SPARK-1652: Remove incorrect deprecation warning in spark-submit

This is a straightforward fix.

Author: Patrick Wendell <pwendell@gmail.com>

This patch had conflicts when merged, resolved by
Committer: Patrick Wendell <pwendell@gmail.com>

Closes #578 from pwendell/spark-submit-yarn and squashes the following commits:

96027c7 [Patrick Wendell] Test fixes
b5be173 [Patrick Wendell] Review feedback
4ac9cac [Patrick Wendell] SPARK-1652: spark-submit for yarn prints warnings even though calling as expected
Improved build configuration

1, Fix SPARK-1441: compile spark core error with hadoop 0.23.x
2, Fix SPARK-1491: maven hadoop-provided profile fails to build
3, Fix org.scala-lang: * ,org.apache.avro:* inconsistent versions dependency
4, A modified on the sql/catalyst/pom.xml,sql/hive/pom.xml,sql/core/pom.xml (Four spaces formatted into two spaces)

Author: witgo <witgo@qq.com>

Closes #480 from witgo/format_pom and squashes the following commits:

03f652f [witgo] review commit
b452680 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
bee920d [witgo] revert fix SPARK-1629: Spark Core missing commons-lang dependence
7382a07 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
6902c91 [witgo] fix SPARK-1629: Spark Core missing commons-lang dependence
0da4bc3 [witgo] merge master
d1718ed [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
e345919 [witgo] add avro dependency to yarn-alpha
77fad08 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
62d0862 [witgo] Fix org.scala-lang: * inconsistent versions dependency
1a162d7 [witgo] Merge branch 'master' of https://github.com/apache/spark into format_pom
934f24d [witgo] review commit
cf46edc [witgo] exclude jruby
06e7328 [witgo] Merge branch 'SparkBuild' into format_pom
99464d2 [witgo] fix maven hadoop-provided profile fails to build
0c6c1fc [witgo] Fix compile spark core error with hadoop 0.23.x
6851bec [witgo] Maintain consistent SparkBuild.scala, pom.xml
HOTFIX: Bug in release script
Minor fix to python table caching API.

Author: Michael Armbrust <michael@databricks.com>

Closes #585 from marmbrus/pythonCacheTable and squashes the following commits:

7ec1f91 [Michael Armbrust] Minor fix to python table caching API.
[SPARK-1636][MLLIB] Move main methods to examples

* `NaiveBayes` -> `SparseNaiveBayes`
* `KMeans` -> `DenseKMeans`
* `SVMWithSGD` and `LogisticRegerssionWithSGD` -> `BinaryClassification`
* `ALS` -> `MovieLensALS`
* `LinearRegressionWithSGD`, `LassoWithSGD`, and `RidgeRegressionWithSGD` -> `LinearRegression`
* `DecisionTree` -> `DecisionTreeRunner`

`scopt` is used for parsing command-line parameters. `scopt` has MIT license and it only depends on `scala-library`.

Example help message:

~~~
BinaryClassification: an example app for binary classification.
Usage: BinaryClassification [options] <input>

  --numIterations <value>
        number of iterations
  --stepSize <value>
        initial step size, default: 1.0
  --algorithm <value>
        algorithm (SVM,LR), default: LR
  --regType <value>
        regularization type (L1,L2), default: L2
  --regParam <value>
        regularization parameter, default: 0.1
  <input>
        input paths to labeled examples in LIBSVM format
~~~

Author: Xiangrui Meng <meng@databricks.com>

Closes #584 from mengxr/mllib-main and squashes the following commits:

7b58c60 [Xiangrui Meng] minor
6e35d7e [Xiangrui Meng] make imports explicit and fix code style
c6178c9 [Xiangrui Meng] update TS PCA/SVD to use new spark-submit
6acff75 [Xiangrui Meng] use scopt for DecisionTreeRunner
be86069 [Xiangrui Meng] use main instead of extending App
b3edf68 [Xiangrui Meng] move DecisionTree's main method to examples
8bfaa5a [Xiangrui Meng] change NaiveBayesParams to Params
fe23dcb [Xiangrui Meng] remove main from KMeans and add DenseKMeans as an example
67f4448 [Xiangrui Meng] remove main methods from linear regression algorithms and add LinearRegression example
b066bbc [Xiangrui Meng] remove main from ALS and add MovieLensALS example
b040f3b [Xiangrui Meng] change BinaryClassificationParams to Params
577945b [Xiangrui Meng] remove unused imports from NB
3d299bc [Xiangrui Meng] remove main from LR/SVM and add an example app for binary classification
f70878e [Xiangrui Meng] remove main from NaiveBayes and add an example NaiveBayes app
01ec2cd [Xiangrui Meng] Merge branch 'master' into mllib-main
9420692 [Xiangrui Meng] add scopt to examples dependencies
HOTFIX: minor change to release script
HOTFIX: minor change to release script
SPARK-1557 Set permissions on event log files/directories

