Unified package definition format in Spark SQL

According to discussions in comments of PR #208, this PR unifies package definition format in Spark SQL.

Some broken links in ScalaDoc and typos detected along the way are also fixed.

Author: Cheng Lian <lian.cs.zju@gmail.com>

Closes #225 from liancheng/packageDefinition and squashes the following commits:

75c47b3 [Cheng Lian] Fixed file line length
4f87968 [Cheng Lian] Unified package definition format in Spark SQL
[SQL] Un-ignore a test that is now passing.

Add golden answer for aforementioned test.

Also, fix golden test generation from sbt/sbt by setting the classpath correctly.

Author: Michael Armbrust <michael@databricks.com>

Closes #244 from marmbrus/partTest and squashes the following commits:

37a33c9 [Michael Armbrust] Un-ignore a test that is now passing, add golden answer for aforementioned test.  Fix golden test generation from sbt/sbt.
[SQL] Add a custom serializer for maps since they do not have a no-arg constructor.

Author: Michael Armbrust <michael@databricks.com>

Closes #243 from marmbrus/mapSer and squashes the following commits:

54045f7 [Michael Armbrust] Add a custom serializer for maps since they do not have a no-arg constructor.
SPARK-1324: SparkUI Should Not Bind to SPARK_PUBLIC_DNS

/cc @aarondav and @andrewor14

Author: Patrick Wendell <pwendell@gmail.com>

Closes #231 from pwendell/ui-binding and squashes the following commits:

e8025f8 [Patrick Wendell] SPARK-1324: SparkUI Should Not Bind to SPARK_PUBLIC_DNS
Spark 1095 : Adding explicit return types to all public methods

Excluded those that are self-evident and the cases that are discussed in the mailing list.

Author: NirmalReddy <nirmal_reddy2000@yahoo.com>
Author: NirmalReddy <nirmal.reddy@imaginea.com>

Closes #168 from NirmalReddy/Spark-1095 and squashes the following commits:

ac54b29 [NirmalReddy] import misplaced
8c5ff3e [NirmalReddy] Changed syntax of unit returning methods
02d0778 [NirmalReddy] fixed explicit types in all the other packages
1c17773 [NirmalReddy] fixed explicit types in core package
SPARK-1325. The maven build error for Spark Tools

This is just a slight variation on https://github.com/apache/spark/pull/234 and alternative suggestion for SPARK-1325. `scala-actors` is not necessary. `SparkBuild.scala` should be updated to reflect the direct dependency on `scala-reflect` and `scala-compiler`. And the `repl` build, which has the same dependencies, should also be consistent between Maven / SBT.

Author: Sean Owen <sowen@cloudera.com>
Author: witgo <witgo@qq.com>

Closes #240 from srowen/SPARK-1325 and squashes the following commits:

25bd7db [Sean Owen] Add necessary dependencies scala-reflect and scala-compiler to tools. Update repl dependencies, which are similar, to be consistent between Maven / SBT in this regard too.
[SPARK-1327] GLM needs to check addIntercept for intercept and weights

GLM needs to check addIntercept for intercept and weights. The current implementation always uses the first weight as intercept. Added a test for training without adding intercept.

JIRA: https://spark-project.atlassian.net/browse/SPARK-1327

Author: Xiangrui Meng <meng@databricks.com>

Closes #236 from mengxr/glm and squashes the following commits:

bcac1ac [Xiangrui Meng] add two tests to ensure {Lasso, Ridge}.setIntercept will throw an exceptions
a104072 [Xiangrui Meng] remove protected to be compatible with 0.9
0e57aa4 [Xiangrui Meng] update Lasso and RidgeRegression to parse the weights correctly from GLM mark createModel protected mark predictPoint protected
d7f629f [Xiangrui Meng] fix a bug in GLM when intercept is not used
Cut down the granularity of travis tests.

This PR amortizes the cost of downloading all the jars and compiling core across more test cases.  In one anecdotal run this change takes the cumulative time down from ~80 minutes to ~40 minutes.

Author: Michael Armbrust <michael@databricks.com>

Closes #255 from marmbrus/travis and squashes the following commits:

506b22d [Michael Armbrust] Cut down the granularity of travis tests so we can amortize the cost of compilation.
SPARK-1330 removed extra echo from comput_classpath.sh

remove the extra echo which prevents spark-class from working.  Note that I did not update the comment above it, which is also wrong because I'm not sure what it should do.

Should hive only be included if explicitly built with sbt hive/assembly or should sbt assembly build it?

Author: Thomas Graves <tgraves@apache.org>

Closes #241 from tgravescs/SPARK-1330 and squashes the following commits:

b10d708 [Thomas Graves] SPARK-1330 removed extra echo from comput_classpath.sh
SPARK-1335. Also increase perm gen / code cache for scalatest when invoked via Maven build

I am observing build failures when the Maven build reaches tests in the new SQL components. (I'm on Java 7 / OSX 10.9). The failure is the usual complaint from scala, that it's out of permgen space, or that JIT out of code cache space.

