065b531 [Burak Yavuz] [SPARK-4409] First pass after code review
a8120d2 [Burak Yavuz] [SPARK-4409] Finished updates to API according to SPARK-4614
f798c82 [Burak Yavuz] [SPARK-4409] Updated API according to SPARK-4614
c75f3cd [Burak Yavuz] [SPARK-4409] Added JavaAPI Tests, and fixed a couple of bugs
d662f9d [Burak Yavuz] [SPARK-4409] Modified according to remote repo
83dfe37 [Burak Yavuz] [SPARK-4409] Scalastyle error fixed
a14c0da [Burak Yavuz] [SPARK-4409] Initial commit to add methods
SPARK-4968: takeOrdered to skip reduce step in case mappers return no partitions

takeOrdered should skip reduce step in case mapped RDDs have no partitions. This prevents the mentioned exception :

4. run query
SELECT * FROM testTable WHERE market = 'market2' ORDER BY End_Time DESC LIMIT 100;
Error trace
java.lang.UnsupportedOperationException: empty collection
at org.apache.spark.rdd.RDD$$anonfun$reduce$1.apply(RDD.scala:863)
at org.apache.spark.rdd.RDD$$anonfun$reduce$1.apply(RDD.scala:863)
at scala.Option.getOrElse(Option.scala:120)
at org.apache.spark.rdd.RDD.reduce(RDD.scala:863)
at org.apache.spark.rdd.RDD.takeOrdered(RDD.scala:1136)

Author: Yash Datta <Yash.Datta@guavus.com>

Closes #3830 from saucam/fix_takeorder and squashes the following commits:

5974d10 [Yash Datta] SPARK-4968: takeOrdered to skip reduce step in case mappers return no partitions
SPARK-4156 [MLLIB] EM algorithm for GMMs

Implementation of Expectation-Maximization for Gaussian Mixture Models.

This is my maiden contribution to Apache Spark, so I apologize now if I have done anything incorrectly; having said that, this work is my own, and I offer it to the project under the project's open source license.

Author: Travis Galoppo <tjg2107@columbia.edu>
Author: Travis Galoppo <travis@localhost.localdomain>
Author: tgaloppo <tjg2107@columbia.edu>
Author: FlytxtRnD <meethu.mathew@flytxt.com>

Closes #3022 from tgaloppo/master and squashes the following commits:

aaa8f25 [Travis Galoppo] MLUtils: changed privacy of EPSILON from [util] to [mllib]
709e4bf [Travis Galoppo] fixed usage line to include optional maxIterations parameter
acf1fba [Travis Galoppo] Fixed parameter comment in GaussianMixtureModel Made maximum iterations an optional parameter to DenseGmmEM
9b2fc2a [Travis Galoppo] Style improvements Changed ExpectationSum to a private class
b97fe00 [Travis Galoppo] Minor fixes and tweaks.
1de73f3 [Travis Galoppo] Removed redundant array from array creation
578c2d1 [Travis Galoppo] Removed unused import
227ad66 [Travis Galoppo] Moved prediction methods into model class.
308c8ad [Travis Galoppo] Numerous changes to improve code
cff73e0 [Travis Galoppo] Replaced accumulators with RDD.aggregate
20ebca1 [Travis Galoppo] Removed unusued code
42b2142 [Travis Galoppo] Added functionality to allow setting of GMM starting point. Added two cluster test to testing suite.
8b633f3 [Travis Galoppo] Style issue
9be2534 [Travis Galoppo] Style issue
d695034 [Travis Galoppo] Fixed style issues
c3b8ce0 [Travis Galoppo] Merge branch 'master' of https://github.com/tgaloppo/spark   Adds predict() method
2df336b [Travis Galoppo] Fixed style issue
b99ecc4 [tgaloppo] Merge pull request #1 from FlytxtRnD/predictBranch
f407b4c [FlytxtRnD] Added predict() to return the cluster labels and membership values
97044cf [Travis Galoppo] Fixed style issues
dc9c742 [Travis Galoppo] Moved MultivariateGaussian utility class
e7d413b [Travis Galoppo] Moved multivariate Gaussian utility class to mllib/stat/impl Improved comments
9770261 [Travis Galoppo] Corrected a variety of style and naming issues.
8aaa17d [Travis Galoppo] Added additional train() method to companion object for cluster count and tolerance parameters.
676e523 [Travis Galoppo] Fixed to no longer ignore delta value provided on command line
e6ea805 [Travis Galoppo] Merged with master branch; update test suite with latest context changes. Improved cluster initialization strategy.
86fb382 [Travis Galoppo] Merge remote-tracking branch 'upstream/master'
719d8cc [Travis Galoppo] Added scala test suite with basic test
c1a8e16 [Travis Galoppo] Made GaussianMixtureModel class serializable Modified sum function for better performance
5c96c57 [Travis Galoppo] Merge remote-tracking branch 'upstream/master'
c15405c [Travis Galoppo] SPARK-4156
Added setMinCount to Word2Vec.scala

Wanted to customize the private minCount variable in the Word2Vec class. Added
a method to do so.

Author: ganonp <ganonp@gmail.com>

Closes #3693 from ganonp/my-custom-spark and squashes the following commits:

ad534f2 [ganonp] made norm method public
5110a6f [ganonp] Reorganized
854958b [ganonp] Fixed Indentation for setMinCount
12ed8f9 [ganonp] Update Word2Vec.scala
76bdf5a [ganonp] Update Word2Vec.scala
ffb88bb [ganonp] Update Word2Vec.scala
5eb9100 [ganonp] Added setMinCount to Word2Vec.scala
[SPARK-4972][MLlib] Updated the scala doc for lasso and ridge regression for the change of LeastSquaresGradient

In #SPARK-4907, we added factor of 2 into the LeastSquaresGradient. We updated the scala doc for lasso and ridge regression here.

Author: DB Tsai <dbtsai@alpinenow.com>

Closes #3808 from dbtsai/doc and squashes the following commits:

ec3c989 [DB Tsai] first commit