This adds minimal setting of event log directory/files permissions.  To have a secure environment the user must manually create the top level event log directory and set permissions up.   We can add logic to do that automatically later if we want.

Author: Thomas Graves <tgraves@apache.org>

Closes #538 from tgravescs/SPARK-1557 and squashes the following commits:

e471d8e [Thomas Graves] rework
d8b6620 [Thomas Graves] update use of octal
3ca9b79 [Thomas Graves] Updated based on comments
5a09709 [Thomas Graves] add in missing import
3150ed6 [Thomas Graves] SPARK-1557 Set permissions on event log files/directories
SPARK-1509: add zipWithIndex zipWithUniqueId methods to java api

Author: witgo <witgo@qq.com>

Closes #423 from witgo/zipWithIndex and squashes the following commits:

039ec04 [witgo] Merge branch 'master' of https://github.com/apache/spark into zipWithIndex
24d74c9 [witgo] review commit
763a5e4 [witgo] Merge branch 'master' of https://github.com/apache/spark into zipWithIndex
59747d1 [witgo] review commit
7bf4d06 [witgo] Merge branch 'master' of https://github.com/apache/spark into zipWithIndex
daa8f84 [witgo] review commit
4070613 [witgo] Merge branch 'master' of https://github.com/apache/spark into zipWithIndex
18e6c97 [witgo] java api zipWithIndex test
11e2e7f [witgo] add zipWithIndex zipWithUniqueId methods to java api
SPARK-1588.  Restore SPARK_YARN_USER_ENV and SPARK_JAVA_OPTS for YARN.

Author: Sandy Ryza <sandy@cloudera.com>

Closes #586 from sryza/sandy-spark-1588 and squashes the following commits:

35eb38e [Sandy Ryza] Scalify
b361684 [Sandy Ryza] SPARK-1588.  Restore SPARK_YARN_USER_ENV and SPARK_JAVA_OPTS for YARN.
[SPARK-1674] fix interrupted system call error in pyspark's RDD.pipe

`RDD.pipe`'s doctest throws interrupted system call exception on Mac. It can be fixed by wrapping `pipe.stdout.readline` in an iterator.

Author: Xiangrui Meng <meng@databricks.com>

Closes #594 from mengxr/pyspark-pipe and squashes the following commits:

cc32ac9 [Xiangrui Meng] fix interrupted system call error in pyspark's RDD.pipe
[SPARK-1646] Micro-optimisation of ALS

This change replaces some Scala `for` and `foreach` constructs with `while` constructs.  There may be a slight performance gain on the order of 1-2% when training an ALS model.

I trained an ALS model on the Movielens 10M-rating dataset repeatedly both with and without these changes.  All 7 runs in both columns were done in a Scala `for` loop like this:

    for (iter <- 0 to 10) {
      val before = System.currentTimeMillis()
      val model = ALS.train(rats, 20, 10)
      val after = System.currentTimeMillis()
      println("%d ms".format(after-before))
      println("rmse %g".format(computeRmse(model, rats, numRatings)))
    }

The timings were done on a multiuser machine, and I stopped one set of timings after 7 had been completed.  It would be nice if somebody with dedicated hardware could confirm my timings.

    After           Before
    121980 ms       122041 ms
    117069 ms       117127 ms
    115332 ms       117523 ms
    115381 ms       117402 ms
    114635 ms       116550 ms
    114140 ms       114076 ms
    112993 ms       117200 ms

Ratios are about 1.0005, 1.0005, 1.019, 1.0175, 1.01671, 0.99944, and 1.03723.  I therefore suspect these changes make for a slight performance gain on the order of 1-2%.