I see that various build scripts increase these both for SBT. This change simply adds these settings to scalatest's arguments. Works for me and seems a bit more consistent.

(I also snuck in cures for new build warnings from new scaladoc. Felt too trivial for a new PR, although it's separate. Just something I also saw while examining the build output.)

Author: Sean Owen <sowen@cloudera.com>

Closes #253 from srowen/SPARK-1335 and squashes the following commits:

c0f2d31 [Sean Owen] Appease scalastyle with a newline at the end of the file
a02679c [Sean Owen] Fix scaladoc errors due to missing links, which are generating build warnings, from some recent doc changes. We apparently can't generate links outside the module.
b2c6a09 [Sean Owen] Add perm gen, code cache settings to scalatest, mirroring SBT settings elsewhere, which allows tests to complete in at least one environment where they are failing. (Also removed a duplicate -Xms setting elsewhere.)
[SPARK-1268] Adding XOR and AND-NOT operations to spark.util.collection.BitSet

Symmetric difference (xor) in particular is useful for computing some distance metrics (e.g. Hamming). Unit tests added.

Author: Petko Nikolov <nikolov@soundcloud.com>

Closes #172 from petko-nikolov/bitset-imprv and squashes the following commits:

451f28b [Petko Nikolov] fixed style mistakes
5beba18 [Petko Nikolov] rm outer loop in andNot test
0e61035 [Petko Nikolov] conform to spark style; rm redundant asserts; more unit tests added; use arraycopy instead of loop
d53cdb9 [Petko Nikolov] rm incidentally added space
4e1df43 [Petko Nikolov] adding xor and and-not to BitSet; unit tests added
[SPARK-1210] Prevent ContextClassLoader of Actor from becoming ClassLoader of Executo...

...r.

Constructor of `org.apache.spark.executor.Executor` should not set context class loader of current thread, which is backend Actor's thread.

Run the following code in local-mode REPL.

```
scala> case class Foo(i: Int)
scala> val ret = sc.parallelize((1 to 100).map(Foo), 10).collect
```

This causes errors as follows:

```
ERROR actor.OneForOneStrategy: [L$line5.$read$$iwC$$iwC$$iwC$$iwC$Foo;
java.lang.ArrayStoreException: [L$line5.$read$$iwC$$iwC$$iwC$$iwC$Foo;
     at scala.runtime.ScalaRunTime$.array_update(ScalaRunTime.scala:88)
     at org.apache.spark.SparkContext$$anonfun$runJob$3.apply(SparkContext.scala:870)
     at org.apache.spark.SparkContext$$anonfun$runJob$3.apply(SparkContext.scala:870)
     at org.apache.spark.scheduler.JobWaiter.taskSucceeded(JobWaiter.scala:56)
     at org.apache.spark.scheduler.DAGScheduler.handleTaskCompletion(DAGScheduler.scala:859)
     at org.apache.spark.scheduler.DAGScheduler.processEvent(DAGScheduler.scala:616)
     at org.apache.spark.scheduler.DAGScheduler$$anonfun$start$1$$anon$2$$anonfun$receive$1.applyOrElse(DAGScheduler.scala:207)
     at akka.actor.ActorCell.receiveMessage(ActorCell.scala:498)
     at akka.actor.ActorCell.invoke(ActorCell.scala:456)
     at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:237)
     at akka.dispatch.Mailbox.run(Mailbox.scala:219)
     at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:386)
     at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
     at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
     at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
     at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
```

This is because the class loaders to deserialize result `Foo` instances might be different from backend Actor's, and the Actor's class loader should be the same as Driver's.

Author: Takuya UESHIN <ueshin@happy-camper.st>

Closes #15 from ueshin/wip/wrongcontextclassloader and squashes the following commits:

d79e8c0 [Takuya UESHIN] Change a parent class loader of ExecutorURLClassLoader.
c6c09b6 [Takuya UESHIN] Add a test to collect objects of class defined in repl.
43e0feb [Takuya UESHIN] Prevent ContextClassLoader of Actor from becoming ClassLoader of Executor.
Make sed do -i '' on OSX

I don't have access to an OSX machine, so if someone could test this that would be great.

Author: Nick Lanham <nick@afternight.org>

Closes #258 from nicklan/osx-sed-fix and squashes the following commits:

a6f158f [Nick Lanham] Also make mktemp work on OSX
558fd6e [Nick Lanham] Make sed do -i '' on OSX
SPARK-1096, a space after comment start style checker.