Author: Tor Myklebust <tmyklebu@gmail.com>

Closes #568 from tmyklebu/alsopt and squashes the following commits:

5ded80f [Tor Myklebust] Fix style.
79595ff [Tor Myklebust] Fix style error.
4ef0313 [Tor Myklebust] Merge branch 'master' of github.com:apache/spark into alsopt
114fb74 [Tor Myklebust] Turn some 'for' loops into 'while' loops.
dcf583a [Tor Myklebust] Remove the partitioner member variable; instead, thread that needle everywhere it needs to go.
23d6f91 [Tor Myklebust] Stop making the partitioner configurable.
495784f [Tor Myklebust] Merge branch 'master' of https://github.com/apache/spark
674933a [Tor Myklebust] Fix style.
40edc23 [Tor Myklebust] Fix missing space.
f841345 [Tor Myklebust] Fix daft bug creating 'pairs', also for -> foreach.
5ec9e6c [Tor Myklebust] Clean a couple of things up using 'map'.
36a0f43 [Tor Myklebust] Make the partitioner private.
d872b09 [Tor Myklebust] Add negative id ALS test.
df27697 [Tor Myklebust] Support custom partitioners.  Currently we use the same partitioner for users and products.
c90b6d8 [Tor Myklebust] Scramble user and product ids before bucketing.
c774d7d [Tor Myklebust] Make the partitioner a member variable and use it instead of modding directly.
Args for worker rather than master

Args for worker rather than master

Author: Chen Chao <crazyjvm@gmail.com>

Closes #587 from CrazyJvm/patch-6 and squashes the following commits:

b54b89f [Chen Chao] Args for worker rather than master
Handle the vals that never used

In XORShiftRandom.scala, use val "million" instead of constant "1e6.toInt".
Delete vals that never used in other files.

Author: WangTao <barneystinson@aliyun.com>

Closes #565 from WangTaoTheTonic/master and squashes the following commits:

17cacfc [WangTao] Handle the unused assignment, method parameters and symbol inspected by Intellij IDEA
37b4090 [WangTao] Handle the vals that never used
SPARK-1004.  PySpark on YARN

This reopens https://github.com/apache/incubator-spark/pull/640 against the new repo

Author: Sandy Ryza <sandy@cloudera.com>

Closes #30 from sryza/sandy-spark-1004 and squashes the following commits:

89889d4 [Sandy Ryza] Move unzipping py4j to the generate-resources phase so that it gets included in the jar the first time
5165a02 [Sandy Ryza] Fix docs
fd0df79 [Sandy Ryza] PySpark on YARN
Fix SPARK-1629: Spark should inline use of commons-lang `SystemUtils.IS_...

...OS_WINDOWS`

Author: witgo <witgo@qq.com>

Closes #569 from witgo/SPARK-1629 and squashes the following commits:

31520eb [witgo] Merge branch 'master' of https://github.com/apache/spark into SPARK-1629
fcaafd7 [witgo] merge mastet
49e248e [witgo] Fix SPARK-1629: Spark should inline use of commons-lang `SystemUtils.IS_OS_WINDOWS`
SPARK-1691: Support quoted arguments inside of spark-submit.

This is a fairly straightforward fix. The bug was reported by @vanzin and the fix was proposed by @deanwampler and myself. Please take a look!

Author: Patrick Wendell <pwendell@gmail.com>

Closes #609 from pwendell/quotes and squashes the following commits:

8bed767 [Patrick Wendell] SPARK-1691: Support quoted arguments inside of spark-submit.
[SQL] SPARK-1661 - Fix regex_serde test

The JIRA in question is actually reporting a bug with Shark, but I wanted to make sure Spark SQL did not have similar problems.  This fixes a bug in our parsing code that was preventing the test from executing, but it looks like the RegexSerDe is working in Spark SQL.

Author: Michael Armbrust <michael@databricks.com>

Closes #595 from marmbrus/fixRegexSerdeTest and squashes the following commits:

a4dc612 [Michael Armbrust] Add files created by hive to gitignore.
efa6402 [Michael Armbrust] Fix Hive serde_regex test.
fix the spelling mistake

Author: wangfei <wangfei_hello@126.com>

Closes #614 from scwf/pxcw and squashes the following commits:

d1016ba [wangfei] fix spelling mistake
 SPARK-1659: improvements spark-submit usage

Author: witgo <witgo@qq.com>

Closes #581 from witgo/SPARK-1659 and squashes the following commits:

0b2cf98 [witgo] Delete spark-submit obsolete usage: "--arg ARG"