Author: Prashant Sharma <prashant.s@imaginea.com>

Closes #124 from ScrapCodes/SPARK-1096/scalastyle-comment-check and squashes the following commits:

214135a [Prashant Sharma] Review feedback.
5eba88c [Prashant Sharma] Fixed style checks for ///+ comments.
e54b2f8 [Prashant Sharma] improved message, work around.
83e7144 [Prashant Sharma] removed dependency on scalastyle in plugin, since scalastyle sbt plugin already depends on the right version. Incase we update the plugin we will have to adjust our spark-style project to depend on right scalastyle version.
810a1d6 [Prashant Sharma] SPARK-1096, a space after comment style checker.
ba33193 [Prashant Sharma] scala style as a project
fix path for jar, make sed actually work on OSX

Author: Nick Lanham <nick@afternight.org>

Closes #264 from nicklan/make-distribution-fixes and squashes the following commits:

172b981 [Nick Lanham] fix path for jar, make sed actually work on OSX
SPARK-1345 adding missing dependency on avro for hadoop 0.23 to the new ...

...sql pom files

Author: Thomas Graves <tgraves@apache.org>

Closes #263 from tgravescs/SPARK-1345 and squashes the following commits:

b43a2a0 [Thomas Graves] SPARK-1345 adding missing dependency on avro for hadoop 0.23 to the new sql pom files
SPARK-1126.  spark-app preliminary

This is a starting version of the spark-app script for running compiled binaries against Spark.  It still needs tests and some polish.  The only testing I've done so far has been using it to launch jobs in yarn-standalone mode against a pseudo-distributed cluster.

This leaves out the changes required for launching python scripts.  I think it might be best to save those for another JIRA/PR (while keeping to the design so that they won't require backwards-incompatible changes).

Author: Sandy Ryza <sandy@cloudera.com>

Closes #86 from sryza/sandy-spark-1126 and squashes the following commits:

d428d85 [Sandy Ryza] Commenting, doc, and import fixes from Patrick's comments
e7315c6 [Sandy Ryza] Fix failing tests
34de899 [Sandy Ryza] Change --more-jars to --jars and fix docs
299ddca [Sandy Ryza] Fix scalastyle
a94c627 [Sandy Ryza] Add newline at end of SparkSubmit
04bc4e2 [Sandy Ryza] SPARK-1126. spark-submit script
Implement the RLike & Like in catalyst

This PR includes:
1) Unify the unit test for expression evaluation
2) Add implementation of RLike & Like

Author: Cheng Hao <hao.cheng@intel.com>

Closes #224 from chenghao-intel/string_expression and squashes the following commits:

84f72e9 [Cheng Hao] fix bug in RLike/Like & Simplify the unit test
aeeb1d7 [Cheng Hao] Simplify the implementation/unit test of RLike/Like
319edb7 [Cheng Hao] change to spark code style
91cfd33 [Cheng Hao] add implementation for rlike/like
2c8929e [Cheng Hao] Update the unit test for expression evaluation
[SPARK-1186] : Enrich the Spark Shell to support additional arguments.

Enrich the Spark Shell functionality to support the following options.

```
Usage: spark-shell [OPTIONS]

OPTIONS:
    -h  --help              : Print this help information.
    -c  --cores             : The maximum number of cores to be used by the Spark Shell.
    -em --executor-memory   : The memory used by each executor of the Spark Shell, the number
                              is followed by m for megabytes or g for gigabytes, e.g. "1g".
    -dm --driver-memory     : The memory used by the Spark Shell, the number is followed
                              by m for megabytes or g for gigabytes, e.g. "1g".
    -m  --master            : A full string that describes the Spark Master, defaults to "local"
                              e.g. "spark://localhost:7077".
    --log-conf              : Enables logging of the supplied SparkConf as INFO at start of the
                              Spark Context.

e.g.
    spark-shell -m spark://localhost:7077 -c 4 -dm 512m -em 2g
```

**Note**: this commit reflects the changes applied to _master_ based on [5d98cfc1].

[ticket: SPARK-1186] : Enrich the Spark Shell to support additional arguments.
                        https://spark-project.atlassian.net/browse/SPARK-1186

Author      : bernardo.gomezpalcio@gmail.com

Author: Bernardo Gomez Palacio <bernardo.gomezpalacio@gmail.com>

Closes #116 from berngp/feature/enrich-spark-shell and squashes the following commits:

c5f455f [Bernardo Gomez Palacio] [SPARK-1186] : Enrich the Spark Shell to support additional arguments.
Don't swallow all kryo errors, only those that indicate we are out of data.

Author: Michael Armbrust <michael@databricks.com>

Closes #142 from marmbrus/kryoErrors and squashes the following commits:

9c72d1f [Michael Armbrust] Make the test more future proof.
78f5a42 [Michael Armbrust] Don't swallow all kryo errors, only those that indicate we are out of data.